Research

Our breakthrough insights and products arise out of decades of real-world clinical knowledge and academic research.

The Sema4 team is comprised of leading scientists in complex genomics, cancer research and development, systems and network biology, and population genomics. Explore all publications by our researchers.

RESEARCH HIGHLIGHTS

Robert Sebra, Eric Schadt, et al. | Nature Methods | 29 June 2015

Putting Genomes Together to Understand the Complexity of Life

Assembly and diploid architecture of an individual human genome via single-molecule technologies

We carried out the first study to sequence a human diploid genome using what are known as long-read DNA sequencing technologies, delivering the highest quality reference genome to date. Assembling a more accurate and complete genome is critical to our understanding of complex phenotypes such as human disease that have a genetic component.
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Robert Sebra, Eric Schadt, et al. | Nature Biotechnology | 1 July 2015

Pioneering a Novel Genome Assembly Approach

A hybrid approach for the automated finishing of bacterial genomes

One of the challenges in the field of genomics today is assembling complete genomes de novo, as opposed to using existing reference genomes to put a given genome together. By forcing the use of a reference genome, structural features in a given genome can be missed if they are absent in the reference, so the potential for discovery and clinical impact is reduced. We pioneered the first de novo assembly approach to assembling genomes using a combination of long and short read DNA sequencing technologies, demonstrating the ability to complete genomes de novo in an automated fashion, a necessary first step to achieve the vision of more comprehensive precision medicine
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Andrew V. Uzilov, Marc Fink, Yeygeniy Antipin, Katie Raustad, Robert Sebra, Shuyu Dan Li, Eric Schadt, Rong Chen, et al. | Genome Medicine | 1 June 2016

The Clinical Utility of Understanding Complex Genomes

Development and clinical application of an integrative genomic approach to personalized cancer therapy

Personalized therapy provides the best outcome of cancer care and its implementation in the clinic has been greatly facilitated by recent convergence of enormous progress in basic cancer research, rapid advancement of new tumor profiling technologies, and an expanding compendium of targeted cancer therapeutics. We developed and carried out a personalized cancer therapy study, generating extensive DNA and RNA data on cancer patients to molecularly characterize the makeup of a patient’s tumor, what the potential drivers of the tumor are, and what existing therapies, clinical trials, or de novo treatment strategies may apply. From our study, we validated the utility of such a program by demonstrating therapeutic recommendations for 91% of patients in the study.
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Eric Schadt, et al. | Cell | 25 April 2013

Modeling the Complexity of Human Disease

Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease

Complex human diseases such as Alzheimer’s disease (AD) are not the result of defects in a single gene or the result of a single environmental factor, but rather are the result of many (even hundreds or thousands) genes interacting in complex ways with many environmental factors that result in the development, progression and severity of disease. Thus, just as weather systems, financial markets, and solar systems are modeled using advanced mathematical modeling techniques to understand the interactions among the many thousands of variables that define these complex systems, living systems must be similarly modeled to achieve an understanding of disease. Here we presented one of the first holistic molecular models for AD, elucidating the complexity of this disease at the molecular and cellular levels. By taking this objective, data driven approach to understanding AD, we were able to uncover that immune cells in the brain (microglia) were a key causal determinant for AD.
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Rong Chen, Lisa Edelmann, Eric Schadt, et al. | Nature Biotechnology | 11 April 2016

Investigating Resilience to Disease Through Population Genomics

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we described a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. To accomplish this, we carried out the largest genomics study carried out at the time, analyzing over 589,000 genomes in search of individuals harboring highly penetrant, deleterious mutations in their DNA that should have caused catastrophic illness in childhood, but these individuals never manifested clinical disease and thus are protected.The protecting mechanism, if uncovered, offers a direct therapeutic path for disease. In our search we identified 13 individuals resilient to severe Mendelian childhood diseases, including diseases such as cystic fibrosis, where we identified individuals harboring the most damaging cystic fibrosis mutations, but never having manifested disease into their 40’s and 50’s.

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Eric Schadt, Erick Scott, Samantha Violante, et al. | Nature Biotechnology | 13 March 2017

Using Mobile Health Apps to Conduct Clinical Research

The Asthma Mobile Health Study, A Large-Scale Clinical Observational Study Using ResearchKit

The feasibility of using mobile health applications to conduct observational clinical studies requires rigorous validation. The Asthma Mobile Health Study (AMHS) is one of the few studies to examine the value and validity of the novel mobile health research platform, ResearchKit. We demonstrated that a broad-scale study can be conducted in its entirety via a smartphone application, including remote recruitment, consent, enrollment, and secure bi-directional data flow between investigators and participants. For AMHS, we prospectively collected detailed, multi-dimensional, longitudinal data on an asthma cohort more efficiently than traditional epidemiological studies by automating, standardizing, and accelerating various costly and time-consuming processes. Our study’s rapid recruitment and participants’ willingness to share de-identified data broadly highlight users’ acceptance of this methodology for low-risk health studies.

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Publications

Lisa Edelmann’s Articles

Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA.
Reiner J, Karger L, Cohen N, Mehta L, Edelmann L, Scott SA
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH
A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects.
Zhang J, Lachance V, Schaffner A, Li X, Fedick A, Kaye LE, Liao J, Rosenfeld J, Yachelevich N, Chu ML, Mitchell WG, Boles RG, Moran E, Tokita M, Gorman E, Bagley K, Zhang W, Xia F, Leduc M, Yang Y, Eng C, Wong LJ, Schiffmann R, Diaz GA, Kornreich R, Thummel R, Wasserstein M, Yue Z, Edelmann L
Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment.
Zhang J, Fedick A, Wasserman S, Zhao G, Edelmann L, Bottinger EP, Kornreich R, Scott SA
Setleis syndrome due to inheritance of the 1p36.22p36.21 duplication: evidence for lack of penetrance.
Lee BH, Kasparis C, Chen B, Mei H, Edelmann L, Moss C, Weaver DD, Desnick RJ
Myeloid Dysregulation in a Human Induced Pluripotent Stem Cell Model of PTPN11-Associated Juvenile Myelomonocytic Leukemia.
Mulero-Navarro S, Sevilla A, Roman AC, Lee DF, D’Souza SL, Pardo S, Riess I, Su J, Cohen N, Schaniel C, Rodriguez NA, Baccarini A, Brown BD, Cavé H, Caye A, Strullu M, Yalcin S, Park CY, Dhandapany PS, Yongchao G, Edelmann L, Bahieg S, Raynal P, Flex E, Tartaglia M, Moore KA, Lemischka IR, Gelb BD
ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
Wang J, Liao J, Zhang J, Cheng WY, Hakenberg J, Ma M, Webb BD, Ramasamudram-Chakravarthi R, Karger L, Mehta L, Kornreich R, Diaz GA, Li S, Edelmann L, Chen R
Chromosome 1p36.22p36.21 duplications/triplication causes Setleis syndrome (focal facial dermal dysplasia type III).
Weaver DD, Norby AR, Rosenfeld JA, Proud VK, Spangler BE, Ming JE, Chisholm E, Zackai EH, Lee BH, Edelmann L, Desnick RJ
Evaluation of the Affymetrix CytoScan(®) Dx Assay for developmental delay.
Webb BD, Scharf RJ, Spear EA, Edelmann LJ, Stroustrup A
A PTPN11 allele encoding a catalytically impaired SHP2 protein in a patient with a Noonan syndrome phenotype.
Edwards JJ, Martinelli S, Pannone L, Lo IF, Shi L, Edelmann L, Tartaglia M, Luk HM, Gelb BD
Analytical validation of whole exome and whole genome sequencing for clinical applications.
Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE
Setleis syndrome: genetic and clinical findings in a new case with epilepsy.
Giordano L, Desnick RJ, Molinaro A, Uliana V, Forzano F, Edelmann L, Nazarenko I, Pinelli L, Accorsi P, Faravelli F
An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy.
Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, Eversley C, Kornreich R, Desnick RJ, Edelmann L
Phelan-McDermid syndrome: a review of the literature and practice parameters for medical assessment and monitoring.
Kolevzon A, Angarita B, Bush L, Wang AT, Frank Y, Yang A, Rapaport R, Saland J, Srivastava S, Farrell C, Edelmann LJ, Buxbaum JD
46,XY disorder of sex development and developmental delay associated with a novel 9q33.3 microdeletion encompassing NR5A1.
Brandt T, Blanchard L, Desai K, Nimkarn S, Cohen N, Edelmann L, Mehta L
Effect of copy number variants on outcomes for infants with single ventricle heart defects.
Carey AS, Liang L, Edwards J, Brandt T, Mei H, Sharp AJ, Hsu DT, Newburger JW, Ohye RG, Chung WK, Russell MW, Rosenfeld JA, Shaffer LG, Parides MK, Edelmann L, Gelb BD
Localization of BRCA1 protein in breast cancer tissue and cell lines with mutations.
Tulchin N, Ornstein L, Dikman S, Strauchen J, Jaffer S, Nagi C, Bleiweiss I, Kornreich R, Edelmann L, Brown K, Bodian C, Nair VD, Chambon M, Woods NT, Monteiro AN
Phenotypic heterogeneity in a family with a small atypical microduplication of chromosome 22q11.2 involving TBX1.
Weisfeld-Adams JD, Edelmann L, Gadi IK, Mehta L
Complex autism spectrum disorder in a patient with a 17q12 microduplication.
Brandt T, Desai K, Grodberg D, Mehta L, Cohen N, Tryfon A, Kolevzon A, Soorya L, Buxbaum JD, Edelmann L
Role of copy number variants in structural birth defects.
Southard AE, Edelmann LJ, Gelb BD
Copy number variation and warfarin dosing: evaluation of CYP2C9, VKORC1, CYP4F2, GGCX and CALU.
Scott SA, Patel M, Martis S, Lubitz SA, van der Zee S, Yoo C, Edelmann L, Halperin JL, Desnick RJ
Experience with carrier screening and prenatal diagnosis for 16 Ashkenazi Jewish genetic diseases.
Scott SA, Edelmann L, Liu L, Luo M, Desnick RJ, Kornreich R
Type 1 Gaucher disease: significant disease manifestations in “asymptomatic” homozygotes.
Balwani M, Fuerstman L, Kornreich R, Edelmann L, Desnick RJ
Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome.
Scott SA, Cohen N, Brandt T, Warburton PE, Edelmann L
Genes essential for cell viability that are linked to tumor suppressor genes play a role in cancer susceptibility.
Wang Y, Huang B, Edelmann L, Kolodner RD, Edelmann W
Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome.
Carvajal-Vergara X, Sevilla A, D’Souza SL, Ang YS, Schaniel C, Lee DF, Yang L, Kaplan AD, Adler ED, Rozov R, Ge Y, Cohen N, Edelmann LJ, Chang B, Waghray A, Su J, Pardo S, Lichtenbelt KD, Tartaglia M, Gelb BD, Lemischka IR
Dual-color, break-apart FISH assay on paraffin-embedded tissues as an adjunct to diagnosis of Xp11 translocation renal cell carcinoma and alveolar soft part sarcoma.
Zhong M, De Angelo P, Osborne L, Keane-Tarchichi M, Goldfischer M, Edelmann L, Yang Y, Linehan WM, Merino MJ, Aisner S, Hameed M
Amniotic fluid cells are more efficiently reprogrammed to pluripotency than adult cells.
Galende E, Karakikes I, Edelmann L, Desnick RJ, Kerenyi T, Khoueiry G, Lafferty J, McGinn JT, Brodman M, Fuster V, Hajjar RJ, Polgar K
Cis lethal genetic interactions attenuate and alter p53 tumorigenesis.
Wang Y, Zhang W, Edelmann L, Kolodner RD, Kucherlapati R, Edelmann W
A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region.
McInnes LA, Nakamine A, Pilorge M, Brandt T, Jiménez González P, Fallas M, Manghi ER, Edelmann L, Glessner J, Hakonarson H, Betancur C, Buxbaum JD
Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization.
Scott SA, Cohen N, Brandt T, Toruner G, Desnick RJ, Edelmann L
Development of genomic DNA reference materials for genetic testing of disorders common in people of ashkenazi jewish descent.
Kalman L, Wilson JA, Buller A, Dixon J, Edelmann L, Geller L, Highsmith WE, Holtegaard L, Kornreich R, Rohlfs EM, Payeur TL, Sellers T, Toji L, Muralidharan K
Clinical utility of array CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies.
Edelmann L, Hirschhorn K
Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: efficient identification of known microduplications and identification of a novel microduplication in ASMT.
Cai G, Edelmann L, Goldsmith JE, Cohen N, Nakamine A, Reichert JG, Hoffman EJ, Zurawiecki DM, Silverman JM, Hollander E, Soorya L, Anagnostou E, Betancur C, Buxbaum JD
Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations.
Scott SA, Edelmann L, Kornreich R, Desnick RJ
Multiple hemangiomas in a patient with a t(3q;4p) translocation: an infrequent association with Wolf-Hirschhorn syndrome.
Pardo S, Blitman N, Han B, Cohen N, Edelmann L, Hirschhorn K
CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population.
Scott SA, Edelmann L, Kornreich R, Erazo M, Desnick RJ
An atypical deletion of the Williams-Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism.
Edelmann L, Prosnitz A, Pardo S, Bhatt J, Cohen N, Lauriat T, Ouchanov L, González PJ, Manghi ER, Bondy P, Esquivel M, Monge S, Delgado MF, Splendore A, Francke U, Burton BK, McInnes LA
Mutation in Rpa1 results in defective DNA double-strand break repair, chromosomal instability and cancer in mice.
Wang Y, Putnam CD, Kane MF, Zhang W, Edelmann L, Russell R, Carrión DV, Chin L, Kucherlapati R, Kolodner RD, Edelmann W
Cystic fibrosis carrier screening: validation of a novel method using BeadChip technology.
Edelmann L, Hashmi G, Song Y, Han Y, Kornreich R, Desnick RJ
Premarital and prenatal screening for cystic fibrosis: experience in the Ashkenazi Jewish population.
Kornreich R, Ekstein J, Edelmann L, Desnick RJ
Loss of DNA mismatch repair function and cancer predisposition in the mouse: animal models for human hereditary nonpolyposis colorectal cancer.
Edelmann L, Edelmann W
Familial dysautonomia: detection of the IKBKAP IVS20(+6T –> C) and R696P mutations and frequencies among Ashkenazi Jews.
Dong J, Edelmann L, Bajwa AM, Kornreich R, Desnick RJ
Carrier screening for mucolipidosis type IV in the American Ashkenazi Jewish population.
Edelmann L, Dong J, Desnick RJ, Kornreich R

Jun Zhu’s Articles

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy.
Pollak J, Rai KG, Funk CC, Arora S, Lee E, Zhu J, Price ND, Paddison PJ, Ramirez JM, Rostomily RC
Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition.
Collazo-Lorduy A, Castillo-Martin M, Wang L, Patel V, Iyer G, Jordan E, Al-Ahmadie H, Leonard I, Oh WK, Zhu J, McBride RB, Cordon-Cardo C, Solit DB, Sfakianos JP, Galsky MD
Gene expression elucidates functional impact of polygenic risk for schizophrenia.
Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P
EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer.
Katsyv I, Wang M, Song WM, Zhou X, Zhao Y, Park S, Zhu J, Zhang B, Irie HY
Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression.
Gong Y, Wang L, Chippada-Venkata U, Dai X, Oh WK, Zhu J
Impact of non-neoplastic vs intratumoural hepatitis B viral DNA and replication on hepatocellular carcinoma recurrence.
Wang Q, Lin L, Yoo S, Wang W, Blank S, Fiel MI, Kadri H, Luan W, Warren L, Zhu J, Hiotis SP
Disease-specific classification using deconvoluted whole blood gene expression.
Wang L, Oh WK, Zhu J
A 2-Gene Panel Derived From Prostate Cancer-Enhanced Transcripts in Whole Blood Is Prognostic for Survival and Predicts Treatment Benefit in Metastatic Castration-Resistant Prostate Cancer.
Heck MM, Thalgott M, Schmid SC, Oh WK, Gong Y, Wang L, Zhu J, Seitz AK, Porst D, Höppner M, Retz M, Gschwend JE, Nawroth R
Discover the network mechanisms underlying the connections between aging and age-related diseases.
Yang J, Huang T, Song WM, Petralia F, Mobbs CV, Zhang B, Zhao Y, Schadt EE, Zhu J, Tu Z
Meditation and vacation effects have an impact on disease-associated molecular phenotypes.
Epel ES, Puterman E, Lin J, Blackburn EH, Lum PY, Beckmann ND, Zhu J, Lee E, Gilbert A, Rissman RA, Tanzi RE, Schadt EE
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R
Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders.
Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X
Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease.
Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Al Adham Z, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM
Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage.
Moyon S, Huynh JL, Dutta D, Zhang F, Ma D, Yoo S, Lawrence R, Wegner M, John GR, Emery B, Lubetzki C, Franklin RJ, Fan G, Zhu J, Dupree JL, Casaccia P
Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.
Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, GTEx Consortium., Zhu J
A Next Generation Multiscale View of Inborn Errors of Metabolism.
Argmann CA, Houten SM, Zhu J, Schadt EE
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.
Lee E, Ito K, Zhao Y, Schadt EE, Irie HY, Zhu J
Characterization of Genetic Networks Associated with Alzheimer’s Disease.
Zhang B, Tran L, Emilsson V, Zhu J
Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.
Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, Lee J, Pollard SM, Zhu J, Delrow JJ, Clurman BE, Olson JM, Paddison PJ
Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer.
Bansal N, Petrie K, Christova R, Chung CY, Leibovitch BA, Howell L, Gil V, Sbirkov Y, Lee E, Wexler J, Ariztia EV, Sharma R, Zhu J, Bernstein E, Zhou MM, Zelent A, Farias E, Waxman S
Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, GTEx Consortium., Schadt EE, Zhu J, Tu Z
A robust blood gene expression-based prognostic model for castration-resistant prostate cancer.
Wang L, Gong Y, Chippada-Venkata U, Heck MM, Retz M, Nawroth R, Galsky M, Tsao CK, Schadt E, de Bono J, Olmos D, Zhu J, Oh WK
KRAS as a predictor of poor prognosis and benefit from postoperative FOLFOX chemotherapy in patients with stage II and III colorectal cancer.
Deng Y, Wang L, Tan S, Kim GP, Dou R, Chen D, Cai Y, Fu X, Wang L, Zhu J, Wang J
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
GTEx Consortium.
Molecular portraits of epithelial, mesenchymal, and hybrid States in lung adenocarcinoma and their relevance to survival.
Schliekelman MJ, Taguchi A, Zhu J, Dai X, Rodriguez J, Celiktas M, Zhang Q, Chin A, Wong CH, Wang H, McFerrin L, Selamat SA, Yang C, Kroh EM, Garg KS, Behrens C, Gazdar AF, Laird-Offringa IA, Tewari M, Wistuba II, Thiery JP, Hanash SM
Integrative network analysis reveals molecular mechanisms of blood pressure regulation.
Huan T, Meng Q, Saleh MA, Norlander AE, Joehanes R, Zhu J, Chen BH, Zhang B, Johnson AD, Ying S, Courchesne P, Raghavachari N, Wang R, Liu P, International Consortium for Blood Pressure GWAS (ICBP)., O’Donnell CJ, Vasan R, Munson PJ, Madhur MS, Harrison DG, Yang X, Levy D
Integrative network analysis reveals molecular mechanisms of blood pressure regulation.
Huan T, Meng Q, Saleh MA, Norlander AE, Joehanes R, Zhu J, Chen BH, Zhang B, Johnson AD, Ying S, Courchesne P, Raghavachari N, Wang R, Liu P, O’Donnell CJ, Vasan R, Munson PJ, Madhur MS, Harrison DG, Yang X, Levy D
A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits.
Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, Peng Z, Tu Z, Yang X, Meng Q, Friend S, Huang L
Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.
Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, Huang T, Tu Z, Foronjy RF, Spira A, Schadt EE, Powell CA, Zhu J
MODMatcher: multi-omics data matcher for integrative genomic analysis.
Yoo S, Huang T, Campbell JD, Lee E, Tu Z, Geraci MW, Powell CA, Schadt EE, Spira A, Zhu J
Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.
Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T, Suver C, Molony C, Melquist S, Johnson AD, Fan G, Stone DJ, Schadt EE, Casaccia P, Emilsson V, Zhu J
Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease.
Mäkinen VP, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, Huan T, Segrè AV, Ghosh S, Vivar J, Nikpay M, Stewart AF, Nelson CP, Willenborg C, Erdmann J, Blakenberg S, O’Donnell CJ, März W, Laaksonen R, Epstein SE, Kathiresan S, Shah SH, Hazen SL, Reilly MP, Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium., Lusis AJ, Samani NJ, Schunkert H, Quertermous T, McPherson R, Yang X, Assimes TL
An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy.
Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, Eversley C, Kornreich R, Desnick RJ, Edelmann L
Biomarkers for bladder cancer management: present and future.
Ye F, Wang L, Castillo-Martin M, McBride R, Galsky MD, Zhu J, Boffetta P, Zhang DY, Cordon-Cardo C
Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains.
Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD, Haroutunian V, Zhu J, Donovan MJ, Sharp AJ, Casaccia P
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma.
Wu C, Zhu J, Zhang X
A systems biology framework identifies molecular underpinnings of coronary heart disease.
Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, Ying S, Munson PJ, Raghavachari N, Wang R, Liu P, Courchesne P, Hwang SJ, Assimes TL, McPherson R, Samani NJ, Schunkert H, Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, International Consortium for Blood Pressure GWAS (ICBP)., Meng Q, Suver C, O’Donnell CJ, Derry J, Yang X, Levy D
The Genotype-Tissue Expression (GTEx) project.
GTEx Consortium.
Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease.
Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V
Modeling causality for pairs of phenotypes in system genetics.
Neto EC, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS
Cancer-Specific requirement for BUB1B/BUBR1 in human brain tumor isolates and genetically transformed cells.
Ding Y, Hubert CG, Herman J, Corrin P, Toledo CM, Skutt-Kakaria K, Vazquez J, Basom R, Zhang B, Risler JK, Pollard SM, Nam DH, Delrow JJ, Zhu J, Lee J, DeLuca J, Olson JM, Paddison PJ
11β-HSD1 inhibition reduces atherosclerosis in mice by altering proinflammatory gene expression in the vasculature.
Luo MJ, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, Plump A, Balkovec JM, Cheng K, Ding GJ, Kawka DW, Koo GC, Grand CB, Luo Q, Maletic MM, Malkowitz L, Shah K, Singer I, Waddell ST, Wu KK, Yuan J, Zhu J, Stepaniants S, Yang X, Lum PY, Wang IM
Functional genomics- and network-driven systems biology approaches for pharmacogenomics and toxicogenomics.
Yang X, Zhang B, Zhu J
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.
Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.
Wu C, Zhu J, Zhang X
Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers.
Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, Meng Q, Peters M, He Y, Ni C, Slipetz D, Crackower MA, Houshyar H, Tan CM, Asante-Appiah E, O’Neill G, Luo MJ, Thieringer R, Yuan J, Chiu CS, Lum PY, Lamb J, Boie Y, Wilkinson HA, Schadt EE, Dai H, Roberts C
Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.
Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.
Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE
Construction of regulatory networks using expression time-series data of a genotyped population.
Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE
Inferring causal genomic alterations in breast cancer using gene expression data.
Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.
Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, Zhang B, Castro V, Zhu J, Sieberts SK, Wang S, Molony C, Heymsfield SB, Kemp DM, Reitman ML, Lum PY, Schadt EE, Kaplan LM
Forkhead transcription factor foxq1 promotes epithelial-mesenchymal transition and breast cancer metastasis.
Zhang H, Meng F, Liu G, Zhang B, Zhu J, Wu F, Ethier SP, Miller F, Wu G
Bayesian models for detecting epistatic interactions from genetic data.
Zhang Y, Jiang B, Zhu J, Liu JS
Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.
Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE
An integrative multi-network and multi-classifier approach to predict genetic interactions.
Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, Kumar V, Schadt EE
Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY
Identification and validation of genes affecting aortic lesions in mice.
Yang X, Peterson L, Thieringer R, Deignan JL, Wang X, Zhu J, Wang S, Zhong H, Stepaniants S, Beaulaurier J, Wang IM, Rosa R, Cumiskey AM, Luo JM, Luo Q, Shah K, Xiao J, Nickle D, Plump A, Schadt EE, Lusis AJ, Lum PY
Simultaneous clustering of multiple gene expression and physical interaction datasets.
Narayanan M, Vetta A, Schadt EE, Zhu J
Characterizing dynamic changes in the human blood transcriptional network.
Zhu J, Chen Y, Leonardson AS, Wang K, Lamb JR, Emilsson V, Schadt EE
A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.
Zhang W, Zhu J, Schadt EE, Liu JS
The effect of food intake on gene expression in human peripheral blood.
Leonardson AS, Zhu J, Chen Y, Wang K, Lamb JR, Reitman M, Emilsson V, Schadt EE
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
Wang K, Narayanan M, Zhong H, Tompa M, Schadt EE, Zhu J
Ppargamma2 is a key driver of longevity in the mouse.
Argmann C, Dobrin R, Heikkinen S, Auburtin A, Pouilly L, Cock TA, Koutnikova H, Zhu J, Schadt EE, Auwerx J
Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments.
Schadt EE, Zhang B, Zhu J
Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.
Tu Z, Argmann C, Wong KK, Mitnaul LJ, Edwards S, Sach IC, Zhu J, Schadt EE
Disentangling molecular relationships with a causal inference test.
Millstein J, Zhang B, Zhu J, Schadt EE
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks.
Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, Torosyan G, Majid S, Falkard B, Kleinhanz RR, Karlsson J, Castellani LW, Mumick S, Wang K, Xie T, Coon M, Zhang C, Estrada-Smith D, Farber CR, Wang SS, van Nas A, Ghazalpour A, Zhang B, Macneil DJ, Lamb JR, Dipple KM, Reitman ML, Mehrabian M, Lum PY, Schadt EE, Lusis AJ, Drake TA
Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.
Dobrin R, Zhu J, Molony C, Argman C, Parrish ML, Carlson S, Allan MF, Pomp D, Schadt EE
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE
Mapping the genetic architecture of gene expression in human liver.
Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R
Variations in DNA elucidate molecular networks that cause disease.
Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy MF, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE
Genetics of gene expression and its effect on disease.
Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S, Magnusson KP, Stefansson H, Fossdal R, Kristjansson K, Gislason HG, Stefansson T, Leifsson BG, Thorsteinsdottir U, Lamb JR, Gulcher JR, Reitman ML, Kong A, Schadt EE, Stefansson K
A systems biology approach to drug discovery.
Zhu J, Zhang B, Schadt EE
Statistical power of phylo-HMM for evolutionarily conserved element detection.
Fan X, Zhu J, Schadt EE, Liu JS
Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations.
Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, Sachs JR, Schadt EE
Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes.
Lum PY, Chen Y, Zhu J, Lamb J, Melmed S, Wang S, Drake TA, Lusis AJ, Schadt EE
Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels.
Cervino AC, Li G, Edwards S, Zhu J, Laurie C, Tokiwa G, Lum PY, Wang S, Castellani LW, Lusis AJ, Carlson S, Sachs AB, Schadt EE
An integrative genomics approach to infer causal associations between gene expression and disease.
Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ
An integrative genomics approach to the reconstruction of gene networks in segregating populations.
Zhu J, Lum PY, Lamb J, GuhaThakurta D, Edwards SW, Thieringer R, Berger JP, Wu MS, Thompson J, Sachs AB, Schadt EE
Database search based on Bayesian alignment.
Zhu J, Lüthy R, Lawrence CE
Bayesian adaptive sequence alignment algorithms.
Zhu J, Liu JS, Lawrence CE
Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome.
Zhu J, Penczek PA, Schröder R, Frank J
Bayesian adaptive alignment and inference.
Zhu J, Liu J, Lawrence C
Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice.
Lata KR, Agrawal RK, Penczek P, Grassucci R, Zhu J, Frank J
A common-lines based method for determining orientations for N > 3 particle projections simultaneously.
Penczek PA, Zhu J, Frank J
SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A
A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome.
Frank J, Verschoor A, Li Y, Zhu J, Lata RK, Radermacher M, Penczek P, Grassucci R, Agrawal RK, Srivastava S
A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome.
Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK

Eric Schadt’s Articles

Rationale and Design of Family-Based Approach in a Minority Community Integrating Systems-Biology for Promotion of Health (FAMILIA).
Bansilal S, Vedanthan R, Kovacic JC, Soto AV, Latina J, Björkegren JLM, Jaslow R, Santana M, Sartori S, Giannarelli C, Mani V, Hajjar R, Schadt E, Kasarskis A, Fayad ZA, Fuster V
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, Patel A, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MY, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I
Heterozygous Pathogenic Variant in DACT1 Causes an Autosomal-Dominant Syndrome with Features Overlapping Townes-Brocks Syndrome.
Webb BD, Metikala S, Wheeler PG, Sherpa MD, Houten SM, Horb ME, Schadt EE
The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit.
Chan YY, Wang P, Rogers L, Tignor N, Zweig M, Hershman SG, Genes N, Scott ER, Krock E, Badgeley M, Edgar R, Violante S, Wright R, Powell CA, Dudley JT, Schadt EE
Genomic profiling reveals mutational landscape in parathyroid carcinomas.
Pandya C, Uzilov AV, Bellizzi J, Lau CY, Moe AS, Strahl M, Hamou W, Newman LC, Fink MY, Antipin Y, Yu W, Stevenson M, Cavaco BM, Teh BT, Thakker RV, Morreau H, Schadt EE, Sebra R, Li SD, Arnold A, Chen R
Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease.
Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, König IR, Eicher JD, Johnson AD, Hamby SE, Betsholtz C, Ruusalepp A, Franzén O, Schadt EE, Björkegren JL, Weeke PE, Auer PL, Schick UM, Lu Y, Zhang H, Dube MP, Goel A, Farrall M, Peloso GM, Won HH, Do R, van Iperen E, Kruppa J, Mahajan A, Scott RA, Willenborg C, Braund PS, van Capelleveen JC, Doney AS, Donnelly LA, Asselta R, Merlini PA, Duga S, Marziliano N, Denny JC, Shaffer C, El-Mokhtari NE, Franke A, Heilmann S, Hengstenberg C, Hoffmann P, Holmen OL, Hveem K, Jansson JH, Jöckel KH, Kessler T, Kriebel J, Laugwitz KL, Marouli E, Martinelli N, McCarthy MI, Van Zuydam NR, Meisinger C, Esko T, Mihailov E, Escher SA, Alver M, Moebus S, Morris AD, Virtamo J, Nikpay M, Olivieri O, Provost S, AlQarawi A, Robertson NR, Akinsansya KO, Reilly DF, Vogt TF, Yin W, Asselbergs FW, Kooperberg C, Jackson RD, Stahl E, Müller-Nurasyid M, Strauch K, Varga TV, Waldenberger M, Wellcome Trust Case Control Consortium., Zeng L, Chowdhury R, Salomaa V, Ford I, Jukema JW, Amouyel P, Kontto J, MORGAM Investigators., Nordestgaard BG, Ferrières J, Saleheen D, Sattar N, Surendran P, Wagner A, Young R, Howson JM, Butterworth AS, Danesh J, Ardissino D, Bottinger EP, Erbel R, Franks PW, Girelli D, Hall AS, Hovingh GK, Kastrati A, Lieb W, Meitinger T, Kraus WE, Shah SH, McPherson R, Orho-Melander M, Melander O, Metspalu A, Palmer CN, Peters A, Rader DJ, Reilly MP, Loos RJ, Reiner AP, Roden DM, Tardif JC, Thompson JR, Wareham NJ, Watkins H, Willer CJ, Samani NJ, Schunkert H, Deloukas P, Kathiresan S, Myocardial Infarction Genetics and CARDIoGRAM Exome Consortia Investigators.
Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks.
Akerman I, Tu Z, Beucher A, Rolando DM, Sauty-Colace C, Benazra M, Nakic N, Yang J, Wang H, Pasquali L, Moran I, Garcia-Hurtado J, Castro N, Gonzalez-Franco R, Stewart AF, Bonner C, Piemonti L, Berney T, Groop L, Kerr-Conte J, Pattou F, Argmann C, Schadt E, Ravassard P, Ferrer J
Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project.
Sanderson SC, Linderman MD, Suckiel SA, Zinberg R, Wasserstein M, Kasarskis A, Diaz GA, Schadt EE
High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors.
Di Narzo AF, Telesco SE, Brodmerkel C, Argmann C, Peters LA, Li K, Kidd B, Dudley J, Cho J, Schadt EE, Kasarskis A, Dobrin R, Hao K
Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.
Jones GT, Tromp G, Kuivaniemi H, Gretarsdottir S, Baas AF, Giusti B, Strauss E, Van’t Hof FN, Webb TR, Erdman R, Ritchie MD, Elmore JR, Verma A, Pendergrass S, Kullo IJ, Ye Z, Peissig PL, Gottesman O, Verma SS, Malinowski J, Rasmussen-Torvik LJ, Borthwick KM, Smelser DT, Crosslin DR, de Andrade M, Ryer EJ, McCarty CA, Böttinger EP, Pacheco JA, Crawford DC, Carrell DS, Gerhard GS, Franklin DP, Carey DJ, Phillips VL, Williams MJ, Wei W, Blair R, Hill AA, Vasudevan TM, Lewis DR, Thomson IA, Krysa J, Hill GB, Roake J, Merriman TR, Oszkinis G, Galora S, Saracini C, Abbate R, Pulli R, Pratesi C, Saratzis A, Verissimo AR, Bumpstead S, Badger SA, Clough RE, Cockerill G, Hafez H, Scott DJ, Futers TS, Romaine SP, Bridge K, Griffin KJ, Bailey MA, Smith A, Thompson MM, van Bockxmeer FM, Matthiasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Lindholt JS, Hughes A, Bradley DT, Stirrups K, Golledge J, Norman PE, Powell JT, Humphries SE, Hamby SE, Goodall AH, Nelson CP, Sakalihasan N, Courtois A, Ferrell RE, Eriksson P, Folkersen L, Franco-Cereceda A, Eicher JD, Johnson AD, Betsholtz C, Ruusalepp A, Franzén O, Schadt EE, Björkegren JL, Lipovich L, Drolet AM, Verhoeven EL, Zeebregts CJ, Geelkerken RH, van Sambeek MR, van Sterkenburg SM, de Vries JP, Stefansson K, Thompson JR, de Bakker PI, Deloukas P, Sayers RD, Harrison SC, van Rij AM, Samani NJ, Bown MJ
Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.
Mendelson MM, Marioni RE, Joehanes R, Liu C, Hedman ÅK, Aslibekyan S, Demerath EW, Guan W, Zhi D, Yao C, Huan T, Willinger C, Chen B, Courchesne P, Multhaup M, Irvin MR, Cohain A, Schadt EE, Grove ML, Bressler J, North K, Sundström J, Gustafsson S, Shah S, McRae AF, Harris SE, Gibson J, Redmond P, Corley J, Murphy L, Starr JM, Kleinbrink E, Lipovich L, Visscher PM, Wray NR, Krauss RM, Fallin D, Feinberg A, Absher DM, Fornage M, Pankow JS, Lind L, Fox C, Ingelsson E, Arnett DK, Boerwinkle E, Liang L, Levy D, Deary IJ
variancePartition: interpreting drivers of variation in complex gene expression studies.
Hoffman GE, Schadt EE
Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease.
Wang M, Roussos P, McKenzie A, Zhou X, Kajiwara Y, Brennand KJ, De Luca GC, Crary JF, Casaccia P, Buxbaum JD, Ehrlich M, Gandy S, Goate A, Katsel P, Schadt E, Haroutunian V, Zhang B
Gene expression elucidates functional impact of polygenic risk for schizophrenia.
Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P
Corrigendum: Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).
Peterson CT, Lucas J, John-Williams LS, Thompson JW, Moseley MA, Patel S, Peterson SN, Porter V, Schadt EE, Mills PJ, Tanzi RE, Doraiswamy PM, Chopra D
Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project.
Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Wasserstein M, Kasarskis A, Schadt EE, Zinberg RE
Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).
Peterson CT, Lucas J, John-Williams LS, Thompson JW, Moseley MA, Patel S, Peterson SN, Porter V, Schadt EE, Mills PJ, Tanzi RE, Doraiswamy PM, Chopra D
Discover the network mechanisms underlying the connections between aging and age-related diseases.
Yang J, Huang T, Song WM, Petralia F, Mobbs CV, Zhang B, Zhao Y, Schadt EE, Zhu J, Tu Z
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.
Franzén O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, Foroughi-Asl H, Giambartolomei C, Fullard JF, Sukhavasi K, Köks S, Gan LM, Giannarelli C, Kovacic JC, Betsholtz C, Losic B, Michoel T, Hao K, Roussos P, Skogsberg J, Ruusalepp A, Schadt EE, Björkegren JL
CD47-blocking antibodies restore phagocytosis and prevent atherosclerosis.
Kojima Y, Volkmer JP, McKenna K, Civelek M, Lusis AJ, Miller CL, Direnzo D, Nanda V, Ye J, Connolly AJ, Schadt EE, Quertermous T, Betancur P, Maegdefessel L, Matic LP, Hedin U, Weissman IL, Leeper NJ
The Self-Directed Biological Transformation Initiative and Well-Being.
Mills PJ, Wilson KL, Pung MA, Weiss L, Patel S, Doraiswamy PM, Peterson C, Porter V, Schadt E, Chopra D, Tanzi RE
Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.
Miller CL, Pjanic M, Wang T, Nguyen T, Cohain A, Lee JD, Perisic L, Hedin U, Kundu RK, Majmudar D, Kim JB, Wang O, Betsholtz C, Ruusalepp A, Franzén O, Assimes TL, Montgomery SB, Schadt EE, Björkegren JL, Quertermous T
Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT
Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn’s Disease Cohort Inform IBD Genetic Association Loci.
Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, Telesco S, Kidd B, Walker J, Dudley J, Cho J, Schadt EE, Kasarskis A, Curran M, Dobrin R, Hao K
A new molecular signature method for prediction of driver cancer pathways from transcriptional data.
Rykunov D, Beckmann ND, Li H, Uzilov A, Schadt EE, Reva B
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R
Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT
Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease.
Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Al Adham Z, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH
Family-Based Approaches to Cardiovascular Health Promotion.
Vedanthan R, Bansilal S, Soto AV, Kovacic JC, Latina J, Jaslow R, Santana M, Gorga E, Kasarskis A, Hajjar R, Schadt EE, Björkegren JL, Fayad ZA, Fuster V
Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease.
Talukdar HA, Foroughi Asl H, Jain RK, Ermel R, Ruusalepp A, Franzén O, Kidd BA, Readhead B, Giannarelli C, Kovacic JC, Ivert T, Dudley JT, Civelek M, Lusis AJ, Schadt EE, Skogsberg J, Michoel T, Björkegren JL
In utero exposures to environmental organic pollutants disrupt epigenetic marks linked to fetoplacental development.
Kappil MA, Li Q, Li A, Dassanayake PS, Xia Y, Nanes JA, Landrigan PJ, Stodgell CJ, Aagaard KM, Schadt EE, Dole N, Varner M, Moye J, Kasten C, Miller RK, Ma Y, Chen J, Lambertini L
New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.
Lu Y, Day FR, Gustafsson S, Buchkovich ML, Na J, Bataille V, Cousminer DL, Dastani Z, Drong AW, Esko T, Evans DM, Falchi M, Feitosa MF, Ferreira T, Hedman ÅK, Haring R, Hysi PG, Iles MM, Justice AE, Kanoni S, Lagou V, Li R, Li X, Locke A, Lu C, Mägi R, Perry JR, Pers TH, Qi Q, Sanna M, Schmidt EM, Scott WR, Shungin D, Teumer A, Vinkhuyzen AA, Walker RW, Westra HJ, Zhang M, Zhang W, Zhao JH, Zhu Z, Afzal U, Ahluwalia TS, Bakker SJ, Bellis C, Bonnefond A, Borodulin K, Buchman AS, Cederholm T, Choh AC, Choi HJ, Curran JE, de Groot LC, De Jager PL, Dhonukshe-Rutten RA, Enneman AW, Eury E, Evans DS, Forsen T, Friedrich N, Fumeron F, Garcia ME, Gärtner S, Han BG, Havulinna AS, Hayward C, Hernandez D, Hillege H, Ittermann T, Kent JW, Kolcic I, Laatikainen T, Lahti J, Mateo Leach I, Lee CG, Lee JY, Liu T, Liu Y, Lobbens S, Loh M, Lyytikäinen LP, Medina-Gomez C, Michaëlsson K, Nalls MA, Nielson CM, Oozageer L, Pascoe L, Paternoster L, Polašek O, Ripatti S, Sarzynski MA, Shin CS, Narančić NS, Spira D, Srikanth P, Steinhagen-Thiessen E, Sung YJ, Swart KM, Taittonen L, Tanaka T, Tikkanen E, van der Velde N, van Schoor NM, Verweij N, Wright AF, Yu L, Zmuda JM, Eklund N, Forrester T, Grarup N, Jackson AU, Kristiansson K, Kuulasmaa T, Kuusisto J, Lichtner P, Luan J, Mahajan A, Männistö S, Palmer CD, Ried JS, Scott RA, Stancáková A, Wagner PJ, Demirkan A, Döring A, Gudnason V, Kiel DP, Kühnel B, Mangino M, Mcknight B, Menni C, O’Connell JR, Oostra BA, Shuldiner AR, Song K, Vandenput L, van Duijn CM, Vollenweider P, White CC, Boehnke M, Boettcher Y, Cooper RS, Forouhi NG, Gieger C, Grallert H, Hingorani A, Jørgensen T, Jousilahti P, Kivimaki M, Kumari M, Laakso M, Langenberg C, Linneberg A, Luke A, Mckenzie CA, Palotie A, Pedersen O, Peters A, Strauch K, Tayo BO, Wareham NJ, Bennett DA, Bertram L, Blangero J, Blüher M, Bouchard C, Campbell H, Cho NH, Cummings SR, Czerwinski SA, Demuth I, Eckardt R, Eriksson JG, Ferrucci L, Franco OH, Froguel P, Gansevoort RT, Hansen T, Harris TB, Hastie N, Heliövaara M, Hofman A, Jordan JM, Jula A, Kähönen M, Kajantie E, Knekt PB, Koskinen S, Kovacs P, Lehtimäki T, Lind L, Liu Y, Orwoll ES, Osmond C, Perola M, Pérusse L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Rivadeneira F, Rudan I, Salomaa V, Sørensen TI, Stumvoll M, Tönjes A, Towne B, Tranah GJ, Tremblay A, Uitterlinden AG, van der Harst P, Vartiainen E, Viikari JS, Vitart V, Vohl MC, Völzke H, Walker M, Wallaschofski H, Wild S, Wilson JF, Yengo L, Bishop DT, Borecki IB, Chambers JC, Cupples LA, Dehghan A, Deloukas P, Fatemifar G, Fox C, Furey TS, Franke L, Han J, Hunter DJ, Karjalainen J, Karpe F, Kaplan RC, Kooner JS, McCarthy MI, Murabito JM, Morris AP, Bishop JA, North KE, Ohlsson C, Ong KK, Prokopenko I, Richards JB, Schadt EE, Spector TD, Widén E, Willer CJ, Yang J, Ingelsson E, Mohlke KL, Hirschhorn JN, Pospisilik JA, Zillikens MC, Lindgren C, Kilpeläinen TO, Loos RJ
Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z, GTEx Consortium.
A Next Generation Multiscale View of Inborn Errors of Metabolism.
Argmann CA, Houten SM, Zhu J, Schadt EE
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.
Lee E, Ito K, Zhao Y, Schadt EE, Irie HY, Zhu J
Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.
Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, Wasserstein M, Kasarskis A, Schadt EE
Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.
Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, Wasserstein M, Kasarskis A, Schadt EE
Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.
Knowles JW, Xie W, Zhang Z, Chennamsetty I, Assimes TL, Paananen J, Hansson O, Pankow J, Goodarzi MO, Carcamo-Orive I, Morris AP, Chen YD, Mäkinen VP, Ganna A, Mahajan A, Guo X, Abbasi F, Greenawalt DM, Lum P, Molony C, Lind L, Lindgren C, Raffel LJ, Tsao PS, RISC (Relationship between Insulin Sensitivity and Cardiovascular Disease) Consortium., EUGENE (European Network on Functional Genomics of Type Diabetes) Study., GUARDIAN (Genetics UndeRlying DIAbetes in HispaNics) Consortium., SAPPHIRe (Stanford Asian and Pacific Program for Hypertension and Insulin Resistance) Study., Schadt EE, Rotter JI, Sinaiko A, Reaven G, Yang X, Hsiung CA, Groop L, Cordell HJ, Laakso M, Hao K, Ingelsson E, Frayling TM, Weedon MN, Walker M, Quertermous T
IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS.
Ma M, Wang C, Glicksberg BS, Schadt EE, Li SD, Chen R
METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS.
Tignor N, Wang P, Genes N, Rogers L, Hershman SG, Scott ER, Zweig M, Yvonne Chan YF, Schadt EE
EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.
Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE
Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
Pereira E, Camacho-Vanegas O, Anand S, Sebra R, Catalina Camacho S, Garnar-Wortzel L, Nair N, Moshier E, Wooten M, Uzilov A, Chen R, Prasad-Hayes M, Zakashansky K, Beddoe AM, Schadt E, Dottino P, Martignetti JA
Correction: A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen.
Chao MC, Zhu S, Kimura S, Davis BM, Schadt EE, Fang G, Waldor MK
A Cytosine Methyltransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen [corrected].
Chao MC, Zhu S, Kimura S, Davis BM, Schadt EE, Fang G, Waldor MK
Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A
How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study.
Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE
Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis.
Wagschal A, Najafi-Shoushtari SH, Wang L, Goedeke L, Sinha S, deLemos AS, Black JC, Ramírez CM, Li Y, Tewhey R, Hatoum I, Shah N, Lu Y, Kristo F, Psychogios N, Vrbanac V, Lu YC, Hla T, de Cabo R, Tsang JS, Schadt E, Sabeti PC, Kathiresan S, Cohen DE, Whetstine J, Chung RT, Fernández-Hernando C, Kaplan LM, Bernards A, Gerszten RE, Näär AM
Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, GTEx Consortium., Schadt EE, Zhu J, Tu Z
Prediction of Causal Candidate Genes in Coronary Artery Disease Loci.
Brænne I, Civelek M, Vilne B, Di Narzo A, Johnson AD, Zhao Y, Reiz B, Codoni V, Webb TR, Foroughi Asl H, Hamby SE, Zeng L, Trégouët DA, Hao K, Topol EJ, Schadt EE, Yang X, Samani NJ, Björkegren JL, Erdmann J, Schunkert H, Lusis AJ, Leducq Consortium CAD Genomics‡.
An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium., Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO
A robust blood gene expression-based prognostic model for castration-resistant prostate cancer.
Wang L, Gong Y, Chippada-Venkata U, Heck MM, Retz M, Nawroth R, Galsky M, Tsao CK, Schadt E, de Bono J, Olmos D, Zhu J, Oh WK
Preparing the next generation of genomicists: a laboratory-style course in medical genomics.
Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, Mahajan M, Shah H, Suckiel S, Zweig M, Schadt EE
Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE
Modern Methods for Delineating Metagenomic Complexity.
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE
Improved integrative framework combining association data with gene expression features to prioritize Crohn’s disease genes.
Ning K, Gettler K, Zhang W, Ng SM, Bowen BM, Hyams J, Stephens MC, Kugathasan S, Denson LA, Schadt EE, Hoffman GE, Cho JH
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G
Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss.
Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, Naidich TP, Rodenburg RJ, Houten SM, Schadt EE
Prothymosin α variants isolated from CD8+ T cells and cervicovaginal fluid suppress HIV-1 replication through type I interferon induction.
Teixeira A, Yen B, Gusella GL, Thomas AG, Mullen MP, Aberg J, Chen X, Hoshida Y, van Bakel H, Schadt E, Basler CF, García-Sastre A, Mosoian A
Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.
Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT
Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease.
Foroughi Asl H, Talukdar HA, Kindt AS, Jain RK, Ermel R, Ruusalepp A, Nguyen KD, Dobrin R, Reilly DF, Schunkert H, Samani NJ, Braenne I, Erdmann J, Melander O, Qi J, Ivert T, Skogsberg J, Schadt EE, Michoel T, Björkegren JL, CARDIoGRAM Consortium.
Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.
Knowles JW, Xie W, Zhang Z, Chennamsetty I, Assimes TL, Paananen J, Hansson O, Pankow J, Goodarzi MO, Carcamo-Orive I, Morris AP, Chen YD, Mäkinen VP, Ganna A, Mahajan A, Guo X, Abbasi F, Greenawalt DM, Lum P, Molony C, Lind L, Lindgren C, Raffel LJ, Tsao PS, RISC (Relationship between Insulin Sensitivity and Cardiovascular Disease) Consortium., EUGENE2 (European Network on Functional Genomics of Type 2 Diabetes) Study., GUARDIAN (Genetics UndeRlying DIAbetes in HispaNics) Consortium., SAPPHIRe (Stanford Asian and Pacific Program for Hypertension and Insulin Resistance) Study., Schadt EE, Rotter JI, Sinaiko A, Reaven G, Yang X, Hsiung CA, Groop L, Cordell HJ, Laakso M, Hao K, Ingelsson E, Frayling TM, Weedon MN, Walker M, Quertermous T
Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans.
Ferguson JF, Meyer NJ, Qu L, Xue C, Liu Y, DerOhannessian SL, Rushefski M, Paschos GK, Tang S, Schadt EE, Li M, Christie JD, Reilly MP
Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders.
Björkegren JL, Kovacic JC, Dudley JT, Schadt EE
Genetic studies of body mass index yield new insights for obesity biology.
Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, Powell C, Vedantam S, Buchkovich ML, Yang J, Croteau-Chonka DC, Esko T, Fall T, Ferreira T, Gustafsson S, Kutalik Z, Luan J, Mägi R, Randall JC, Winkler TW, Wood AR, Workalemahu T, Faul JD, Smith JA, Hua Zhao J, Zhao W, Chen J, Fehrmann R, Hedman ÅK, Karjalainen J, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bolton JL, Bragg-Gresham JL, Buyske S, Demirkan A, Deng G, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Goel A, Gong J, Jackson AU, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Mangino M, Mateo Leach I, Medina-Gomez C, Medland SE, Nalls MA, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Shungin D, Stančáková A, Strawbridge RJ, Ju Sung Y, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Isaacs A, Albrecht E, Ärnlöv J, Arscott GM, Attwood AP, Bandinelli S, Barrett A, Bas IN, Bellis C, Bennett AJ, Berne C, Blagieva R, Blüher M, Böhringer S, Bonnycastle LL, Böttcher Y, Boyd HA, Bruinenberg M, Caspersen IH, Ida Chen YD, Clarke R, Daw EW, de Craen AJ, Delgado G, Dimitriou M, Doney AS, Eklund N, Estrada K, Eury E, Folkersen L, Fraser RM, Garcia ME, Geller F, Giedraitis V, Gigante B, Go AS, Golay A, Goodall AH, Gordon SD, Gorski M, Grabe HJ, Grallert H, Grammer TB, Gräßler J, Grönberg H, Groves CJ, Gusto G, Haessler J, Hall P, Haller T, Hallmans G, Hartman CA, Hassinen M, Hayward C, Heard-Costa NL, Helmer Q, Hengstenberg C, Holmen O, Hottenga JJ, James AL, Jeff JM, Johansson Å, Jolley J, Juliusdottir T, Kinnunen L, Koenig W, Koskenvuo M, Kratzer W, Laitinen J, Lamina C, Leander K, Lee NR, Lichtner P, Lind L, Lindström J, Sin Lo K, Lobbens S, Lorbeer R, Lu Y, Mach F, Magnusson PK, Mahajan A, McArdle WL, McLachlan S, Menni C, Merger S, Mihailov E, Milani L, Moayyeri A, Monda KL, Morken MA, Mulas A, Müller G, Müller-Nurasyid M, Musk AW, Nagaraja R, Nöthen MM, Nolte IM, Pilz S, Rayner NW, Renstrom F, Rettig R, Ried JS, Ripke S, Robertson NR, Rose LM, Sanna S, Scharnagl H, Scholtens S, Schumacher FR, Scott WR, Seufferlein T, Shi J, Vernon Smith A, Smolonska J, Stanton AV, Steinthorsdottir V, Stirrups K, Stringham HM, Sundström J, Swertz MA, Swift AJ, Syvänen AC, Tan ST, Tayo BO, Thorand B, Thorleifsson G, Tyrer JP, Uh HW, Vandenput L, Verhulst FC, Vermeulen SH, Verweij N, Vonk JM, Waite LL, Warren HR, Waterworth D, Weedon MN, Wilkens LR, Willenborg C, Wilsgaard T, Wojczynski MK, Wong A, Wright AF, Zhang Q, LifeLines Cohort Study., Brennan EP, Choi M, Dastani Z, Drong AW, Eriksson P, Franco-Cereceda A, Gådin JR, Gharavi AG, Goddard ME, Handsaker RE, Huang J, Karpe F, Kathiresan S, Keildson S, Kiryluk K, Kubo M, Lee JY, Liang L, Lifton RP, Ma B, McCarroll SA, McKnight AJ, Min JL, Moffatt MF, Montgomery GW, Murabito JM, Nicholson G, Nyholt DR, Okada Y, Perry JR, Dorajoo R, Reinmaa E, Salem RM, Sandholm N, Scott RA, Stolk L, Takahashi A, Tanaka T, Van’t Hooft FM, Vinkhuyzen AA, Westra HJ, Zheng W, Zondervan KT, ADIPOGen Consortium., AGEN-BMI Working Group., CARDIOGRAMplusC4D Consortium., CKDGen Consortium., GLGC., ICBP., MAGIC Investigators., MuTHER Consortium., MIGen Consortium., PAGE Consortium., ReproGen Consortium., GENIE Consortium., International Endogene Consortium., Heath AC, Arveiler D, Bakker SJ, Beilby J, Bergman RN, Blangero J, Bovet P, Campbell H, Caulfield MJ, Cesana G, Chakravarti A, Chasman DI, Chines PS, Collins FS, Crawford DC, Cupples LA, Cusi D, Danesh J, de Faire U, den Ruijter HM, Dominiczak AF, Erbel R, Erdmann J, Eriksson JG, Farrall M, Felix SB, Ferrannini E, Ferrières J, Ford I, Forouhi NG, Forrester T, Franco OH, Gansevoort RT, Gejman PV, Gieger C, Gottesman O, Gudnason V, Gyllensten U, Hall AS, Harris TB, Hattersley AT, Hicks AA, Hindorff LA, Hingorani AD, Hofman A, Homuth G, Hovingh GK, Humphries SE, Hunt SC, Hyppönen E, Illig T, Jacobs KB, Jarvelin MR, Jöckel KH, Johansen B, Jousilahti P, Jukema JW, Jula AM, Kaprio J, Kastelein JJ, Keinanen-Kiukaanniemi SM, Kiemeney LA, Knekt P, Kooner JS, Kooperberg C, Kovacs P, Kraja AT, Kumari M, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lyssenko V, Männistö S, Marette A, Matise TC, McKenzie CA, McKnight B, Moll FL, Morris AD, Morris AP, Murray JC, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Madden PA, Pasterkamp G, Peden JF, Peters A, Postma DS, Pramstaller PP, Price JF, Qi L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ridker PM, Rioux JD, Ritchie MD, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schunkert H, Schwarz PE, Sever P, Shuldiner AR, Sinisalo J, Stolk RP, Strauch K, Tönjes A, Trégouët DA, Tremblay A, Tremoli E, Virtamo J, Vohl MC, Völker U, Waeber G, Willemsen G, Witteman JC, Zillikens MC, Adair LS, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bornstein SR, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PI, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hui J, Hunter DJ, Hveem K, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, März W, Melbye M, Metspalu A, Moebus S, Munroe PB, Njølstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Pérusse L, Peters U, Power C, Quertermous T, Rauramaa R, Rivadeneira F, Saaristo TE, Saleheen D, Sattar N, Schadt EE, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Thorsteinsdottir U, Stumvoll M, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Walker M, Wallaschofski H, Wareham NJ, Watkins H, Weir DR, Wichmann HE, Wilson JF, Zanen P, Borecki IB, Deloukas P, Fox CS, Heid IM, O’Connell JR, Strachan DP, Stefansson K, van Duijn CM, Abecasis GR, Franke L, Frayling TM, McCarthy MI, Visscher PM, Scherag A, Willer CJ, Boehnke M, Mohlke KL, Lindgren CM, Beckmann JS, Barroso I, North KE, Ingelsson E, Hirschhorn JN, Loos RJ, Speliotes EK
New genetic loci link adipose and insulin biology to body fat distribution.
Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, Strawbridge RJ, Pers TH, Fischer K, Justice AE, Workalemahu T, Wu JM, Buchkovich ML, Heard-Costa NL, Roman TS, Drong AW, Song C, Gustafsson S, Day FR, Esko T, Fall T, Kutalik Z, Luan J, Randall JC, Scherag A, Vedantam S, Wood AR, Chen J, Fehrmann R, Karjalainen J, Kahali B, Liu CT, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bragg-Gresham JL, Buyske S, Demirkan A, Ehret GB, Feitosa MF, Goel A, Jackson AU, Johnson T, Kleber ME, Kristiansson K, Mangino M, Mateo Leach I, Medina-Gomez C, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Stančáková A, Ju Sung Y, Tanaka T, Teumer A, Van Vliet-Ostaptchouk JV, Yengo L, Zhang W, Albrecht E, Ärnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Böhringer S, Bonnet F, Böttcher Y, Bruinenberg M, Carba DB, Caspersen IH, Clarke R, Daw EW, Deelen J, Deelman E, Delgado G, Doney AS, Eklund N, Erdos MR, Estrada K, Eury E, Friedrich N, Garcia ME, Giedraitis V, Gigante B, Go AS, Golay A, Grallert H, Grammer TB, Gräßler J, Grewal J, Groves CJ, Haller T, Hallmans G, Hartman CA, Hassinen M, Hayward C, Heikkilä K, Herzig KH, Helmer Q, Hillege HL, Holmen O, Hunt SC, Isaacs A, Ittermann T, James AL, Johansson I, Juliusdottir T, Kalafati IP, Kinnunen L, Koenig W, Kooner IK, Kratzer W, Lamina C, Leander K, Lee NR, Lichtner P, Lind L, Lindström J, Lobbens S, Lorentzon M, Mach F, Magnusson PK, Mahajan A, McArdle WL, Menni C, Merger S, Mihailov E, Milani L, Mills R, Moayyeri A, Monda KL, Mooijaart SP, Mühleisen TW, Mulas A, Müller G, Müller-Nurasyid M, Nagaraja R, Nalls MA, Narisu N, Glorioso N, Nolte IM, Olden M, Rayner NW, Renstrom F, Ried JS, Robertson NR, Rose LM, Sanna S, Scharnagl H, Scholtens S, Sennblad B, Seufferlein T, Sitlani CM, Vernon Smith A, Stirrups K, Stringham HM, Sundström J, Swertz MA, Swift AJ, Syvänen AC, Tayo BO, Thorand B, Thorleifsson G, Tomaschitz A, Troffa C, van Oort FV, Verweij N, Vonk JM, Waite LL, Wennauer R, Wilsgaard T, Wojczynski MK, Wong A, Zhang Q, Hua Zhao J, Brennan EP, Choi M, Eriksson P, Folkersen L, Franco-Cereceda A, Gharavi AG, Hedman ÅK, Hivert MF, Huang J, Kanoni S, Karpe F, Keildson S, Kiryluk K, Liang L, Lifton RP, Ma B, McKnight AJ, McPherson R, Metspalu A, Min JL, Moffatt MF, Montgomery GW, Murabito JM, Nicholson G, Nyholt DR, Olsson C, Perry JR, Reinmaa E, Salem RM, Sandholm N, Schadt EE, Scott RA, Stolk L, Vallejo EE, Westra HJ, Zondervan KT, ADIPOGen Consortium., CARDIOGRAMplusC4D Consortium., CKDGen Consortium., GEFOS Consortium., GENIE Consortium., GLGC., ICBP., International Endogene Consortium., LifeLines Cohort Study., MAGIC Investigators., MuTHER Consortium., PAGE Consortium., ReproGen Consortium., Amouyel P, Arveiler D, Bakker SJ, Beilby J, Bergman RN, Blangero J, Brown MJ, Burnier M, Campbell H, Chakravarti A, Chines PS, Claudi-Boehm S, Collins FS, Crawford DC, Danesh J, de Faire U, de Geus EJ, Dörr M, Erbel R, Eriksson JG, Farrall M, Ferrannini E, Ferrières J, Forouhi NG, Forrester T, Franco OH, Gansevoort RT, Gieger C, Gudnason V, Haiman CA, Harris TB, Hattersley AT, Heliövaara M, Hicks AA, Hingorani AD, Hoffmann W, Hofman A, Homuth G, Humphries SE, Hyppönen E, Illig T, Jarvelin MR, Johansen B, Jousilahti P, Jula AM, Kaprio J, Kee F, Keinanen-Kiukaanniemi SM, Kooner JS, Kooperberg C, Kovacs P, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lyssenko V, Männistö S, Marette A, Matise TC, McKenzie CA, McKnight B, Musk AW, Möhlenkamp S, Morris AD, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Palmer LJ, Penninx BW, Peters A, Pramstaller PP, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ridker PM, Ritchie MD, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PE, Shuldiner AR, Staessen JA, Steinthorsdottir V, Stolk RP, Strauch K, Tönjes A, Tremblay A, Tremoli E, Vohl MC, Völker U, Vollenweider P, Wilson JF, Witteman JC, Adair LS, Bochud M, Boehm BO, Bornstein SR, Bouchard C, Cauchi S, Caulfield MJ, Chambers JC, Chasman DI, Cooper RS, Dedoussis G, Ferrucci L, Froguel P, Grabe HJ, Hamsten A, Hui J, Hveem K, Jöckel KH, Kivimaki M, Kuh D, Laakso M, Liu Y, März W, Munroe PB, Njølstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Pérusse L, Peters U, Power C, Quertermous T, Rauramaa R, Rivadeneira F, Saaristo TE, Saleheen D, Sinisalo J, Slagboom PE, Snieder H, Spector TD, Thorsteinsdottir U, Stumvoll M, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Veronesi G, Walker M, Wareham NJ, Watkins H, Wichmann HE, Abecasis GR, Assimes TL, Berndt SI, Boehnke M, Borecki IB, Deloukas P, Franke L, Frayling TM, Groop LC, Hunter DJ, Kaplan RC, O’Connell JR, Qi L, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Willer CJ, Visscher PM, Yang J, Hirschhorn JN, Zillikens MC, McCarthy MI, Speliotes EK, North KE, Fox CS, Barroso I, Franks PW, Ingelsson E, Heid IM, Loos RJ, Cupples LA, Morris AP, Lindgren CM, Mohlke KL
Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma.
Sia D, Losic B, Moeini A, Cabellos L, Hao K, Revill K, Bonal D, Miltiadous O, Zhang Z, Hoshida Y, Cornella H, Castillo-Martin M, Pinyol R, Kasai Y, Roayaie S, Thung SN, Fuster J, Schwartz ME, Waxman S, Cordon-Cardo C, Schadt E, Mazzaferro V, Llovet JM
Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.
Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, Huang T, Tu Z, Foronjy RF, Spira A, Schadt EE, Powell CA, Zhu J
Exploring the associations between microRNA expression profiles and environmental pollutants in human placenta from the National Children’s Study (NCS).
Li Q, Kappil MA, Li A, Dassanayake PS, Darrah TH, Friedman AE, Friedman M, Lambertini L, Landrigan P, Stodgell CJ, Xia Y, Nanes JA, Aagaard KM, Schadt EE, Murray JC, Clark EB, Dole N, Culhane J, Swanson J, Varner M, Moye J, Kasten C, Miller RK, Chen J
Systems biology of asthma and allergic diseases: a multiscale approach.
Bunyavanich S, Schadt EE
Causal inference in biology networks with integrated belief propagation.
Chang R, Karr JR, Schadt EE
Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders.
Schadt EE, Buchanan S, Brennand KJ, Merchant KM
TGFβ receptor 1: an immune susceptibility gene in HPV-associated cancer.
Levovitz C, Chen D, Ivansson E, Gyllensten U, Finnigan JP, Alshawish S, Zhang W, Schadt EE, Posner MR, Genden EM, Boffetta P, Sikora AG
iPSC-derived dopamine neurons reveal differences between monozygotic twins discordant for Parkinson’s disease.
Woodard CM, Campos BA, Kuo SH, Nirenberg MJ, Nestor MW, Zimmer M, Mosharov EV, Sulzer D, Zhou H, Paull D, Clark L, Schadt EE, Sardi SP, Rubin L, Eggan K, Brock M, Lipnick S, Rao M, Chang S, Li A, Noggle SA
A role for noncoding variation in schizophrenia.
Roussos P, Mitchell AC, Voloudakis G, Fullard JF, Pothula VM, Tsang J, Stahl EA, Georgakopoulos A, Ruderfer DM, Charney A, Okada Y, Siminovitch KA, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Plenge RM, Raychaudhuri S, Fromer M, Purcell SM, Brennand KJ, Robakis NK, Schadt EE, Akbarian S, Sklar P
Geroscience: linking aging to chronic disease.
Kennedy BK, Berger SL, Brunet A, Campisi J, Cuervo AM, Epel ES, Franceschi C, Lithgow GJ, Morimoto RI, Pessin JE, Rando TA, Richardson A, Schadt EE, Wyss-Coray T, Sierra F
lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R.
Hoffman GE, Mezey JG, Schadt EE
Downregulation of carnitine acyl-carnitine translocase by miRNAs 132 and 212 amplifies glucose-stimulated insulin secretion.
Soni MS, Rabaglia ME, Bhatnagar S, Shang J, Ilkayeva O, Mynatt R, Zhou YP, Schadt EE, Thornberry NA, Muoio DM, Keller MP, Attie AD
Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.
Shang MM, Talukdar HA, Hofmann JJ, Niaudet C, Asl HF, Jain RK, Rossignoli A, Cedergren C, Silveira A, Gigante B, Leander K, de Faire U, Hamsten A, Ruusalepp A, Melander O, Ivert T, Michoel T, Schadt EE, Betsholtz C, Skogsberg J, Björkegren JL
Biomarkers for combat-related PTSD: focus on molecular networks from high-dimensional data.
Neylan TC, Schadt EE, Yehuda R
MODMatcher: multi-omics data matcher for integrative genomic analysis.
Yoo S, Huang T, Campbell JD, Lee E, Tu Z, Geraci MW, Powell CA, Schadt EE, Spira A, Zhu J
Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis.
Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, Ziniti JP, Cohain A, Linderman M, Torgerson DG, Eng CS, Pino-Yanes M, Padhukasahasram B, Yang JJ, Mathias RA, Beaty TH, Li X, Graves P, Romieu I, Navarro Bdel R, Salam MT, Vora H, Nicolae DL, Ober C, Martinez FD, Bleecker ER, Meyers DA, Gauderman WJ, Gilliland F, Burchard EG, Barnes KC, Williams LK, London SJ, Zhang B, Raby BA, Weiss ST
Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease.
Sivendran S, Chang R, Pham L, Phelps RG, Harcharik ST, Hall LD, Bernardo SG, Moskalenko MM, Sivendran M, Fu Y, de Moll EH, Pan M, Moon JY, Arora S, Cohain A, DiFeo A, Ferringer TC, Tismenetsky M, Tsui CL, Friedlander PA, Parides MK, Banchereau J, Chaussabel D, Lebwohl MG, Wolchok JD, Bhardwaj N, Burakoff SJ, Oh WK, Palucka K, Merad M, Schadt EE, Saenger YM
Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.
Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T, Suver C, Molony C, Melquist S, Johnson AD, Fan G, Stone DJ, Schadt EE, Casaccia P, Emilsson V, Zhu J
The role of macromolecular damage in aging and age-related disease.
Richardson AG, Schadt EE
Translational genomics. Clues from the resilient.
Friend SH, Schadt EE
Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.
Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, Plagnol V
Analytical validation of whole exome and whole genome sequencing for clinical applications.
Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE
Mutations in tetratricopeptide repeat domain 7A result in a severe form of very early onset inflammatory bowel disease.
Avitzur Y, Guo C, Mastropaolo LA, Bahrami E, Chen H, Zhao Z, Elkadri A, Dhillon S, Murchie R, Fattouh R, Huynh H, Walker JL, Wales PW, Cutz E, Kakuta Y, Dudley J, Kammermeier J, Powrie F, Shah N, Walz C, Nathrath M, Kotlarz D, Puchaka J, Krieger JR, Racek T, Kirchner T, Walters TD, Brumell JH, Griffiths AM, Rezaei N, Rashtian P, Najafi M, Monajemzadeh M, Pelsue S, McGovern DP, Uhlig HH, Schadt E, Klein C, Snapper SB, Muise AM
Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci.
Tragante V, Barnes MR, Ganesh SK, Lanktree MB, Guo W, Franceschini N, Smith EN, Johnson T, Holmes MV, Padmanabhan S, Karczewski KJ, Almoguera B, Barnard J, Baumert J, Chang YP, Elbers CC, Farrall M, Fischer ME, Gaunt TR, Gho JM, Gieger C, Goel A, Gong Y, Isaacs A, Kleber ME, Mateo Leach I, McDonough CW, Meijs MF, Melander O, Nelson CP, Nolte IM, Pankratz N, Price TS, Shaffer J, Shah S, Tomaszewski M, van der Most PJ, Van Iperen EP, Vonk JM, Witkowska K, Wong CO, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Brown M, Burt A, Cooper-DeHoff RM, Connell JM, Cruickshanks KJ, Curtis SP, Davey-Smith G, Delles C, Gansevoort RT, Guo X, Haiqing S, Hastie CE, Hofker MH, Hovingh GK, Kim DS, Kirkland SA, Klein BE, Klein R, Li YR, Maiwald S, Newton-Cheh C, O’Brien ET, Onland-Moret NC, Palmas W, Parsa A, Penninx BW, Pettinger M, Vasan RS, Ranchalis JE, M Ridker P, Rose LM, Sever P, Shimbo D, Steele L, Stolk RP, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Wyatt S, Young JH, Zwinderman AH, Bezzina CR, Boerwinkle E, Casas JP, Caulfield MJ, Chakravarti A, Chasman DI, Davidson KW, Doevendans PA, Dominiczak AF, FitzGerald GA, Gums JG, Fornage M, Hakonarson H, Halder I, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJ, Koenig W, Kumari M, März W, Murray SS, O’Connell JR, Oldehinkel AJ, Pankow JS, Rader DJ, Redline S, Reilly MP, Schadt EE, Kottke-Marchant K, Snieder H, Snyder M, Stanton AV, Tobin MD, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Watkins H, Johnson AD, Reiner AP, Zhu X, de Bakker PI, Levy D, Asselbergs FW, Munroe PB, Keating BJ
Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis.
Kojima Y, Downing K, Kundu R, Miller C, Dewey F, Lancero H, Raaz U, Perisic L, Hedin U, Schadt E, Maegdefessel L, Quertermous T, Leeper NJ
Causal effects of body mass index on cardiometabolic traits and events: a Mendelian randomization analysis.
Holmes MV, Lange LA, Palmer T, Lanktree MB, North KE, Almoguera B, Buxbaum S, Chandrupatla HR, Elbers CC, Guo Y, Hoogeveen RC, Li J, Li YR, Swerdlow DI, Cushman M, Price TS, Curtis SP, Fornage M, Hakonarson H, Patel SR, Redline S, Siscovick DS, Tsai MY, Wilson JG, van der Schouw YT, FitzGerald GA, Hingorani AD, Casas JP, de Bakker PI, Rich SS, Schadt EE, Asselbergs FW, Reiner AP, Keating BJ
Unifying immunology with informatics and multiscale biology.
Kidd BA, Peters LA, Schadt EE, Dudley JT
Autotransporters but not pAA are critical for rabbit colonization by Shiga toxin-producing Escherichia coli O104:H4.
Munera D, Ritchie JM, Hatzios SK, Bronson R, Fang G, Schadt EE, Davis BM, Waldor MK
Personalized ovarian cancer disease surveillance and detection of candidate therapeutic drug target in circulating tumor DNA.
Martignetti JA, Camacho-Vanegas O, Priedigkeit N, Camacho C, Pereira E, Lin L, Garnar-Wortzel L, Miller D, Losic B, Shah H, Liao J, Ma J, Lahiri P, Chee M, Schadt E, Dottino P
Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study.
Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE
Characterization of the human ESC transcriptome by hybrid sequencing.
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH
Fine-mapping, gene expression and splicing analysis of the disease associated LRRK2 locus.
Trabzuni D, Ryten M, Emmett W, Ramasamy A, Lackner KJ, Zeller T, Walker R, Smith C, Lewis PA, Mamais A, de Silva R, Vandrovcova J, International Parkinson Disease Genomics Consortium (IPDGC)., Hernandez D, Nalls MA, Sharma M, Garnier S, Lesage S, Simon-Sanchez J, Gasser T, Heutink P, Brice A, Singleton A, Cai H, Schadt E, Wood NW, Bandopadhyay R, Weale ME, Hardy J, Plagnol V
A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry.
Monda KL, Chen GK, Taylor KC, Palmer C, Edwards TL, Lange LA, Ng MC, Adeyemo AA, Allison MA, Bielak LF, Chen G, Graff M, Irvin MR, Rhie SK, Li G, Liu Y, Liu Y, Lu Y, Nalls MA, Sun YV, Wojczynski MK, Yanek LR, Aldrich MC, Ademola A, Amos CI, Bandera EV, Bock CH, Britton A, Broeckel U, Cai Q, Caporaso NE, Carlson CS, Carpten J, Casey G, Chen WM, Chen F, Chen YD, Chiang CW, Coetzee GA, Demerath E, Deming-Halverson SL, Driver RW, Dubbert P, Feitosa MF, Feng Y, Freedman BI, Gillanders EM, Gottesman O, Guo X, Haritunians T, Harris T, Harris CC, Hennis AJ, Hernandez DG, McNeill LH, Howard TD, Howard BV, Howard VJ, Johnson KC, Kang SJ, Keating BJ, Kolb S, Kuller LH, Kutlar A, Langefeld CD, Lettre G, Lohman K, Lotay V, Lyon H, Manson JE, Maixner W, Meng YA, Monroe KR, Morhason-Bello I, Murphy AB, Mychaleckyj JC, Nadukuru R, Nathanson KL, Nayak U, N’diaye A, Nemesure B, Wu SY, Leske MC, Neslund-Dudas C, Neuhouser M, Nyante S, Ochs-Balcom H, Ogunniyi A, Ogundiran TO, Ojengbede O, Olopade OI, Palmer JR, Ruiz-Narvaez EA, Palmer ND, Press MF, Rampersaud E, Rasmussen-Torvik LJ, Rodriguez-Gil JL, Salako B, Schadt EE, Schwartz AG, Shriner DA, Siscovick D, Smith SB, Wassertheil-Smoller S, Speliotes EK, Spitz MR, Sucheston L, Taylor H, Tayo BO, Tucker MA, Van Den Berg DJ, Edwards DR, Wang Z, Wiencke JK, Winkler TW, Witte JS, Wrensch M, Wu X, Yang JJ, Levin AM, Young TR, Zakai NA, Cushman M, Zanetti KA, Zhao JH, Zhao W, Zheng Y, Zhou J, Ziegler RG, Zmuda JM, Fernandes JK, Gilkeson GS, Kamen DL, Hunt KJ, Spruill IJ, Ambrosone CB, Ambs S, Arnett DK, Atwood L, Becker DM, Berndt SI, Bernstein L, Blot WJ, Borecki IB, Bottinger EP, Bowden DW, Burke G, Chanock SJ, Cooper RS, Ding J, Duggan D, Evans MK, Fox C, Garvey WT, Bradfield JP, Hakonarson H, Grant SF, Hsing A, Chu L, Hu JJ, Huo D, Ingles SA, John EM, Jordan JM, Kabagambe EK, Kardia SL, Kittles RA, Goodman PJ, Klein EA, Kolonel LN, Le Marchand L, Liu S, McKnight B, Millikan RC, Mosley TH, Padhukasahasram B, Williams LK, Patel SR, Peters U, Pettaway CA, Peyser PA, Psaty BM, Redline S, Rotimi CN, Rybicki BA, Sale MM, Schreiner PJ, Signorello LB, Singleton AB, Stanford JL, Strom SS, Thun MJ, Vitolins M, Zheng W, Moore JH, Williams SM, Ketkar S, Zhu X, Zonderman AB, NABEC Consortium., UKBEC Consortium., BioBank Japan Project., AGEN Consortium., Kooperberg C, Papanicolaou GJ, Henderson BE, Reiner AP, Hirschhorn JN, Loos RJ, North KE, Haiman CA
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson WO, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimäki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt MF, Mohlke KL, O’Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E
Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease.
Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V
Loci influencing blood pressure identified using a cardiovascular gene-centric array.
Ganesh SK, Tragante V, Guo W, Guo Y, Lanktree MB, Smith EN, Johnson T, Castillo BA, Barnard J, Baumert J, Chang YP, Elbers CC, Farrall M, Fischer ME, Franceschini N, Gaunt TR, Gho JM, Gieger C, Gong Y, Isaacs A, Kleber ME, Mateo Leach I, McDonough CW, Meijs MF, Mellander O, Molony CM, Nolte IM, Padmanabhan S, Price TS, Rajagopalan R, Shaffer J, Shah S, Shen H, Soranzo N, van der Most PJ, Van Iperen EP, Van Setten J, Vonk JM, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Boer JM, Boerwinkle E, Burkley B, Burt A, Chakravarti A, Chen W, Cooper-Dehoff RM, Curtis SP, Dreisbach A, Duggan D, Ehret GB, Fabsitz RR, Fornage M, Fox E, Furlong CE, Gansevoort RT, Hofker MH, Hovingh GK, Kirkland SA, Kottke-Marchant K, Kutlar A, Lacroix AZ, Langaee TY, Li YR, Lin H, Liu K, Maiwald S, Malik R, CARDIOGRAM, METASTROKE., Murugesan G, Newton-Cheh C, O’Connell JR, Onland-Moret NC, Ouwehand WH, Palmas W, Penninx BW, Pepine CJ, Pettinger M, Polak JF, Ramachandran VS, Ranchalis J, Redline S, Ridker PM, Rose LM, Scharnag H, Schork NJ, Shimbo D, Shuldiner AR, Srinivasan SR, Stolk RP, Taylor HA, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Winkelmann BR, Wyatt S, Young JH, Boehm BO, Caulfield MJ, Chasman DI, Davidson KW, Doevendans PA, Fitzgerald GA, Gums JG, Hakonarson H, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJ, Koenig W, LifeLines Cohort Study., März W, Mitchell BD, Murray SS, Oldehinkel AJ, Rader DJ, Reilly MP, Reiner AP, Schadt EE, Silverstein RL, Snieder H, Stanton AV, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Johnson AD, Munroe PB, de Bakker PI, Zhu X, Levy D, Keating BJ, Asselbergs FW
CR1 and the “vanishing amyloid” hypothesis of Alzheimer’s disease.
Gandy S, Haroutunian V, DeKosky ST, Sano M, Schadt EE
Loss of CDKN2B promotes p53-dependent smooth muscle cell apoptosis and aneurysm formation.
Leeper NJ, Raiesdana A, Kojima Y, Kundu RK, Cheng H, Maegdefessel L, Toh R, Ahn GO, Ali ZA, Anderson DR, Miller CL, Roberts SC, Spin JM, de Almeida PE, Wu JC, Xu B, Cheng K, Quertermous M, Kundu S, Kortekaas KE, Berzin E, Downing KP, Dalman RL, Tsao PS, Schadt EE, Owens GK, Quertermous T
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A
Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium., Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, DIAGRAM Consortium., CARDIOGENICS Consortium., Doney AS, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, MuTHER Consortium., Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AF, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wellcome Trust Case Control Consortium., Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O’Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CN, Roberts R, Watkins H, Schunkert H, Samani NJ
Improving breast cancer survival analysis through competition-based multidimensional modeling.
Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, Wong W, Schadt E
Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.
Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.
Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, Clark TA, Schadt E, Turner SW, Korlach J, Serrano L
Seventy-five genetic loci influencing the human red blood cell.
van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, Paul DS, Elling U, Allayee H, Li X, Radhakrishnan A, Tan ST, Voss K, Weichenberger CX, Albers CA, Al-Hussani A, Asselbergs FW, Ciullo M, Danjou F, Dina C, Esko T, Evans DM, Franke L, Gögele M, Hartiala J, Hersch M, Holm H, Hottenga JJ, Kanoni S, Kleber ME, Lagou V, Langenberg C, Lopez LM, Lyytikäinen LP, Melander O, Murgia F, Nolte IM, O’Reilly PF, Padmanabhan S, Parsa A, Pirastu N, Porcu E, Portas L, Prokopenko I, Ried JS, Shin SY, Tang CS, Teumer A, Traglia M, Ulivi S, Westra HJ, Yang J, Zhao JH, Anni F, Abdellaoui A, Attwood A, Balkau B, Bandinelli S, Bastardot F, Benyamin B, Boehm BO, Cookson WO, Das D, de Bakker PI, de Boer RA, de Geus EJ, de Moor MH, Dimitriou M, Domingues FS, Döring A, Engström G, Eyjolfsson GI, Ferrucci L, Fischer K, Galanello R, Garner SF, Genser B, Gibson QD, Girotto G, Gudbjartsson DF, Harris SE, Hartikainen AL, Hastie CE, Hedblad B, Illig T, Jolley J, Kähönen M, Kema IP, Kemp JP, Liang L, Lloyd-Jones H, Loos RJ, Meacham S, Medland SE, Meisinger C, Memari Y, Mihailov E, Miller K, Moffatt MF, Nauck M, Novatchkova M, Nutile T, Olafsson I, Onundarson PT, Parracciani D, Penninx BW, Perseu L, Piga A, Pistis G, Pouta A, Puc U, Raitakari O, Ring SM, Robino A, Ruggiero D, Ruokonen A, Saint-Pierre A, Sala C, Salumets A, Sambrook J, Schepers H, Schmidt CO, Silljé HH, Sladek R, Smit JH, Starr JM, Stephens J, Sulem P, Tanaka T, Thorsteinsdottir U, Tragante V, van Gilst WH, van Pelt LJ, van Veldhuisen DJ, Völker U, Whitfield JB, Willemsen G, Winkelmann BR, Wirnsberger G, Algra A, Cucca F, d’Adamo AP, Danesh J, Deary IJ, Dominiczak AF, Elliott P, Fortina P, Froguel P, Gasparini P, Greinacher A, Hazen SL, Jarvelin MR, Khaw KT, Lehtimäki T, Maerz W, Martin NG, Metspalu A, Mitchell BD, Montgomery GW, Moore C, Navis G, Pirastu M, Pramstaller PP, Ramirez-Solis R, Schadt E, Scott J, Shuldiner AR, Smith GD, Smith JG, Snieder H, Sorice R, Spector TD, Stefansson K, Stumvoll M, Tang WH, Toniolo D, Tönjes A, Visscher PM, Vollenweider P, Wareham NJ, Wolffenbuttel BH, Boomsma DI, Beckmann JS, Dedoussis GV, Deloukas P, Ferreira MA, Sanna S, Uda M, Hicks AA, Penninger JM, Gieger C, Kooner JS, Ouwehand WH, Soranzo N, Chambers JC
A systematic approach to multifactorial cardiovascular disease: causal analysis.
Schwartz SM, Schwartz HT, Horvath S, Schadt E, Lee SI
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE
Non-O1 Vibrio cholerae unlinked to cholera in Haiti.
Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D’Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, International IBD Genetics Consortium (IIBDGC)., Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH
Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.
Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, David P, Brown M, Wang S, Link DR, Olson J, Travers K, Schadt E, Bushman FD
Mapping cis- and trans-regulatory effects across multiple tissues in twins.
Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett J, Sekowska M, Wilk A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M, Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni L, Tsoka S, Bataille V, Durbin R, Nestle FO, O’Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KR, Schadt EE, Stefansson K, Smith GD, McCarthy MI, Deloukas P, Dermitzakis ET, Spector TD, Multiple Tissue Human Expression Resource (MuTHER) Consortium.
Genetics. A GPS for navigating DNA.
Schadt E, Chang R
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.
Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY
Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis.
Wang CY, Stapleton DS, Schueler KL, Rabaglia ME, Oler AT, Keller MP, Kendziorski CM, Broman KW, Yandell BS, Schadt EE, Attie AD
Eric Schadt. Interview by H. Craig Mak.
Schadt E
This I believe: gaining new insights through integrating “old” data.
Loos RJ, Schadt EE
Leveraging models of cell regulation and GWAS data in integrative network-based association studies.
Califano A, Butte AJ, Friend S, Ideker T, Schadt E
Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers.
Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, Meng Q, Peters M, He Y, Ni C, Slipetz D, Crackower MA, Houshyar H, Tan CM, Asante-Appiah E, O’Neill G, Luo MJ, Thieringer R, Yuan J, Chiu CS, Lum PY, Lamb J, Boie Y, Wilkinson HA, Schadt EE, Dai H, Roberts C
A hybrid approach for the automated finishing of bacterial genomes.
Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE
The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.
Salm MP, Horswell SD, Hutchison CE, Speedy HE, Yang X, Liang L, Schadt EE, Cookson WO, Wierzbicki AS, Naoumova RP, Shoulders CC
Genome scans for transmission ratio distortion regions in mice.
Casellas J, Gularte RJ, Farber CR, Varona L, Mehrabian M, Schadt EE, Lusis AJ, Attie AD, Yandell BS, Medrano JF
Bayesian method to predict individual SNP genotypes from gene expression data.
Schadt EE, Woo S, Hao K
Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia.
Smith CC, Wang Q, Chin CS, Salerno S, Damon LE, Levis MJ, Perl AE, Travers KJ, Wang S, Hunt JP, Zarrinkar PP, Schadt EE, Kasarskis A, Kuriyan J, Shah NP
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.
Saxena R, Elbers CC, Guo Y, Peter I, Gaunt TR, Mega JL, Lanktree MB, Tare A, Castillo BA, Li YR, Johnson T, Bruinenberg M, Gilbert-Diamond D, Rajagopalan R, Voight BF, Balasubramanyam A, Barnard J, Bauer F, Baumert J, Bhangale T, Böhm BO, Braund PS, Burton PR, Chandrupatla HR, Clarke R, Cooper-DeHoff RM, Crook ED, Davey-Smith G, Day IN, de Boer A, de Groot MC, Drenos F, Ferguson J, Fox CS, Furlong CE, Gibson Q, Gieger C, Gilhuijs-Pederson LA, Glessner JT, Goel A, Gong Y, Grant SF, Grobbee DE, Hastie C, Humphries SE, Kim CE, Kivimaki M, Kleber M, Meisinger C, Kumari M, Langaee TY, Lawlor DA, Li M, Lobmeyer MT, Maitland-van der Zee AH, Meijs MF, Molony CM, Morrow DA, Murugesan G, Musani SK, Nelson CP, Newhouse SJ, O’Connell JR, Padmanabhan S, Palmen J, Patel SR, Pepine CJ, Pettinger M, Price TS, Rafelt S, Ranchalis J, Rasheed A, Rosenthal E, Ruczinski I, Shah S, Shen H, Silbernagel G, Smith EN, Spijkerman AW, Stanton A, Steffes MW, Thorand B, Trip M, van der Harst P, van der A DL, van Iperen EP, van Setten J, van Vliet-Ostaptchouk JV, Verweij N, Wolffenbuttel BH, Young T, Zafarmand MH, Zmuda JM, Look AHEAD Research Group., DIAGRAM consortium., Boehnke M, Altshuler D, McCarthy M, Kao WH, Pankow JS, Cappola TP, Sever P, Poulter N, Caulfield M, Dominiczak A, Shields DC, Bhatt DL, Zhang L, Curtis SP, Danesh J, Casas JP, van der Schouw YT, Onland-Moret NC, Doevendans PA, Dorn GW 2nd, Farrall M, FitzGerald GA, Hamsten A, Hegele R, Hingorani AD, Hofker MH, Huggins GS, Illig T, Jarvik GP, Johnson JA, Klungel OH, Knowler WC, Koenig W, März W, Meigs JB, Melander O, Munroe PB, Mitchell BD, Bielinski SJ, Rader DJ, Reilly MP, Rich SS, Rotter JI, Saleheen D, Samani NJ, Schadt EE, Shuldiner AR, Silverstein R, Kottke-Marchant K, Talmud PJ, Watkins H, Asselbergs FW, de Bakker PI, McCaffery J, Wijmenga C, Sabatine MS, Wilson JG, Reiner A, Bowden DW, Hakonarson H, Siscovick DS, Keating BJ
A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models.
Langfelder P, Castellani LW, Zhou Z, Paul E, Davis R, Schadt EE, Lusis AJ, Horvath S, Mehrabian M
Systems genetics of susceptibility to obesity-induced diabetes in mice.
Davis RC, van Nas A, Castellani LW, Zhao Y, Zhou Z, Wen P, Yu S, Qi H, Rosales M, Schadt EE, Broman KW, Péterfy M, Lusis AJ
NEW: network-enabled wisdom in biology, medicine, and health care.
Schadt EE, Björkegren JL
Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ
The changing privacy landscape in the era of big data.
Schadt EE
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.
Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE
Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.
Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
Dastani Z, Hivert MF, Timpson N, Perry JR, Yuan X, Scott RA, Henneman P, Heid IM, Kizer JR, Lyytikäinen LP, Fuchsberger C, Tanaka T, Morris AP, Small K, Isaacs A, Beekman M, Coassin S, Lohman K, Qi L, Kanoni S, Pankow JS, Uh HW, Wu Y, Bidulescu A, Rasmussen-Torvik LJ, Greenwood CM, Ladouceur M, Grimsby J, Manning AK, Liu CT, Kooner J, Mooser VE, Vollenweider P, Kapur KA, Chambers J, Wareham NJ, Langenberg C, Frants R, Willems-Vandijk K, Oostra BA, Willems SM, Lamina C, Winkler TW, Psaty BM, Tracy RP, Brody J, Chen I, Viikari J, Kähönen M, Pramstaller PP, Evans DM, St Pourcain B, Sattar N, Wood AR, Bandinelli S, Carlson OD, Egan JM, Böhringer S, van Heemst D, Kedenko L, Kristiansson K, Nuotio ML, Loo BM, Harris T, Garcia M, Kanaya A, Haun M, Klopp N, Wichmann HE, Deloukas P, Katsareli E, Couper DJ, Duncan BB, Kloppenburg M, Adair LS, Borja JB, DIAGRAM+ Consortium., MAGIC Consortium., GLGC Investigators., MuTHER Consortium., Wilson JG, Musani S, Guo X, Johnson T, Semple R, Teslovich TM, Allison MA, Redline S, Buxbaum SG, Mohlke KL, Meulenbelt I, Ballantyne CM, Dedoussis GV, Hu FB, Liu Y, Paulweber B, Spector TD, Slagboom PE, Ferrucci L, Jula A, Perola M, Raitakari O, Florez JC, Salomaa V, Eriksson JG, Frayling TM, Hicks AA, Lehtimäki T, Smith GD, Siscovick DS, Kronenberg F, van Duijn C, Loos RJ, Waterworth DM, Meigs JB, Dupuis J, Richards JB, Voight BF, Scott LJ, Steinthorsdottir V, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Hofmann OM, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Morris AD, Palmer CN, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Pedersen O, Barroso I, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, Soranzo N, Wheeler E, Glazer NL, Bouatia-Naji N, Mägi R, Randall J, Elliott P, Rybin D, Dehghan A, Hottenga JJ, Song K, Goel A, Lajunen T, Doney A, Cavalcanti-Proença C, Kumari M, Timpson NJ, Zabena C, Ingelsson E, An P, O’Connell J, Luan J, Elliott A, McCarroll SA, Roccasecca RM, Pattou F, Sethupathy P, Ariyurek Y, Barter P, Beilby JP, Ben-Shlomo Y, Bergmann S, Bochud M, Bonnefond A, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Chen YD, Chines P, Clarke R, Coin LJ, Cooper MN, Crisponi L, Day IN, de Geus EJ, Delplanque J, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Grundy S, Gwilliam R, Hallmans G, Hammond N, Han X, Hartikainen AL, Hayward C, Heath SC, Hercberg S, Hillman DR, Hingorani AD, Hui J, Hung J, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Mahley R, Mangino M, Martínez-Larrad MT, McAteer JB, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Mukherjee S, Naitza S, Neville MJ, Orrù M, Pakyz R, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Pfeiffer AF, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Seedorf U, Sharp SJ, Shields B, Sigurðsson G, Sijbrands EJ, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tönjes A, Uitterlinden AG, van Dijk KW, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Ward KL, Watkins H, Wild SH, Willemsen G, Witteman JC, Yarnell JW, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, DIAGRAM Consortium., GIANT Consortium., Global B Pgen Consortium., Borecki IB, Meneton P, Magnusson PK, Nathan DM, Williams GH, Silander K, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Serrano-Ríos M, Lind L, Palmer LJ, Hu FB 1st, Franks PW, Ebrahim S, Marmot M, Kao WH, Pramstaller PP, Wright AF, Stumvoll M, Hamsten A, Procardis Consortium., Buchanan TA, Valle TT, Rotter JI, Penninx BW, Boomsma DI, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Peltonen L, Mooser V, Sladek R, MAGIC investigators., GLGC Consortium., Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Chasman DI, Johansen CT, Fouchier SW, Peloso GM, Barbalic M, Ricketts SL, Bis JC, Feitosa MF, Orho-Melander M, Melander O, Li X, Li M, Cho YS, Go MJ, Kim YJ, Lee JY, Park T, Kim K, Sim X, Ong RT, Croteau-Chonka DC, Lange LA, Smith JD, Ziegler A, Zhang W, Zee RY, Whitfield JB, Thompson JR, Surakka I, Spector TD, Smit JH, Sinisalo J, Scott J, Saharinen J, Sabatti C, Rose LM, Roberts R, Rieder M, Parker AN, Pare G, O’Donnell CJ, Nieminen MS, Nickerson DA, Montgomery GW, McArdle W, Masson D, Martin NG, Marroni F, Lucas G, Luben R, Lokki ML, Lettre G, Launer LJ, Lakatta EG, Laaksonen R, Kyvik KO, König IR, Khaw KT, Kaplan LM, Johansson Å, Janssens AC, Igl W, Hovingh GK, Hengstenberg C, Havulinna AS, Hastie ND, Harris TB, Haritunians T, Hall AS, Groop LC, Gonzalez E, Freimer NB, Erdmann J, Ejebe KG, Döring A, Dominiczak AF, Demissie S, Deloukas P, de Faire U, Crawford G, Chen YD, Caulfield MJ, Boekholdt SM, Assimes TL, Quertermous T, Seielstad M, Wong TY, Tai ES, Feranil AB, Kuzawa CW, Taylor HA Jr, Gabriel SB, Holm H, Gudnason V, Krauss RM, Ordovas JM, Munroe PB, Kooner JS, Tall AR, Hegele RA, Kastelein JJ, Schadt EE, Strachan DP, Reilly MP, Samani NJ, Schunkert H, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, Kathiresan S
Integrative genomics strategies to elucidate the complexity of drug response.
Kasarskis A, Yang X, Schadt E
Construction of regulatory networks using expression time-series data of a genotyped population.
Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE
Clinicopathologic and gene expression parameters predict liver cancer prognosis.
Hao K, Lamb J, Zhang C, Xie T, Wang K, Zhang B, Chudin E, Lee NP, Mao M, Zhong H, Greenawalt D, Ferguson MD, Ng IO, Sham PC, Poon RT, Molony C, Schadt EE, Dai H, Luk JM
The arrestin domain-containing 3 protein regulates body mass and energy expenditure.
Patwari P, Emilsson V, Schadt EE, Chutkow WA, Lee S, Marsili A, Zhang Y, Dobrin R, Cohen DE, Larsen PR, Zavacki AM, Fong LG, Young SG, Lee RT
Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake.
Millstein J, Winrow CJ, Kasarskis A, Owens JR, Zhou L, Summa KC, Fitzpatrick K, Zhang B, Vitaterna MH, Schadt EE, Renger JJ, Turek FW
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE, Coin LJ, Deng G, Gieger C, Heard-Costa NL, Hottenga JJ, Kühnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Mateo Leach I, O’Reilly PF, Peden JF, Rahmioglu N, Soininen P, Speliotes EK, Yuan X, Thorleifsson G, Alizadeh BZ, Atwood LD, Borecki IB, Brown MJ, Charoen P, Cucca F, Das D, de Geus EJ, Dixon AL, Döring A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen AL, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppönen E, Janssen HL, Johnson T, Kangas AJ, Kema IP, Kühn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin JP, Loos RJ, Martin NG, Moffatt MF, Montgomery GW, Munroe PB, Musunuru K, Nakamura Y, O’Donnell CJ, Olafsson I, Penninx BW, Pouta A, Prins BP, Prokopenko I, Puls R, Ruokonen A, Savolainen MJ, Schlessinger D, Schouten JN, Seedorf U, Sen-Chowdhry S, Siminovitch KA, Smit JH, Spector TD, Tan W, Teslovich TM, Tukiainen T, Uitterlinden AG, Van der Klauw MM, Vasan RS, Wallace C, Wallaschofski H, Wichmann HE, Willemsen G, Würtz P, Xu C, Yerges-Armstrong LM, Alcohol Genome-wide Association (AlcGen) Consortium., Diabetes Genetics Replication and Meta-analyses (DIAGRAM+) Study., Genetic Investigation of Anthropometric Traits (GIANT) Consortium., Global Lipids Genetics Consortium., Genetics of Liver Disease (GOLD) Consortium., International Consortium for Blood Pressure (ICBP-GWAS)., Meta-analyses of Glucose and Insulin-Related Traits Consortium (MAGIC)., Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietiläinen KH, Schumann G, Snieder H, Sternberg MJ, Stolk RP, Thomas HC, Thorsteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JC, Wolffenbuttel BH, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, Völzke H, Schadt EE, Scott J, Järvelin MR, Elliott P, Kooner JS
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK
Inferring causal genomic alterations in breast cancer using gene expression data.
Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.
Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, Zhang B, Castro V, Zhu J, Sieberts SK, Wang S, Molony C, Heymsfield SB, Kemp DM, Reitman ML, Lum PY, Schadt EE, Kaplan LM
Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.
Kilpeläinen TO, Zillikens MC, Stančákova A, Finucane FM, Ried JS, Langenberg C, Zhang W, Beckmann JS, Luan J, Vandenput L, Styrkarsdottir U, Zhou Y, Smith AV, Zhao JH, Amin N, Vedantam S, Shin SY, Haritunians T, Fu M, Feitosa MF, Kumari M, Halldorsson BV, Tikkanen E, Mangino M, Hayward C, Song C, Arnold AM, Aulchenko YS, Oostra BA, Campbell H, Cupples LA, Davis KE, Döring A, Eiriksdottir G, Estrada K, Fernández-Real JM, Garcia M, Gieger C, Glazer NL, Guiducci C, Hofman A, Humphries SE, Isomaa B, Jacobs LC, Jula A, Karasik D, Karlsson MK, Khaw KT, Kim LJ, Kivimäki M, Klopp N, Kühnel B, Kuusisto J, Liu Y, Ljunggren O, Lorentzon M, Luben RN, McKnight B, Mellström D, Mitchell BD, Mooser V, Moreno JM, Männistö S, O’Connell JR, Pascoe L, Peltonen L, Peral B, Perola M, Psaty BM, Salomaa V, Savage DB, Semple RK, Skaric-Juric T, Sigurdsson G, Song KS, Spector TD, Syvänen AC, Talmud PJ, Thorleifsson G, Thorsteinsdottir U, Uitterlinden AG, van Duijn CM, Vidal-Puig A, Wild SH, Wright AF, Clegg DJ, Schadt E, Wilson JF, Rudan I, Ripatti S, Borecki IB, Shuldiner AR, Ingelsson E, Jansson JO, Kaplan RC, Gudnason V, Harris TB, Groop L, Kiel DP, Rivadeneira F, Walker M, Barroso I, Vollenweider P, Waeber G, Chambers JC, Kooner JS, Soranzo N, Hirschhorn JN, Stefansson K, Wichmann HE, Ohlsson C, O’Rahilly S, Wareham NJ, Speliotes EK, Fox CS, Laakso M, Loos RJ
Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques.
Su WL, Kleinhanz RR, Schadt EE
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
Ma H, Schadt EE, Kaplan LM, Zhao H
Identification of a common variant in the TFR2 gene implicated in the physiological regulation of serum iron levels.
Pichler I, Minelli C, Sanna S, Tanaka T, Schwienbacher C, Naitza S, Porcu E, Pattaro C, Busonero F, Zanon A, Maschio A, Melville SA, Grazia Piras M, Longo DL, Guralnik J, Hernandez D, Bandinelli S, Aigner E, Murphy AT, Wroblewski V, Marroni F, Theurl I, Gnewuch C, Schadt E, Mitterer M, Schlessinger D, Ferrucci L, Witcher DR, Hicks AA, Weiss G, Uda M, Pramstaller PP
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
Schunkert H, König IR, Kathiresan S, Reilly MP, Assimes TL, Holm H, Preuss M, Stewart AF, Barbalic M, Gieger C, Absher D, Aherrahrou Z, Allayee H, Altshuler D, Anand SS, Andersen K, Anderson JL, Ardissino D, Ball SG, Balmforth AJ, Barnes TA, Becker DM, Becker LC, Berger K, Bis JC, Boekholdt SM, Boerwinkle E, Braund PS, Brown MJ, Burnett MS, Buysschaert I, Cardiogenics., Carlquist JF, Chen L, Cichon S, Codd V, Davies RW, Dedoussis G, Dehghan A, Demissie S, Devaney JM, Diemert P, Do R, Doering A, Eifert S, Mokhtari NE, Ellis SG, Elosua R, Engert JC, Epstein SE, de Faire U, Fischer M, Folsom AR, Freyer J, Gigante B, Girelli D, Gretarsdottir S, Gudnason V, Gulcher JR, Halperin E, Hammond N, Hazen SL, Hofman A, Horne BD, Illig T, Iribarren C, Jones GT, Jukema JW, Kaiser MA, Kaplan LM, Kastelein JJ, Khaw KT, Knowles JW, Kolovou G, Kong A, Laaksonen R, Lambrechts D, Leander K, Lettre G, Li M, Lieb W, Loley C, Lotery AJ, Mannucci PM, Maouche S, Martinelli N, McKeown PP, Meisinger C, Meitinger T, Melander O, Merlini PA, Mooser V, Morgan T, Mühleisen TW, Muhlestein JB, Münzel T, Musunuru K, Nahrstaedt J, Nelson CP, Nöthen MM, Olivieri O, Patel RS, Patterson CC, Peters A, Peyvandi F, Qu L, Quyyumi AA, Rader DJ, Rallidis LS, Rice C, Rosendaal FR, Rubin D, Salomaa V, Sampietro ML, Sandhu MS, Schadt E, Schäfer A, Schillert A, Schreiber S, Schrezenmeir J, Schwartz SM, Siscovick DS, Sivananthan M, Sivapalaratnam S, Smith A, Smith TB, Snoep JD, Soranzo N, Spertus JA, Stark K, Stirrups K, Stoll M, Tang WH, Tennstedt S, Thorgeirsson G, Thorleifsson G, Tomaszewski M, Uitterlinden AG, van Rij AM, Voight BF, Wareham NJ, Wells GA, Wichmann HE, Wild PS, Willenborg C, Witteman JC, Wright BJ, Ye S, Zeller T, Ziegler A, Cambien F, Goodall AH, Cupples LA, Quertermous T, März W, Hengstenberg C, Blankenberg S, Ouwehand WH, Hall AS, Deloukas P, Thompson JR, Stefansson K, Roberts R, Thorsteinsdottir U, O’Donnell CJ, McPherson R, Erdmann J, CARDIoGRAM Consortium., Samani NJ
Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology.
Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP
Systematic detection of polygenic cis-regulatory evolution.
Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, Schadt EE
Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.
Speliotes EK, Yerges-Armstrong LM, Wu J, Hernaez R, Kim LJ, Palmer CD, Gudnason V, Eiriksdottir G, Garcia ME, Launer LJ, Nalls MA, Clark JM, Mitchell BD, Shuldiner AR, Butler JL, Tomas M, Hoffmann U, Hwang SJ, Massaro JM, O’Donnell CJ, Sahani DV, Salomaa V, Schadt EE, Schwartz SM, Siscovick DS, NASH CRN., GIANT Consortium., MAGIC Investigators., Voight BF, Carr JJ, Feitosa MF, Harris TB, Fox CS, Smith AV, Kao WH, Hirschhorn JN, Borecki IB, GOLD Consortium.
Genome-sequencing anniversary. First steps on a long road.
Schadt E
A model selection approach for expression quantitative trait loci (eQTL) mapping.
Wang P, Dawson JA, Keller MP, Yandell BS, Thornberry NA, Zhang BB, Wang IM, Schadt EE, Attie AD, Kendziorski C
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height.
Lanktree MB, Guo Y, Murtaza M, Glessner JT, Bailey SD, Onland-Moret NC, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson CP, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow JS, Shah S, Taylor K, Barnard J, Peters BJ, Maloney CM, Lobmeyer MT, Stanton A, Zafarmand MH, Romaine SP, Mehta A, van Iperen EP, Gong Y, Price TS, Smith EN, Kim CE, Li YR, Asselbergs FW, Atwood LD, Bailey KM, Bhatt D, Bauer F, Behr ER, Bhangale T, Boer JM, Boehm BO, Bradfield JP, Brown M, Braund PS, Burton PR, Carty C, Chandrupatla HR, Chen W, Connell J, Dalgeorgou C, Boer Ad, Drenos F, Elbers CC, Fang JC, Fox CS, Frackelton EC, Fuchs B, Furlong CE, Gibson Q, Gieger C, Goel A, Grobbee DE, Hastie C, Howard PJ, Huang GH, Johnson WC, Li Q, Kleber ME, Klein BE, Klein R, Kooperberg C, Ky B, Lacroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch FD, Meyer NJ, Monda KL, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse SJ, Otieno FG, Patel SR, Putt ME, Rodriguez S, Safa RN, Sawyer DB, Schreiner PJ, Simpson C, Sivapalaratnam S, Srinivasan SR, Suver C, Swergold G, Sweitzer NK, Thomas KA, Thorand B, Timpson NJ, Tischfield S, Tobin M, Tomaszewski M, Verschuren WM, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda JM, Clarke R, Balmforth AJ, Danesh J, Day IN, Schork NJ, de Bakker PI, Delles C, Duggan D, Hingorani AD, Hirschhorn JN, Hofker MH, Humphries SE, Kivimaki M, Lawlor DA, Kottke-Marchant K, Mega JL, Mitchell BD, Morrow DA, Palmen J, Redline S, Shields DC, Shuldiner AR, Sleiman PM, Smith GD, Farrall M, Jamshidi Y, Christiani DC, Casas JP, Hall AS, Doevendans PA, Christie JD, Berenson GS, Murray SS, Illig T, Dorn GW 2nd, Cappola TP, Boerwinkle E, Sever P, Rader DJ, Reilly MP, Caulfield M, Talmud PJ, Topol E, Engert JC, Wang K, Dominiczak A, Hamsten A, Curtis SP, Silverstein RL, Lange LA, Sabatine MS, Trip M, Saleheen D, Peden JF, Cruickshanks KJ, März W, O’Connell JR, Klungel OH, Wijmenga C, Maitland-van der Zee AH, Schadt EE, Johnson JA, Jarvik GP, Papanicolaou GJ, Hugh Watkins on behalf of PROCARDIS., Grant SF, Munroe PB, North KE, Samani NJ, Koenig W, Gaunt TR, Anand SS, van der Schouw YT, Meena Kumari on behalf of the Whitehall II Study and the WHII 50K Group., Soranzo N, Fitzgerald GA, Reiner A, Hegele RA, Hakonarson H, Keating BJ
The origin of the Haitian cholera outbreak strain.
Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK
Dissecting cis regulation of gene expression in human metabolic tissues.
Dobrin R, Greenawalt DM, Hu G, Kemp DM, Kaplan LM, Schadt EE, Emilsson V
Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.
Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE
Identification of genes and networks driving cardiovascular and metabolic phenotypes in a mouse F2 intercross.
Derry JM, Zhong H, Molony C, MacNeil D, Guhathakurta D, Zhang B, Mudgett J, Small K, El Fertak L, Guimond A, Selloum M, Zhao W, Champy MF, Monassier L, Vogt T, Cully D, Kasarskis A, Schadt EE
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Lango Allen H, Lindgren CM, Luan J, Mägi R, Randall JC, Vedantam S, Winkler TW, Qi L, Workalemahu T, Heid IM, Steinthorsdottir V, Stringham HM, Weedon MN, Wheeler E, Wood AR, Ferreira T, Weyant RJ, Segrè AV, Estrada K, Liang L, Nemesh J, Park JH, Gustafsson S, Kilpeläinen TO, Yang J, Bouatia-Naji N, Esko T, Feitosa MF, Kutalik Z, Mangino M, Raychaudhuri S, Scherag A, Smith AV, Welch R, Zhao JH, Aben KK, Absher DM, Amin N, Dixon AL, Fisher E, Glazer NL, Goddard ME, Heard-Costa NL, Hoesel V, Hottenga JJ, Johansson A, Johnson T, Ketkar S, Lamina C, Li S, Moffatt MF, Myers RH, Narisu N, Perry JR, Peters MJ, Preuss M, Ripatti S, Rivadeneira F, Sandholt C, Scott LJ, Timpson NJ, Tyrer JP, van Wingerden S, Watanabe RM, White CC, Wiklund F, Barlassina C, Chasman DI, Cooper MN, Jansson JO, Lawrence RW, Pellikka N, Prokopenko I, Shi J, Thiering E, Alavere H, Alibrandi MT, Almgren P, Arnold AM, Aspelund T, Atwood LD, Balkau B, Balmforth AJ, Bennett AJ, Ben-Shlomo Y, Bergman RN, Bergmann S, Biebermann H, Blakemore AI, Boes T, Bonnycastle LL, Bornstein SR, Brown MJ, Buchanan TA, Busonero F, Campbell H, Cappuccio FP, Cavalcanti-Proença C, Chen YD, Chen CM, Chines PS, Clarke R, Coin L, Connell J, Day IN, den Heijer M, Duan J, Ebrahim S, Elliott P, Elosua R, Eiriksdottir G, Erdos MR, Eriksson JG, Facheris MF, Felix SB, Fischer-Posovszky P, Folsom AR, Friedrich N, Freimer NB, Fu M, Gaget S, Gejman PV, Geus EJ, Gieger C, Gjesing AP, Goel A, Goyette P, Grallert H, Grässler J, Greenawalt DM, Groves CJ, Gudnason V, Guiducci C, Hartikainen AL, Hassanali N, Hall AS, Havulinna AS, Hayward C, Heath AC, Hengstenberg C, Hicks AA, Hinney A, Hofman A, Homuth G, Hui J, Igl W, Iribarren C, Isomaa B, Jacobs KB, Jarick I, Jewell E, John U, Jørgensen T, Jousilahti P, Jula A, Kaakinen M, Kajantie E, Kaplan LM, Kathiresan S, Kettunen J, Kinnunen L, Knowles JW, Kolcic I, König IR, Koskinen S, Kovacs P, Kuusisto J, Kraft P, Kvaløy K, Laitinen J, Lantieri O, Lanzani C, Launer LJ, Lecoeur C, Lehtimäki T, Lettre G, Liu J, Lokki ML, Lorentzon M, Luben RN, Ludwig B, MAGIC., Manunta P, Marek D, Marre M, Martin NG, McArdle WL, McCarthy A, McKnight B, Meitinger T, Melander O, Meyre D, Midthjell K, Montgomery GW, Morken MA, Morris AP, Mulic R, Ngwa JS, Nelis M, Neville MJ, Nyholt DR, O’Donnell CJ, O’Rahilly S, Ong KK, Oostra B, Paré G, Parker AN, Perola M, Pichler I, Pietiläinen KH, Platou CG, Polasek O, Pouta A, Rafelt S, Raitakari O, Rayner NW, Ridderstråle M, Rief W, Ruokonen A, Robertson NR, Rzehak P, Salomaa V, Sanders AR, Sandhu MS, Sanna S, Saramies J, Savolainen MJ, Scherag S, Schipf S, Schreiber S, Schunkert H, Silander K, Sinisalo J, Siscovick DS, Smit JH, Soranzo N, Sovio U, Stephens J, Surakka I, Swift AJ, Tammesoo ML, Tardif JC, Teder-Laving M, Teslovich TM, Thompson JR, Thomson B, Tönjes A, Tuomi T, van Meurs JB, van Ommen GJ, Vatin V, Viikari J, Visvikis-Siest S, Vitart V, Vogel CI, Voight BF, Waite LL, Wallaschofski H, Walters GB, Widen E, Wiegand S, Wild SH, Willemsen G, Witte DR, Witteman JC, Xu J, Zhang Q, Zgaga L, Ziegler A, Zitting P, Beilby JP, Farooqi IS, Hebebrand J, Huikuri HV, James AL, Kähönen M, Levinson DF, Macciardi F, Nieminen MS, Ohlsson C, Palmer LJ, Ridker PM, Stumvoll M, Beckmann JS, Boeing H, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Collins FS, Cupples LA, Smith GD, Erdmann J, Froguel P, Grönberg H, Gyllensten U, Hall P, Hansen T, Harris TB, Hattersley AT, Hayes RB, Heinrich J, Hu FB, Hveem K, Illig T, Jarvelin MR, Kaprio J, Karpe F, Khaw KT, Kiemeney LA, Krude H, Laakso M, Lawlor DA, Metspalu A, Munroe PB, Ouwehand WH, Pedersen O, Penninx BW, Peters A, Pramstaller PP, Quertermous T, Reinehr T, Rissanen A, Rudan I, Samani NJ, Schwarz PE, Shuldiner AR, Spector TD, Tuomilehto J, Uda M, Uitterlinden A, Valle TT, Wabitsch M, Waeber G, Wareham NJ, Watkins H, Procardis Consortium., Wilson JF, Wright AF, Zillikens MC, Chatterjee N, McCarroll SA, Purcell S, Schadt EE, Visscher PM, Assimes TL, Borecki IB, Deloukas P, Fox CS, Groop LC, Haritunians T, Hunter DJ, Kaplan RC, Mohlke KL, O’Connell JR, Peltonen L, Schlessinger D, Strachan DP, van Duijn CM, Wichmann HE, Frayling TM, Thorsteinsdottir U, Abecasis GR, Barroso I, Boehnke M, Stefansson K, North KE, McCarthy MI, Hirschhorn JN, Ingelsson E, Loos RJ
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, Thorleifsson G, Zillikens MC, Speliotes EK, Mägi R, Workalemahu T, White CC, Bouatia-Naji N, Harris TB, Berndt SI, Ingelsson E, Willer CJ, Weedon MN, Luan J, Vedantam S, Esko T, Kilpeläinen TO, Kutalik Z, Li S, Monda KL, Dixon AL, Holmes CC, Kaplan LM, Liang L, Min JL, Moffatt MF, Molony C, Nicholson G, Schadt EE, Zondervan KT, Feitosa MF, Ferreira T, Lango Allen H, Weyant RJ, Wheeler E, Wood AR, MAGIC., Estrada K, Goddard ME, Lettre G, Mangino M, Nyholt DR, Purcell S, Smith AV, Visscher PM, Yang J, McCarroll SA, Nemesh J, Voight BF, Absher D, Amin N, Aspelund T, Coin L, Glazer NL, Hayward C, Heard-Costa NL, Hottenga JJ, Johansson A, Johnson T, Kaakinen M, Kapur K, Ketkar S, Knowles JW, Kraft P, Kraja AT, Lamina C, Leitzmann MF, McKnight B, Morris AP, Ong KK, Perry JR, Peters MJ, Polasek O, Prokopenko I, Rayner NW, Ripatti S, Rivadeneira F, Robertson NR, Sanna S, Sovio U, Surakka I, Teumer A, van Wingerden S, Vitart V, Zhao JH, Cavalcanti-Proença C, Chines PS, Fisher E, Kulzer JR, Lecoeur C, Narisu N, Sandholt C, Scott LJ, Silander K, Stark K, Tammesoo ML, Teslovich TM, Timpson NJ, Watanabe RM, Welch R, Chasman DI, Cooper MN, Jansson JO, Kettunen J, Lawrence RW, Pellikka N, Perola M, Vandenput L, Alavere H, Almgren P, Atwood LD, Bennett AJ, Biffar R, Bonnycastle LL, Bornstein SR, Buchanan TA, Campbell H, Day IN, Dei M, Dörr M, Elliott P, Erdos MR, Eriksson JG, Freimer NB, Fu M, Gaget S, Geus EJ, Gjesing AP, Grallert H, Grässler J, Groves CJ, Guiducci C, Hartikainen AL, Hassanali N, Havulinna AS, Herzig KH, Hicks AA, Hui J, Igl W, Jousilahti P, Jula A, Kajantie E, Kinnunen L, Kolcic I, Koskinen S, Kovacs P, Kroemer HK, Krzelj V, Kuusisto J, Kvaloy K, Laitinen J, Lantieri O, Lathrop GM, Lokki ML, Luben RN, Ludwig B, McArdle WL, McCarthy A, Morken MA, Nelis M, Neville MJ, Paré G, Parker AN, Peden JF, Pichler I, Pietiläinen KH, Platou CG, Pouta A, Ridderstråle M, Samani NJ, Saramies J, Sinisalo J, Smit JH, Strawbridge RJ, Stringham HM, Swift AJ, Teder-Laving M, Thomson B, Usala G, van Meurs JB, van Ommen GJ, Vatin V, Volpato CB, Wallaschofski H, Walters GB, Widen E, Wild SH, Willemsen G, Witte DR, Zgaga L, Zitting P, Beilby JP, James AL, Kähönen M, Lehtimäki T, Nieminen MS, Ohlsson C, Palmer LJ, Raitakari O, Ridker PM, Stumvoll M, Tönjes A, Viikari J, Balkau B, Ben-Shlomo Y, Bergman RN, Boeing H, Smith GD, Ebrahim S, Froguel P, Hansen T, Hengstenberg C, Hveem K, Isomaa B, Jørgensen T, Karpe F, Khaw KT, Laakso M, Lawlor DA, Marre M, Meitinger T, Metspalu A, Midthjell K, Pedersen O, Salomaa V, Schwarz PE, Tuomi T, Tuomilehto J, Valle TT, Wareham NJ, Arnold AM, Beckmann JS, Bergmann S, Boerwinkle E, Boomsma DI, Caulfield MJ, Collins FS, Eiriksdottir G, Gudnason V, Gyllensten U, Hamsten A, Hattersley AT, Hofman A, Hu FB, Illig T, Iribarren C, Jarvelin MR, Kao WH, Kaprio J, Launer LJ, Munroe PB, Oostra B, Penninx BW, Pramstaller PP, Psaty BM, Quertermous T, Rissanen A, Rudan I, Shuldiner AR, Soranzo N, Spector TD, Syvanen AC, Uda M, Uitterlinden A, Völzke H, Vollenweider P, Wilson JF, Witteman JC, Wright AF, Abecasis GR, Boehnke M, Borecki IB, Deloukas P, Frayling TM, Groop LC, Haritunians T, Hunter DJ, Kaplan RC, North KE, O’Connell JR, Peltonen L, Schlessinger D, Strachan DP, Hirschhorn JN, Assimes TL, Wichmann HE, Thorsteinsdottir U, van Duijn CM, Stefansson K, Cupples LA, Loos RJ, Barroso I, McCarthy MI, Fox CS, Mohlke KL, Lindgren CM
A window into third-generation sequencing.
Schadt EE, Turner S, Kasarskis A
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, Ferreira T, Wood AR, Weyant RJ, Segrè AV, Speliotes EK, Wheeler E, Soranzo N, Park JH, Yang J, Gudbjartsson D, Heard-Costa NL, Randall JC, Qi L, Vernon Smith A, Mägi R, Pastinen T, Liang L, Heid IM, Luan J, Thorleifsson G, Winkler TW, Goddard ME, Sin Lo K, Palmer C, Workalemahu T, Aulchenko YS, Johansson A, Zillikens MC, Feitosa MF, Esko T, Johnson T, Ketkar S, Kraft P, Mangino M, Prokopenko I, Absher D, Albrecht E, Ernst F, Glazer NL, Hayward C, Hottenga JJ, Jacobs KB, Knowles JW, Kutalik Z, Monda KL, Polasek O, Preuss M, Rayner NW, Robertson NR, Steinthorsdottir V, Tyrer JP, Voight BF, Wiklund F, Xu J, Zhao JH, Nyholt DR, Pellikka N, Perola M, Perry JR, Surakka I, Tammesoo ML, Altmaier EL, Amin N, Aspelund T, Bhangale T, Boucher G, Chasman DI, Chen C, Coin L, Cooper MN, Dixon AL, Gibson Q, Grundberg E, Hao K, Juhani Junttila M, Kaplan LM, Kettunen J, König IR, Kwan T, Lawrence RW, Levinson DF, Lorentzon M, McKnight B, Morris AP, Müller M, Suh Ngwa J, Purcell S, Rafelt S, Salem RM, Salvi E, Sanna S, Shi J, Sovio U, Thompson JR, Turchin MC, Vandenput L, Verlaan DJ, Vitart V, White CC, Ziegler A, Almgren P, Balmforth AJ, Campbell H, Citterio L, De Grandi A, Dominiczak A, Duan J, Elliott P, Elosua R, Eriksson JG, Freimer NB, Geus EJ, Glorioso N, Haiqing S, Hartikainen AL, Havulinna AS, Hicks AA, Hui J, Igl W, Illig T, Jula A, Kajantie E, Kilpeläinen TO, Koiranen M, Kolcic I, Koskinen S, Kovacs P, Laitinen J, Liu J, Lokki ML, Marusic A, Maschio A, Meitinger T, Mulas A, Paré G, Parker AN, Peden JF, Petersmann A, Pichler I, Pietiläinen KH, Pouta A, Ridderstråle M, Rotter JI, Sambrook JG, Sanders AR, Schmidt CO, Sinisalo J, Smit JH, Stringham HM, Bragi Walters G, Widen E, Wild SH, Willemsen G, Zagato L, Zgaga L, Zitting P, Alavere H, Farrall M, McArdle WL, Nelis M, Peters MJ, Ripatti S, van Meurs JB, Aben KK, Ardlie KG, Beckmann JS, Beilby JP, Bergman RN, Bergmann S, Collins FS, Cusi D, den Heijer M, Eiriksdottir G, Gejman PV, Hall AS, Hamsten A, Huikuri HV, Iribarren C, Kähönen M, Kaprio J, Kathiresan S, Kiemeney L, Kocher T, Launer LJ, Lehtimäki T, Melander O, Mosley TH Jr, Musk AW, Nieminen MS, O’Donnell CJ, Ohlsson C, Oostra B, Palmer LJ, Raitakari O, Ridker PM, Rioux JD, Rissanen A, Rivolta C, Schunkert H, Shuldiner AR, Siscovick DS, Stumvoll M, Tönjes A, Tuomilehto J, van Ommen GJ, Viikari J, Heath AC, Martin NG, Montgomery GW, Province MA, Kayser M, Arnold AM, Atwood LD, Boerwinkle E, Chanock SJ, Deloukas P, Gieger C, Grönberg H, Hall P, Hattersley AT, Hengstenberg C, Hoffman W, Lathrop GM, Salomaa V, Schreiber S, Uda M, Waterworth D, Wright AF, Assimes TL, Barroso I, Hofman A, Mohlke KL, Boomsma DI, Caulfield MJ, Cupples LA, Erdmann J, Fox CS, Gudnason V, Gyllensten U, Harris TB, Hayes RB, Jarvelin MR, Mooser V, Munroe PB, Ouwehand WH, Penninx BW, Pramstaller PP, Quertermous T, Rudan I, Samani NJ, Spector TD, Völzke H, Watkins H, Wilson JF, Groop LC, Haritunians T, Hu FB, Kaplan RC, Metspalu A, North KE, Schlessinger D, Wareham NJ, Hunter DJ, O’Connell JR, Strachan DP, Wichmann HE, Borecki IB, van Duijn CM, Schadt EE, Thorsteinsdottir U, Peltonen L, Uitterlinden AG, Visscher PM, Chatterjee N, Loos RJ, Boehnke M, McCarthy MI, Ingelsson E, Lindgren CM, Abecasis GR, Stefansson K, Frayling TM, Hirschhorn JN
In the absence of HCV infection, interferon stimulated gene expression in liver is not associated with IL28B genotype.
Shebl FM, Maeder D, Shao Y, Prokunina-Olsson L, Schadt EE, O’Brien TR
Drug discovery in a multidimensional world: systems, patterns, and networks.
Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E
Correction for hidden confounders in the genetic analysis of gene expression.
Listgarten J, Kadie C, Schadt EE, Heckerman D
An integrative multi-network and multi-classifier approach to predict genetic interactions.
Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, Kumar V, Schadt EE
FoxM1 is up-regulated by obesity and stimulates beta-cell proliferation.
Davis DB, Lavine JA, Suhonen JI, Krautkramer KA, Rabaglia ME, Sperger JM, Fernandez LA, Yandell BS, Keller MP, Wang IM, Schadt EE, Attie AD
Computational solutions to large-scale data management and analysis.
Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.
Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus.
Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, Li X, Li H, Kuperwasser N, Ruda VM, Pirruccello JP, Muchmore B, Prokunina-Olsson L, Hall JL, Schadt EE, Morales CR, Lund-Katz S, Phillips MC, Wong J, Cantley W, Racie T, Ejebe KG, Orho-Melander M, Melander O, Koteliansky V, Fitzgerald K, Krauss RM, Cowan CA, Kathiresan S, Rader DJ
Biological, clinical and population relevance of 95 loci for blood lipids.
Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ, Johansen CT, Fouchier SW, Isaacs A, Peloso GM, Barbalic M, Ricketts SL, Bis JC, Aulchenko YS, Thorleifsson G, Feitosa MF, Chambers J, Orho-Melander M, Melander O, Johnson T, Li X, Guo X, Li M, Shin Cho Y, Jin Go M, Jin Kim Y, Lee JY, Park T, Kim K, Sim X, Twee-Hee Ong R, Croteau-Chonka DC, Lange LA, Smith JD, Song K, Hua Zhao J, Yuan X, Luan J, Lamina C, Ziegler A, Zhang W, Zee RY, Wright AF, Witteman JC, Wilson JF, Willemsen G, Wichmann HE, Whitfield JB, Waterworth DM, Wareham NJ, Waeber G, Vollenweider P, Voight BF, Vitart V, Uitterlinden AG, Uda M, Tuomilehto J, Thompson JR, Tanaka T, Surakka I, Stringham HM, Spector TD, Soranzo N, Smit JH, Sinisalo J, Silander K, Sijbrands EJ, Scuteri A, Scott J, Schlessinger D, Sanna S, Salomaa V, Saharinen J, Sabatti C, Ruokonen A, Rudan I, Rose LM, Roberts R, Rieder M, Psaty BM, Pramstaller PP, Pichler I, Perola M, Penninx BW, Pedersen NL, Pattaro C, Parker AN, Pare G, Oostra BA, O’Donnell CJ, Nieminen MS, Nickerson DA, Montgomery GW, Meitinger T, McPherson R, McCarthy MI, McArdle W, Masson D, Martin NG, Marroni F, Mangino M, Magnusson PK, Lucas G, Luben R, Loos RJ, Lokki ML, Lettre G, Langenberg C, Launer LJ, Lakatta EG, Laaksonen R, Kyvik KO, Kronenberg F, König IR, Khaw KT, Kaprio J, Kaplan LM, Johansson A, Jarvelin MR, Janssens AC, Ingelsson E, Igl W, Kees Hovingh G, Hottenga JJ, Hofman A, Hicks AA, Hengstenberg C, Heid IM, Hayward C, Havulinna AS, Hastie ND, Harris TB, Haritunians T, Hall AS, Gyllensten U, Guiducci C, Groop LC, Gonzalez E, Gieger C, Freimer NB, Ferrucci L, Erdmann J, Elliott P, Ejebe KG, Döring A, Dominiczak AF, Demissie S, Deloukas P, de Geus EJ, de Faire U, Crawford G, Collins FS, Chen YD, Caulfield MJ, Campbell H, Burtt NP, Bonnycastle LL, Boomsma DI, Boekholdt SM, Bergman RN, Barroso I, Bandinelli S, Ballantyne CM, Assimes TL, Quertermous T, Altshuler D, Seielstad M, Wong TY, Tai ES, Feranil AB, Kuzawa CW, Adair LS, Taylor HA Jr, Borecki IB, Gabriel SB, Wilson JG, Holm H, Thorsteinsdottir U, Gudnason V, Krauss RM, Mohlke KL, Ordovas JM, Munroe PB, Kooner JS, Tall AR, Hegele RA, Kastelein JJ, Schadt EE, Rotter JI, Boerwinkle E, Strachan DP, Mooser V, Stefansson K, Reilly MP, Samani NJ, Schunkert H, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, van Duijn CM, Peltonen L, Abecasis GR, Boehnke M, Kathiresan S
Genetic variation at the phospholipid transfer protein locus affects its activity and high-density lipoprotein size and is a novel marker of cardiovascular disease susceptibility.
Vergeer M, Boekholdt SM, Sandhu MS, Ricketts SL, Wareham NJ, Brown MJ, de Faire U, Leander K, Gigante B, Kavousi M, Hofman A, Uitterlinden AG, van Duijn CM, Witteman JC, Jukema JW, Schadt EE, van der Schoot E, Kastelein JJ, Khaw KT, Dullaart RP, van Tol A, Trip MD, Dallinga-Thie GM
Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY
Gene bionetwork analysis of ovarian primordial follicle development.
Nilsson EE, Savenkova MI, Schindler R, Zhang B, Schadt EE, Skinner MK
Expression quantitative trait loci: replication, tissue- and sex-specificity in mice.
van Nas A, Ingram-Drake L, Sinsheimer JS, Wang SS, Schadt EE, Drake T, Lusis AJ
Identification and validation of genes affecting aortic lesions in mice.
Yang X, Peterson L, Thieringer R, Deignan JL, Wang X, Zhu J, Wang S, Zhong H, Stepaniants S, Beaulaurier J, Wang IM, Rosa R, Cumiskey AM, Luo JM, Luo Q, Shah K, Xiao J, Nickle D, Plump A, Schadt EE, Lusis AJ, Lum PY
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
Hsu YH, Zillikens MC, Wilson SG, Farber CR, Demissie S, Soranzo N, Bianchi EN, Grundberg E, Liang L, Richards JB, Estrada K, Zhou Y, van Nas A, Moffatt MF, Zhai G, Hofman A, van Meurs JB, Pols HA, Price RI, Nilsson O, Pastinen T, Cupples LA, Lusis AJ, Schadt EE, Ferrari S, Uitterlinden AG, Rivadeneira F, Spector TD, Karasik D, Kiel DP
Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes.
Zhong H, Beaulaurier J, Lum PY, Molony C, Yang X, Macneil DJ, Weingarth DT, Zhang B, Greenawalt D, Dobrin R, Hao K, Woo S, Fabre-Suver C, Qian S, Tota MR, Keller MP, Kendziorski CM, Yandell BS, Castro V, Attie AD, Kaplan LM, Schadt EE
Simultaneous clustering of multiple gene expression and physical interaction datasets.
Narayanan M, Vetta A, Schadt EE, Zhu J
Integrating pathway analysis and genetics of gene expression for genome-wide association studies.
Zhong H, Yang X, Kaplan LM, Molony C, Schadt EE
Assessing the prospects of genome-wide association studies performed in inbred mice.
Su WL, Sieberts SK, Kleinhanz RR, Lux K, Millstein J, Molony C, Schadt EE
Evidence for widespread adaptive evolution of gene expression in budding yeast.
Fraser HB, Moses AM, Schadt EE
Characterizing dynamic changes in the human blood transcriptional network.
Zhu J, Chen Y, Leonardson AS, Wang K, Lamb JR, Emilsson V, Schadt EE
A survey of cancer cell lines reveals highly structured and hierarchical relationships within and between DNA and mRNA that may be the result of selection.
Xie T, Zhang C, Zhang B, Molony C, Oudes A, Roberts C, Dai H, Schadt E, Lamb J
A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.
Zhang W, Zhu J, Schadt EE, Liu JS
Magnitude of stratification in human populations and impacts on genome wide association studies.
Hao K, Chudin E, Greenawalt D, Schadt EE
The quantitative genetics of phenotypic robustness.
Fraser HB, Schadt EE
The effect of food intake on gene expression in human peripheral blood.
Leonardson AS, Zhu J, Chen Y, Wang K, Lamb JR, Reitman M, Emilsson V, Schadt EE
Disruption of the aortic elastic lamina and medial calcification share genetic determinants in mice.
Wang SS, Martin LJ, Schadt EE, Meng H, Wang X, Zhao W, Ingram-Drake L, Nebohacova M, Mehrabian M, Drake TA, Lusis AJ
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
Wang K, Narayanan M, Zhong H, Tompa M, Schadt EE, Zhu J
Ppargamma2 is a key driver of longevity in the mouse.
Argmann C, Dobrin R, Heikkinen S, Auburtin A, Pouilly L, Cock TA, Koutnikova H, Zhu J, Schadt EE, Auwerx J
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.
Hägg S, Skogsberg J, Lundström J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, Bajic VB, Samnegård A, Silveira A, Kaplan LM, Gigante B, Leander K, de Faire U, Rosfors S, Lockowandt U, Liska J, Konrad P, Takolander R, Franco-Cereceda A, Schadt EE, Ivert T, Hamsten A, Tegnér J, Björkegren J
Alternative splicing of TCF7L2 gene in omental and subcutaneous adipose tissue and risk of type 2 diabetes.
Prokunina-Olsson L, Kaplan LM, Schadt EE, Collins FS
Common body mass index-associated variants confer risk of extreme obesity.
Cotsapas C, Speliotes EK, Hatoum IJ, Greenawalt DM, Dobrin R, Lum PY, Suver C, Chudin E, Kemp D, Reitman M, Voight BF, Neale BM, Schadt EE, Hirschhorn JN, Kaplan LM, Daly MJ, GIANT Consortium.
Molecular networks as sensors and drivers of common human diseases.
Schadt EE
The C3a anaphylatoxin receptor is a key mediator of insulin resistance and functions by modulating adipose tissue macrophage infiltration and activation.
Mamane Y, Chung Chan C, Lavallee G, Morin N, Xu LJ, Huang J, Gordon R, Thomas W, Lamb J, Schadt EE, Kennedy BP, Mancini JA
Obesity and genetics regulate microRNAs in islets, liver, and adipose of diabetic mice.
Zhao E, Keller MP, Rabaglia ME, Oler AT, Stapleton DS, Schueler KL, Neto EC, Moon JY, Wang P, Wang IM, Lum PY, Ivanovska I, Cleary M, Greenawalt D, Tsang J, Choi YJ, Kleinhanz R, Shang J, Zhou YP, Howard AD, Zhang BB, Kendziorski C, Thornberry NA, Yandell BS, Schadt EE, Attie AD
On the adjustment for covariates in genetic association analysis: a novel, simple principle to infer direct causal effects.
Vansteelandt S, Goetgeluk S, Lutz S, Waldman I, Lyon H, Schadt EE, Weiss ST, Lange C
Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.
Hao K, Chudin E, McElwee J, Schadt EE
Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments.
Schadt EE, Zhang B, Zhu J
Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.
Tu Z, Argmann C, Wong KK, Mitnaul LJ, Edwards S, Sach IC, Zhu J, Schadt EE
Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history.
Scheinfeldt LB, Biswas S, Madeoy J, Connelly CF, Schadt EE, Akey JM
Disentangling molecular relationships with a causal inference test.
Millstein J, Zhang B, Zhu J, Schadt EE
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks.
Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, Torosyan G, Majid S, Falkard B, Kleinhanz RR, Karlsson J, Castellani LW, Mumick S, Wang K, Xie T, Coon M, Zhang C, Estrada-Smith D, Farber CR, Wang SS, van Nas A, Ghazalpour A, Zhang B, Macneil DJ, Lamb JR, Dipple KM, Reitman ML, Mehrabian M, Lum PY, Schadt EE, Lusis AJ, Drake TA
A network view of disease and compound screening.
Schadt EE, Friend SH, Shaywitz DA
Something wiki this way comes. Interview by Bryn Nelson.
Friend S, Schadt E
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks.
van Nas A, Guhathakurta D, Wang SS, Yehya N, Horvath S, Zhang B, Ingram-Drake L, Chaudhuri G, Schadt EE, Drake TA, Arnold AP, Lusis AJ
Diurnal variation of the human adipose transcriptome and the link to metabolic disease.
Loboda A, Kraft WK, Fine B, Joseph J, Nebozhyn M, Zhang C, He Y, Yang X, Wright C, Morris M, Chalikonda I, Ferguson M, Emilsson V, Leonardson A, Lamb J, Dai H, Schadt E, Greenberg HE, Lum PY
Integrative genomics and drug development.
Lum PY, Derry JM, Schadt EE
The Pro12Ala PPARgamma2 variant determines metabolism at the gene-environment interface.
Heikkinen S, Argmann C, Feige JN, Koutnikova H, Champy MF, Dali-Youcef N, Schadt EE, Laakso M, Auwerx J
Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.
Dobrin R, Zhu J, Molony C, Argman C, Parrish ML, Carlson S, Allan MF, Pomp D, Schadt EE
An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association.
Farber CR, van Nas A, Ghazalpour A, Aten JE, Doss S, Sos B, Schadt EE, Ingram-Drake L, Davis RC, Horvath S, Smith DJ, Drake TA, Lusis AJ
Common variants at 30 loci contribute to polygenic dyslipidemia.
Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, Ferrucci L, Scheet P, Sanna S, Uda M, Yang Q, Lunetta KL, Dupuis J, de Bakker PI, O’Donnell CJ, Chambers JC, Kooner JS, Hercberg S, Meneton P, Lakatta EG, Scuteri A, Schlessinger D, Tuomilehto J, Collins FS, Groop L, Altshuler D, Collins R, Lathrop GM, Melander O, Salomaa V, Peltonen L, Orho-Melander M, Ordovas JM, Boehnke M, Abecasis GR, Mohlke KL, Cupples LA
Uncovering the genetic landscape for multiple sleep-wake traits.
Winrow CJ, Williams DL, Kasarskis A, Millstein J, Laposky AD, Yang HS, Mrazek K, Zhou L, Owens JR, Radzicki D, Preuss F, Schadt EE, Shimomura K, Vitaterna MH, Zhang C, Koblan KS, Renger JJ, Turek FW
Genomics and genome-wide association studies: an integrative approach to expression QTL mapping.
Degnan JH, Lasky-Su J, Raby BA, Xu M, Molony C, Schadt EE, Lange C
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE
Calibrating the performance of SNP arrays for whole-genome association studies.
Hao K, Schadt EE, Storey JD
Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences.
Su WL, Modrek B, GuhaThakurta D, Edwards S, Shah JK, Kulkarni AV, Russell A, Schadt EE, Johnson JM, Castle JC
Mapping the genetic architecture of gene expression in human liver.
Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.
Keller MP, Choi Y, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, Steinberg HA, Chaibub Neto E, Kleinhanz R, Turner S, Hellerstein MK, Schadt EE, Yandell BS, Kendziorski C, Attie AD
On the replication of genetic associations: timing can be everything!
Lasky-Su J, Lyon HN, Emilsson V, Heid IM, Molony C, Raby BA, Lazarus R, Klanderman B, Soto-Quiros ME, Avila L, Silverman EK, Thorleifsson G, Thorsteinsdottir U, Kronenberg F, Vollmert C, Illig T, Fox CS, Levy D, Laird N, Ding X, McQueen MB, Butler J, Ardlie K, Papoutsakis C, Dedoussis G, O’Donnell CJ, Wichmann HE, Celedón JC, Schadt E, Hirschhorn J, Weiss ST, Stefansson K, Lange C
Variations in DNA elucidate molecular networks that cause disease.
Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy MF, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE
Genetics of gene expression and its effect on disease.
Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S, Magnusson KP, Stefansson H, Fossdal R, Kristjansson K, Gislason HG, Stefansson T, Leifsson BG, Thorsteinsdottir U, Lamb JR, Gulcher JR, Reitman ML, Kong A, Schadt EE, Stefansson K
Systems biology and its potential role in radiobiology.
Feinendegen L, Hahnfeldt P, Schadt EE, Stumpf M, Voit EO
A systems biology approach to drug discovery.
Zhu J, Zhang B, Schadt EE
Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.
Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA
Statistical power of phylo-HMM for evolutionarily conserved element detection.
Fan X, Zhu J, Schadt EE, Liu JS
A genome-wide set of congenic mouse strains derived from CAST/Ei on a C57BL/6 background.
Davis RC, Jin A, Rosales M, Yu S, Xia X, Ranola K, Schadt EE, Lusis AJ
Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data.
Wang SS, Schadt EE, Wang H, Wang X, Ingram-Drake L, Shi W, Drake TA, Lusis AJ
Linkage disequilibrium in wild mice.
Laurie CC, Nickerson DA, Anderson AD, Weir BS, Livingston RJ, Dean MD, Smith KL, Schadt EE, Nachman MW
Moving toward a system genetics view of disease.
Sieberts SK, Schadt EE
Pharmacogenetics of metformin response: a step in the path toward personalized medicine.
Reitman ML, Schadt EE
Evidence for novel susceptibility genes for late-onset Alzheimer’s disease from a genome-wide association study of putative functional variants.
Grupe A, Abraham R, Li Y, Rowland C, Hollingworth P, Morgan A, Jehu L, Segurado R, Stone D, Schadt E, Karnoub M, Nowotny P, Tacey K, Catanese J, Sninsky J, Brayne C, Rubinsztein D, Gill M, Lawlor B, Lovestone S, Holmans P, O’Donovan M, Morris JC, Thal L, Goate A, Owen MJ, Williams J
Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations.
Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, Sachs JR, Schadt EE
Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics.
Meng H, Vera I, Che N, Wang X, Wang SS, Ingram-Drake L, Schadt EE, Drake TA, Lusis AJ
DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies.
Hovatta I, Zapala MA, Broide RS, Schadt EE, Libiger O, Schork NJ, Lockhart DJ, Barlow C
Dosage compensation is less effective in birds than in mammals.
Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band MR, Clayton DF, Schadt EE, Lusis AJ, Arnold AP
Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes.
Schadt EE, Lum PY
Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.
GuhaThakurta D, Xie T, Anand M, Edwards SW, Li G, Wang SS, Schadt EE
Integrating genetic and network analysis to characterize genes related to mouse weight.
Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, Castellanos R, Brozell A, Schadt EE, Drake TA, Lusis AJ, Horvath S
Tissue-specific expression and regulation of sexually dimorphic genes in mice.
Yang X, Schadt EE, Wang S, Wang H, Arnold AP, Ingram-Drake L, Drake TA, Lusis AJ
Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice.
Drake TA, Schadt EE, Lusis AJ
Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes.
Lum PY, Chen Y, Zhu J, Lamb J, Melmed S, Wang S, Drake TA, Lusis AJ, Schadt EE
Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity.
Wang S, Yehya N, Schadt EE, Wang H, Drake TA, Lusis AJ
Exploiting naturally occurring DNA variation and molecular profiling data to dissect disease and drug response traits.
Schadt EE
Sequence variation in NPC1L1 and association with improved LDL-cholesterol lowering in response to ezetimibe treatment.
Simon JS, Karnoub MC, Devlin DJ, Arreaza MG, Qiu P, Monks SA, Severino ME, Deutsch P, Palmisano J, Sachs AB, Bayne ML, Plump AS, Schadt EE
Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice.
Hovatta I, Tennant RS, Helton R, Marr RA, Singer O, Redwine JM, Ellison JA, Schadt EE, Verma IM, Lockhart DJ, Barlow C
Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice.
Drake TA, Schadt EE, Davis RC, Lusis AJ
Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels.
Cervino AC, Li G, Edwards S, Zhu J, Laurie C, Tokiwa G, Lum PY, Wang S, Castellani LW, Lusis AJ, Carlson S, Sachs AB, Schadt EE
Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits.
Mehrabian M, Allayee H, Stockton J, Lum PY, Drake TA, Castellani LW, Suh M, Armour C, Edwards S, Lamb J, Lusis AJ, Schadt EE
A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background.
Davis RC, Schadt EE, Smith DJ, Hsieh EW, Cervino AC, van Nas A, Rosales M, Doss S, Meng H, Allayee H, Lusis AJ
Embracing complexity, inching closer to reality.
Schadt EE, Sachs A, Friend S
An integrative genomics approach to infer causal associations between gene expression and disease.
Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ
Cis-acting expression quantitative trait loci in mice.
Doss S, Schadt EE, Drake TA, Lusis AJ
Ultrafine mapping of SNPs from mouse strains C57BL/6J, DBA/2J, and C57BLKS/J for loci contributing to diabetes and atherosclerosis susceptibility.
Davis RC, Schadt EE, Cervino AC, Péterfy M, Lusis AJ
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
Johnson JM, Edwards S, Shoemaker D, Schadt EE
Genomic analysis of metabolic pathway gene expression in mice.
Ghazalpour A, Doss S, Sheth SS, Ingram-Drake LA, Schadt EE, Lusis AJ, Drake TA
The Collaborative Cross, a community resource for the genetic analysis of complex traits.
Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O’Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpää MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F, Complex Trait Consortium.
A comprehensive transcript index of the human genome generated using microarrays and computational approaches.
Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.
Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD
Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice.
Colinayo VV, Qiao JH, Wang X, Krass KL, Schadt E, Lusis AJ, Drake TA
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.
He YD, Dai H, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB
A family-based test for correlation between gene expression and trait values.
Kraft P, Schadt E, Aten J, Horvath S
Genetics of gene expression surveyed in maize, mouse and man.
Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH
Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.
Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM
Applications of codon and rate variation models in molecular phylogeny.
Schadt EE, Sinsheimer JS, Lange K
Codon and rate variation models in molecular phylogeny.
Schadt E, Lange K
Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis.
Lock C, Hermans G, Pedotti R, Brendolan A, Schadt E, Garren H, Langer-Gould A, Strober S, Cannella B, Allard J, Klonowski P, Austin A, Lad N, Kaminski N, Galli SJ, Oksenberg JR, Raine CS, Heller R, Steinman L

Rui Chang’s Articles

Using chiral tactoids as optical probes to study the aggregation behavior of chromonics.
Nayani K, Fu J, Chang R, Park JO, Srinivasarao M
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, Patel A, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MY, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I
Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer binding protein alpha.
Song Z, Xiaoli AM, Zhang Q, Zhang Y, Yang ES, Wang S, Chang R, Zhang ZD, Yang G, Strich R, Pessin JE, Yang F
Metabolic network failures in Alzheimer’s disease-A biochemical road map.
Toledo JB, Arnold M, Kastenmüller G, Chang R, Baillie RA, Han X, Thambisetty M, Tenenbaum JD, Suhre K, Thompson JW, John-Williams LS, MahmoudianDehkordi S, Rotroff DM, Jack JR, Motsinger-Reif A, Risacher SL, Blach C, Lucas JE, Massaro T, Louie G, Zhu H, Dallmann G, Klavins K, Koal T, Kim S, Nho K, Shen L, Casanova R, Varma S, Legido-Quigley C, Moseley MA, Zhu K, Henrion MY, van der Lee SJ, Harms AC, Demirkan A, Hankemeier T, van Duijn CM, Trojanowski JQ, Shaw LM, Saykin AJ, Weiner MW, Doraiswamy PM, Kaddurah-Daouk R, Alzheimer’s Disease Neuroimaging Initiative and the Alzheimer Disease Metabolomics Consortium.
Snail acetylation by histone acetyltransferase p300 in lung cancer.
Chang R, Zhang Y, Zhang P, Zhou Q
Piezo2 senses airway stretch and mediates lung inflation-induced apnoea.
Nonomura K, Woo SH, Chang RB, Gillich A, Qiu Z, Francisco AG, Ranade SS, Liberles SD, Patapoutian A
Wetting of Inkjet Polymer Droplets on Porous Alumina Substrates.
Zhou H, Chang R, Reichmanis E, Song Y
Sensory Neurons that Detect Stretch and Nutrients in the Digestive System.
Williams EK, Chang RB, Strochlic DE, Umans BD, Lowell BB, Liberles SD
Nm23-H1 was involved in regulation of KAI1 expression in high-metastatic lung cancer cells L9981.
You J, Chang R, Liu B, Zu L, Zhou Q
The K+ channel KIR2.1 functions in tandem with proton influx to mediate sour taste transduction.
Ye W, Chang RB, Bushman JD, Tu YH, Mulhall EM, Wilson CE, Cooper AJ, Chick WS, Hill-Eubanks DC, Nelson MT, Kinnamon SC, Liman ER
EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.
Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE
Immune biomarkers are more accurate in prediction of survival in ulcerated than in non-ulcerated primary melanomas.
de Moll EH, Fu Y, Qian Y, Perkins SH, Wieder S, Gnjatic S, Remark R, Bernardo SG, Moskalenko M, Yao J, Ferringer T, Chang R, Chipuk J, Horst BA, Birge MB, Phelps RG, Saenger YM
Spontaneous emergence of chirality in achiral lyotropic chromonic liquid crystals confined to cylinders.
Nayani K, Chang R, Fu J, Ellis PW, Fernandez-Nieves A, Park JO, Srinivasarao M
Design and performance of the APPLE-Knot undulator.
Ji F, Chang R, Zhou Q, Zhang W, Ye M, Sasaki S, Qiao S
Using “Tender” X-ray Ambient Pressure X-Ray Photoelectron Spectroscopy as A Direct Probe of Solid-Liquid Interface.
Axnanda S, Crumlin EJ, Mao B, Rani S, Chang R, Karlsson PG, Edwards MO, Lundqvist M, Moberg R, Ross P, Hussain Z, Liu Z
Vagal Sensory Neuron Subtypes that Differentially Control Breathing.
Chang RB, Strochlic DE, Williams EK, Umans BD, Liberles SD
Causal inference in biology networks with integrated belief propagation.
Chang R, Karr JR, Schadt EE
A near ambient pressure XPS study of subnanometer silver clusters on Al2O3 and TiO2 ultrathin film supports.
Mao BH, Chang R, Shi L, Zhuo QQ, Rani S, Liu XS, Tyo EC, Vajda S, Wang SD, Liu Z
Arbuscular mycorrhizae improve low temperature tolerance in cucumber via alterations in H2O2 accumulation and ATPase activity.
Liu A, Chen S, Chang R, Liu D, Chen H, Ahammed GJ, Lin X, He C
Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease.
Sivendran S, Chang R, Pham L, Phelps RG, Harcharik ST, Hall LD, Bernardo SG, Moskalenko MM, Sivendran M, Fu Y, de Moll EH, Pan M, Moon JY, Arora S, Cohain A, DiFeo A, Ferringer TC, Tismenetsky M, Tsui CL, Friedlander PA, Parides MK, Banchereau J, Chaussabel D, Lebwohl MG, Wolchok JD, Bhardwaj N, Burakoff SJ, Oh WK, Palucka K, Merad M, Schadt EE, Saenger YM
CO2 activation and carbonate intermediates: an operando AP-XPS study of CO2 electrolysis reactions on solid oxide electrochemical cells.
Yu Y, Mao B, Geller A, Chang R, Gaskell K, Liu Z, Eichhorn BW
Defining the role of CD2 in disease progression and overall survival among patients with completely resected stage-II to -III cutaneous melanoma.
Harcharik S, Bernardo S, Moskalenko M, Pan M, Sivendran M, Bell H, Hall LD, Castillo-Martín M, Fox K, Cordon-Cardo C, Chang R, Sivendran S, Phelps RG, Saenger Y
MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.
You J, Li Y, Fang N, Liu B, Zu L, Chang R, Li X, Zhou Q
Overexpression of mitochondrial uncoupling protein conferred resistance to heat stress and Botrytis cinerea infection in tomato.
Chen S, Liu A, Zhang S, Li C, Chang R, Liu D, Ahammed GJ, Lin X
Vasonatrin peptide, a novel protector of dopaminergic neurons against the injuries induced by n-methyl-4-phenylpyridiniums.
Zhao HK, Chen BY, Chang R, Wang JB, Ni F, Yang L, Dong XC, Sun SH, Zhao G, Fang W, Ma QR, Wang XL, Yu J
The suppressive role and aberrent promoter methylation of BTG3 in the progression of hepatocellular carcinoma.
Lv Z, Zou H, Peng K, Wang J, Ding Y, Li Y, Ren X, Wang F, Chang R, Liang L, Ding Y
SPAG9 is overexpressed in human astrocytoma and promotes cell proliferation and invasion.
Yi F, Ni W, Liu W, Pan X, Han X, Yang L, Kong X, Ma R, Chang R
Hyperphosphorylation of tau protein by calpain regulation in retina of Alzheimer’s disease transgenic mouse.
Zhao H, Chang R, Che H, Wang J, Yang L, Fang W, Xia Y, Li N, Ma Q, Wang X
Ozone-induced band bending on metal-oxide surfaces studied under environmental conditions.
Lampimäki M, Zelenay V, Křepelová A, Liu Z, Chang R, Bluhm H, Ammann M
Oxidation and reduction of size-selected subnanometer Pd clusters on Al2O3 surface.
Mao BH, Chang R, Lee S, Axnanda S, Crumlin E, Grass ME, Wang SD, Vajda S, Liu Z
The top cited articles on glioma stem cells in Web of Science.
Yi F, Ma J, Ni W, Chang R, Liu W, Han X, Pan D, Liu X, Qiu J
Importance of the metal-oxide interface in catalysis: in situ studies of the water-gas shift reaction by ambient-pressure X-ray photoelectron spectroscopy.
Mudiyanselage K, Senanayake SD, Feria L, Kundu S, Baber AE, Graciani J, Vidal AB, Agnoli S, Evans J, Chang R, Axnanda S, Liu Z, Sanz JF, Liu P, Rodriguez JA, Stacchiola DJ
[Research advance on mechanism and application of HATs and HDACs in epithelial-mesenchymal transition of lung cancer].
Chang R, You J, Zhou Q
Elevated rates of transaminitis during ipilimumab therapy for metastatic melanoma.
Bernardo SG, Moskalenko M, Pan M, Shah S, Sidhu HK, Sicular S, Harcharik S, Chang R, Friedlander P, Saenger YM
Synchronous evolution of an odor biosynthesis pathway and behavioral response.
Li Q, Korzan WJ, Ferrero DM, Chang RB, Roy DS, Buchi M, Lemon JK, Kaur AW, Stowers L, Fendt M, Liberles SD
Association between obesity and dental caries in Chinese children.
Wu L, Chang R, Mu Y, Deng X, Wu F, Zhang S, Zhou D
Immunoreactivity of Pluripotent Markers SSEA-5 and L1CAM in Human Tumors, Teratomas, and Induced Pluripotent Stem Cells.
Cassidy L, Choi M, Meyer J, Chang R, Seigel GM
Direct work function measurement by gas phase photoelectron spectroscopy and its application on PbS nanoparticles.
Axnanda S, Scheele M, Crumlin E, Mao B, Chang R, Rani S, Faiz M, Wang S, Alivisatos AP, Liu Z
Genetics. A GPS for navigating DNA.
Schadt E, Chang R
Formation of nanometer-sized surface platinum oxide clusters on a stepped Pt(557) single crystal surface induced by oxygen: a high-pressure STM and ambient-pressure XPS study.
Zhu Z, Tao FF, Zheng F, Chang R, Li Y, Heinke L, Liu Z, Salmeron M, Somorjai GA
Systematic search for recipes to generate induced pluripotent stem cells.
Chang R, Shoemaker R, Wang W
[Effects of negative pressure on osteogenesis in human bone marrow-derived stroma cells cultured in vitro].
Yang Z, Zhu YJ, Cheng Y, Shang BS, Chang R, He P, Zhang YG
Lysine acetylation sites in bovine foamy virus transactivator BTas are important for its DNA binding activity.
Chang R, Tan J, Xu F, Han H, Geng Y, Li Y, Qiao W
A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention.
Chang R, Shoemaker R, Wang W
A TRPA1-dependent mechanism for the pungent sensation of weak acids.
Wang YY, Chang RB, Allgood SD, Silver WL, Liman ER
A proton current drives action potentials in genetically identified sour taste cells.
Chang RB, Waters H, Liman ER
TRPA1 is a component of the nociceptive response to CO2.
Wang YY, Chang RB, Liman ER
A requirement for cyclin-dependent kinase 6 in thymocyte development and tumorigenesis.
Hu MG, Deshpande A, Enos M, Mao D, Hinds EA, Hu GF, Chang R, Guo Z, Dose M, Mao C, Tsichlis PN, Gounari F, Hinds PW
The nociceptor ion channel TRPA1 is potentiated and inactivated by permeating calcium ions.
Wang YY, Chang RB, Waters HN, McKemy DD, Liman ER
Secreted APP regulates the function of full-length APP in neurite outgrowth through interaction with integrin beta1.
Young-Pearse TL, Chen AC, Chang R, Marquez C, Selkoe DJ
[Application of proteomic technology in virological research].
Chang R, Liu C, Qiao WT
Modeling semantics of inconsistent qualitative knowledge for quantitative Bayesian network inference.
Chang R, Brauer W, Stetter M
A critical function for beta-amyloid precursor protein in neuronal migration revealed by in utero RNA interference.
Young-Pearse TL, Bai J, Chang R, Zheng JB, LoTurco JJ, Selkoe DJ
Beta-catenin stabilization stalls the transition from double-positive to single-positive stage and predisposes thymocytes to malignant transformation.
Guo Z, Dose M, Kovalovsky D, Chang R, O’Neil J, Look AT, von Boehmer H, Khazaie K, Gounari F
Effects of insulin-like growth factor 1 on synaptic excitability in cultured rat hippocampal neurons.
Xing C, Yin Y, Chang R, Gong X, He X, Xie Z
Potential polyphenol markers of phase change in apple (Malus domestica).
Zhang XZ, Zhao YB, Li CM, Chen DM, Wang GP, Chang RF, Shu HR
Effects of insulin-like growth factor-1 on okadaic acid-induced apoptosis in SH-SY5Y cells.
Xing C, Peng Y, Chang R, Yin Y, Xie Z
A role of insulin-like growth factor 1 in beta amyloid-induced disinhibition of hippocampal neurons.
Xing C, Yin Y, Chang R, He X, Xie Z
Loss of adenomatous polyposis coli gene function disrupts thymic development.
Gounari F, Chang R, Cowan J, Guo Z, Dose M, Gounaris E, Khazaie K
[Using chemical methods to crosslink xenogeneic heart valves: the progress of bioprosthetic heart valves].
Lin L, Tang YW, Chang R, Zhou JY, Cui JW, Hu SS, Zhang FS

Li Li’s Articles

Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis.
Wei C, Li L, Menon MC, Zhang W, Fu J, Kidd B, Keung KL, Woytovich C, Greene I, Xiao W, Salem F, Yi Z, He JC, Dudley JT, Murphy B
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.
Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B
Replicating Cardiovascular Condition-Birth Month Associations.
Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT
Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT
Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.
Miotto R, Li L, Kidd BA, Dudley JT
Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT
Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer.
Yadav KK, Shameer K, Readhead B, Yadav SS, Li L, Kasarskis A, Tewari AK, Dudley JT
Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center.
Li L, Lee NJ, Glicksberg BS, Radbill BD, Dudley JT
PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT.
Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, Jebakaran J, Kovatch P, Sengupta PP, Gelijns S, Moskovitz A, Darrow B, David DL, Kasarskis A, Tatonetti NP, Pinney S, Dudley JT
Identification of type 2 diabetes subgroups through topological analysis of patient similarity.
Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT
A Three-Gene Assay for Monitoring Immune Quiescence in Kidney Transplantation.
Roedder S, Li L, Alonso MN, Hsieh SC, Vu MT, Dai H, Sigdel TK, Bostock I, Macedo C, Metes D, Zeevi A, Shapiro R, Salvatierra O, Scandling J, Alberu J, Engleman E, Sarwal MM
Age-stratified risk of unexpected uterine sarcoma following surgery for presumed benign leiomyoma.
Brohl AS, Li L, Andikyan V, Običan SG, Cioffi A, Hao K, Dudley JT, Ascher-Walsh C, Kasarskis A, Maki RG
Inhibition of intracellular clusterin attenuates cell death in nephropathic cystinosis.
Sansanwal P, Li L, Sarwal MM
Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis.
Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, Yi Z, Xiong H, Woytovich C, Greene I, Overbey J, Rosales I, Bagiella E, Chen R, Ma M, Li L, Ding W, Djamali A, Saminego M, O’Connell PJ, Gallon L, Colvin R, Schroppel B, He JC, Murphy B
An integrative pipeline for multi-modal discovery of disease relationships.
Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R
Disease risk factors identified through shared genetic architecture and electronic medical records.
Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ
Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation.
Kohrt HE, Tian L, Li L, Alizadeh AA, Hsieh S, Tibshirani RJ, Strober S, Sarwal M, Lowsky R
Immune response profiling identifies autoantibodies specific to Moyamoya patients.
Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK
Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection.
Li L, Khush K, Hsieh SC, Ying L, Luikart H, Sigdel T, Roedder S, Yang A, Valantine H, Sarwal MM
Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records.
Li L, Ruau D, Chen R, Weber S, Butte AJ
Complete steroid avoidance is effective and safe in children with renal transplants: a multicenter randomized trial with three-year follow-up.
Sarwal MM, Ettenger RB, Dharnidharka V, Benfield M, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Tang L, Liu J, Li L, Naesens M, Sigdel T, Waskerwitz J, Salvatierra O
A peripheral blood diagnostic test for acute rejection in renal transplantation.
Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM
Stanniocalcin supports the functional adaptation of adult-sized kidneys transplanted into the pediatric recipients.
Lee S, Naesens M, Li L, Sarwal M
A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation.
Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, Esquivel C, Cox K, Chen R, McDiarmid SV, Sarwal MM
Non-HLA antibodies to immunogenic epitopes predict the evolution of chronic renal allograft injury.
Sigdel TK, Li L, Tran TQ, Khatri P, Naesens M, Sansanwal P, Dai H, Hsieh SC, Sarwal MM
Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach.
Sigdel TK, Woo SH, Dai H, Khatri P, Li L, Myers B, Sarwal MM, Lafayette RA
Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.
Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM
The dual role of epithelial-to-mesenchymal transition in chronic allograft injury in pediatric renal transplantation.
Vitalone MJ, Naesens M, Sigdel T, Li L, Hseih S, Sarwal MM
Soluble human leukocyte antigen-G in pediatric renal transplantation.
Zarkhin V, Bezchinsky M, Li L, Sarwal MM
Phenotypic evaluation of B-cell subsets after rituximab for treatment of acute renal allograft rejection in pediatric recipients.
Zarkhin V, Lovelace PA, Li L, Hsieh SC, Sarwal MM
Efficacy and safety of thymoglobulin induction as an alternative approach for steroid-free maintenance immunosuppression in pediatric renal transplantation.
Li L, Chaudhuri A, Chen A, Zhao X, Bezchinsky M, Concepcion W, Salvatierra O Jr, Sarwal MM
Differential immunogenicity and clinical relevance of kidney compartment specific antigens after renal transplantation.
Li L, Sigdel T, Vitalone M, Lee SH, Sarwal M
Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis.
Sansanwal P, Li L, Hsieh SC, Sarwal MM
Expression of soluble HLA-G identifies favorable outcomes in liver transplant recipients.
Zarkhin V, Talisetti A, Li L, Wozniak LJ, McDiarmid SV, Cox K, Esquivel C, Sarwal MM
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD, MAQC Consortium.
Compartmental localization and clinical relevance of MICA antibodies after renal transplantation.
Li L, Chen A, Chaudhuri A, Kambham N, Sigdel T, Chen R, Sarwal MM
Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients.
Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM
BAFF may modulate the rate of B-cell repopulation after rituximab therapy for acute renal transplant rejection.
Zarkhin V, Li L, Sarwal MM
Expression of complement components differs between kidney allografts from living and deceased donors.
Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM
Steroid-free immunosuppression in pediatric renal transplantation: rationale for and [corrected] outcomes following conversion to steroid based therapy.
Sutherland S, Li L, Concepcion W, Salvatierra O, Sarwal MM
Steroid-free immunosuppression since 1999: 129 pediatric renal transplants with sustained graft and patient benefits.
Li L, Chang A, Naesens M, Kambham N, Waskerwitz J, Martin J, Wong C, Alexander S, Grimm P, Concepcion W, Salvatierra O, Sarwal MM
Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures.
Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ
A randomized, prospective trial of rituximab for acute rejection in pediatric renal transplantation.
Zarkhin V, Li L, Kambham N, Sigdel T, Salvatierra O, Sarwal MM
Potential influence of tacrolimus and steroid avoidance on early graft function in pediatric renal transplantation.
Li L, Weintraub L, Concepcion W, Martin JP, Miller K, Salvatierra O, Sarwal MM
Characterization of intra-graft B cells during renal allograft rejection.
Zarkhin V, Kambham N, Li L, Kwok S, Hsieh SC, Salvatierra O, Sarwal MM
Patient selection critical for calcineurin inhibitor withdrawal in pediatric kidney transplantation.
Weintraub L, Li L, Kambham N, Alexander S, Concepcion W, Miller K, Wong C, Salvatierra O, Sarwal M
“To B or not to B?” B-cells and graft rejection.
Zarkhin V, Li L, Sarwal M
Maturation of dose-corrected tacrolimus predose trough levels in pediatric kidney allograft recipients.
Naesens M, Salvatierra O, Li L, Kambham N, Concepcion W, Sarwal M
Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.
Li L, Ying L, Naesens M, Xiao W, Sigdel T, Hsieh S, Martin J, Chen R, Liu K, Mindrinos M, Davis R, Sarwal M
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ
AILUN: reannotating gene expression data automatically.
Chen R, Li L, Butte AJ
Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance.
Brouard S, Mansfield E, Braud C, Li L, Giral M, Hsieh SC, Baeten D, Zhang M, Ashton-Chess J, Braudeau C, Hsieh F, Dupont A, Pallier A, Moreau A, Louis S, Ruiz C, Salvatierra O, Soulillou JP, Sarwal M
Transplant reno-vascular stenoses associated with early erythropoietin use.
Nagarajan S, Mansfield E, Hsieh S, Liu R, Hsieh F, Li L, Salvatierra O Jr, Sarwal MM
Optimizing outcomes for neonatal ARPKD.
Beaunoyer M, Snehal M, Li L, Concepcion W, Salvatierra O Jr, Sarwal M
Subclinical cytomegalovirus and Epstein-Barr virus viremia are associated with adverse outcomes in pediatric renal transplantation.
Li L, Chaudhuri A, Weintraub LA, Hsieh F, Shah S, Alexander S, Salvatierra O Jr, Sarwal MM
A novel, semiquantitative, clinically correlated calcineurin inhibitor toxicity score for renal allograft biopsies.
Kambham N, Nagarajan S, Shah S, Li L, Salvatierra O, Sarwal MM
Designer genes: Filling the gap in transplantation.
Sarwal MM, Li L
Computational prediction of binding hotspots.
Tong W, Li L, Weng Z
RDOCK: refinement of rigid-body protein docking predictions.
Li L, Chen R, Weng Z
ZDOCK predictions for the CAPRI challenge.
Chen R, Tong W, Mintseris J, Li L, Weng Z
ZDOCK: an initial-stage protein-docking algorithm.
Chen R, Li L, Weng Z

Rong Chen’s Articles

Genomic profiling reveals mutational landscape in parathyroid carcinomas.
Pandya C, Uzilov AV, Bellizzi J, Lau CY, Moe AS, Strahl M, Hamou W, Newman LC, Fink MY, Antipin Y, Yu W, Stevenson M, Cavaco BM, Teh BT, Thakker RV, Morreau H, Schadt EE, Sebra R, Li SD, Arnold A, Chen R
Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer.
Chen Y, Camacho SC, Silvers TR, Razak AR, Gabrail NY, Gerecitano JF, Kalir E, Pereira E, Evans BR, Ramus SJ, Huang F, Priedigkeit N, Rodriguez E, Donovan M, Khan F, Kalir T, Sebra R, Uzilov A, Chen R, Sinha R, Halpert R, Billaud JN, Shacham S, McCauley D, Landesman Y, Rashal T, Kauffman M, Mirza MR, Mau-Sørensen M, Dottino P, Martignetti JA
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.
Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O’Connor T, Miotto R, Kidd BA, Chen R, Ma’ayan A, Dudley JT
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.
Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B
Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease.
Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, Balwani M, Doheny D, Peter I, Chen R, Desnick RJ
A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers.
Ayers KL, Mirshahi UL, Wardeh AH, Murray MF, Hao K, Glicksberg BS, Li S, Carey DJ, Chen R
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH
Anabolic actions of Notch on mature bone.
Liu P, Ping Y, Ma M, Zhang D, Liu C, Zaidi S, Gao S, Ji Y, Lou F, Yu F, Lu P, Stachnik A, Bai M, Wei C, Zhang L, Wang K, Chen R, New MI, Rowe DW, Yuen T, Sun L, Zaidi M
The CYP2D6 VCF Translator.
Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA
Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases.
Luo W, Obeidat M, Di Narzo AF, Chen R, Sin DD, Paré PD, Hao K
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.
Hakenberg J, Cheng WY, Thomas P, Wang YC, Uzilov AV, Chen R
IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS.
Ma M, Wang C, Glicksberg BS, Schadt EE, Li SD, Chen R
DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts.
Cheng WY, Hakenberg J, Li SD, Chen R
Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing.
Shoemaker LD, Clark MJ, Patwardhan A, Chandratillake G, Garcia S, Chen R, Morgan AA, Leng N, Kirk S, Chen R, Cook DJ, Snyder M, Steinberg GK
Identification of type 2 diabetes subgroups through topological analysis of patient similarity.
Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT
ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
Wang J, Liao J, Zhang J, Cheng WY, Hakenberg J, Ma M, Webb BD, Ramasamudram-Chakravarthi R, Karger L, Mehta L, Kornreich R, Diaz GA, Li S, Edelmann L, Chen R
Shared genetic etiology underlying Alzheimer’s disease and type 2 diabetes.
Hao K, Di Narzo AF, Ho L, Luo W, Li S, Chen R, Li T, Dubner L, Pasinetti GM
Disease-associated variants in different categories of disease located in distinct regulatory elements.
Ma M, Ru Y, Chuang LS, Hsu NY, Shi LS, Hakenberg J, Cheng WY, Uzilov A, Ding W, Glicksberg BS, Chen R
An integrative pipeline for multi-modal discovery of disease relationships.
Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R
Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis.
Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, Yi Z, Xiong H, Woytovich C, Greene I, Overbey J, Rosales I, Bagiella E, Chen R, Ma M, Li L, Ding W, Djamali A, Saminego M, O’Connell PJ, Gallon L, Colvin R, Schroppel B, He JC, Murphy B
Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
Pereira E, Camacho-Vanegas O, Anand S, Sebra R, Catalina Camacho S, Garnar-Wortzel L, Nair N, Moshier E, Wooten M, Uzilov A, Chen R, Prasad-Hayes M, Zakashansky K, Beddoe AM, Schadt E, Dottino P, Martignetti JA
Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway.
Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, Chen R, Clark MJ, Haraksingh R, FORGE Canada Consortium., Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH, Goldstein DB
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium.
Disease risk factors identified through shared genetic architecture and electronic medical records.
Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ
Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS).
Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte AJ
Systematic functional regulatory assessment of disease-associated variants.
Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M
Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.
Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ
Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus.
Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ
Immune response profiling identifies autoantibodies specific to Moyamoya patients.
Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK
Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records.
Li L, Ruau D, Chen R, Weber S, Butte AJ
Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus.
Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ
Whole genome sequencing in support of wellness and health maintenance.
Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.
Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD
A peripheral blood diagnostic test for acute rejection in renal transplantation.
Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM
Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery.
Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S
Sequencing and analysis of a South Asian-Indian personal genome.
Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G
Human genomic disease variants: a neutral evolutionary explanation.
Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S
Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes.
Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte AJ
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
Patel CJ, Chen R, Butte AJ
Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
Morgan AA, Chen R, Butte AJ
A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation.
Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, Esquivel C, Cox K, Chen R, McDiarmid SV, Sarwal MM
Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes.
Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ
Therapeutic effects of systemic administration of chaperone αB-crystallin associated with binding proinflammatory plasma proteins.
Rothbard JB, Kurnellas MP, Brownell S, Adams CM, Su L, Axtell RC, Chen R, Fathman CG, Robinson WH, Steinman L
Personal omics profiling reveals dynamic molecular and medical phenotypes.
Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O’Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M
Integrative approach to pain genetics identifies pain sensitivity loci across diseases.
Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS
Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.
Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ
Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ
Quantifying multi-ethnic representation in genetic studies of high mortality diseases.
Chen R, Dudley JT, Ruau D, Butte AJ
Performance comparison of whole-genome sequencing platforms.
Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ
Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.
Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM
Performance comparison of exome DNA sequencing technologies.
Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA
Matching cancer genomes to established cell lines for personalized oncology.
Dudley JT, Chen R, Butte AJ
The reference human genome demonstrates high risk of type 1 diabetes and other disorders.
Chen R, Butte AJ
Content-based microarray search using differential expression profiles.
Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association.
Chen R, Davydov EV, Sirota M, Butte AJ
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ
Translational bioinformatics in the cloud: an affordable alternative.
Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ
Likelihood ratios for genome medicine.
Morgan AA, Chen R, Butte AJ
Clinical assessment incorporating a personal genome.
Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB
Compartmental localization and clinical relevance of MICA antibodies after renal transplantation.
Li L, Chen A, Chaudhuri A, Kambham N, Sigdel T, Chen R, Sarwal MM
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets.
Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ
Similarly strong purifying selection acts on human disease genes of all evolutionary ages.
Cai JJ, Borenstein E, Chen R, Petrov DA
Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures.
Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ
Ontology-driven indexing of public datasets for translational bioinformatics.
Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA
GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed.
Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ
Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.
Li L, Ying L, Naesens M, Xiao W, Sigdel T, Hsieh S, Martin J, Chen R, Liu K, Mindrinos M, Davis R, Sarwal M
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ
Integrating statistical pair potentials into protein complex prediction.
Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z
AILUN: reannotating gene expression data automatically.
Chen R, Li L, Butte AJ
Methodologies for extracting functional pharmacogenomic experiments from international repository.
Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ
Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.
Butte AJ, Chen R
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z
Protein-Protein Docking Benchmark 2.0: an update.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z
RDOCK: refinement of rigid-body protein docking predictions.
Li L, Chen R, Weng Z
A protein-protein docking benchmark.
Chen R, Mintseris J, Janin J, Weng Z
ZDOCK: an initial-stage protein-docking algorithm.
Chen R, Li L, Weng Z
ZDOCK predictions for the CAPRI challenge.
Chen R, Tong W, Mintseris J, Li L, Weng Z
A novel shape complementarity scoring function for protein-protein docking.
Chen R, Weng Z
Docking unbound proteins using shape complementarity, desolvation, and electrostatics.
Chen R, Weng Z
Purification and characterization of trichomaglin–a novel ribosome-inactivating protein with abortifacient activity.
Chen R, Xu YZ, Wu J, Pu Z, Jin SW, Liu WY, Xia ZX

Robert Sebra’s Articles

Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both bla_KPC and bla_CTX-M Integrated in Chromosome.
Huang W, Wang G, Sebra R, Zhuge J, Yin C, Aguero-Rosenfeld ME, Schuetz AN, Dimitrova N, Fallon JT
Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR<sup>+</sup> Populations with Stem Cell Properties.
Tome-Garcia J, Tejero R, Nudelman G, Yong RL, Sebra R, Wang H, Fowkes M, Magid M, Walsh M, Silva-Vargas V, Zaslavsky E, Friedel RH, Doetsch F, Tsankova NM
Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography.
Yang S, Hemarajata P, Hindler J, Li F, Adisetiyo H, Aldrovandi G, Sebra R, Kasarskis A, MacCannell D, Didelot X, Russell D, Rubin Z, Humphries R
Genomic profiling reveals mutational landscape in parathyroid carcinomas.
Pandya C, Uzilov AV, Bellizzi J, Lau CY, Moe AS, Strahl M, Hamou W, Newman LC, Fink MY, Antipin Y, Yu W, Stevenson M, Cavaco BM, Teh BT, Thakker RV, Morreau H, Schadt EE, Sebra R, Li SD, Arnold A, Chen R
Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.
Bashir A, Attie O, Sullivan M, Sebra R, Singh KV, Altman D, Pak T, Dutta J, Chacko K, Webster E, Lewis M, Hamula C, Delli Carpini KW, Murray BE, Kasarskis A, van Bakel H, Huprikar S
Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer.
Chen Y, Camacho SC, Silvers TR, Razak AR, Gabrail NY, Gerecitano JF, Kalir E, Pereira E, Evans BR, Ramus SJ, Huang F, Priedigkeit N, Rodriguez E, Donovan M, Khan F, Kalir T, Sebra R, Uzilov A, Chen R, Sinha R, Halpert R, Billaud JN, Shacham S, McCauley D, Landesman Y, Rashal T, Kauffman M, Mirza MR, Mau-Sørensen M, Dottino P, Martignetti JA
Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, bla_KPC, in Klebsiella Species Is Elusive but Not Rare.
Mathers AJ, Stoesser N, Chai W, Carroll J, Barry K, Cherunvanky A, Sebra R, Kasarskis A, Peto TE, Walker AS, Sifri CD, Crook DW, Sheppard AE
Sequence Type 631 Vibrio parahaemolyticus, an Emerging Foodborne Pathogen in North America.
Xu F, Gonzalez-Escalona N, Haendiges J, Myers RA, Ferguson J, Stiles T, Hickey E, Moore M, Hickey JM, Schillaci C, Mank L, DeRosia-Banick K, Matluk N, Robbins A, Sebra RP, Cooper VS, Jones SH, Whistler CA
Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri.
Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS
Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study.
Nair N, Camacho-Vanegas O, Rykunov D, Dashkoff M, Camacho SC, Schumacher CA, Irish JC, Harkins TT, Freeman E, Garcia I, Pereira E, Kendall S, Belfer R, Kalir T, Sebra R, Reva B, Dottino P, Martignetti JA
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.
Olivares-Chauvet P, Mukamel Z, Lifshitz A, Schwartzman O, Elkayam NO, Lubling Y, Deikus G, Sebra RP, Tanay A
Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.
Stoesser N, Sheppard AE, Peirano G, Sebra R, Lynch T, Anson L, Kasarskis A, Motyl MR, Crook DW, Pitout JD
First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.
Stoesser N, Sheppard AE, Peirano G, Sebra RP, Lynch T, Anson LW, Kasarskis A, Motyl MR, Crook DW, Pitout JD
Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
Li J, Li JW, Feng Z, Wang J, An H, Liu Y, Wang Y, Wang K, Zhang X, Miao Z, Liang W, Sebra R, Wang G, Wang WC, Zhang JR
Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans, the Causative Agent of Bat White-Nose Syndrome.
Drees KP, Palmer JM, Sebra R, Lorch JM, Chen C, Wu CC, Bok JW, Keller NP, Blehert DS, Cuomo CA, Lindner DL, Foster JT
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R
Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.
Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, Giess A, Pankhurst LJ, Vaughan A, Grim CJ, Cox HL, Yeh AJ, Modernising Medical Microbiology (MMM) Informatics Group., Sifri CD, Walker AS, Peto TE, Crook DW, Mathers AJ
Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131.
Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, Turner P, Anson LW, Kasarskis A, Batty EM, Kos V, Wilson DJ, Phetsouvanh R, Wyllie D, Sokurenko E, Manges AR, Johnson TJ, Price LB, Peto TE, Johnson JR, Didelot X, Walker AS, Crook DW, Modernizing Medical Microbiology Informatics Group (MMMIG).
Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6.
Qiao W, Yang Y, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, Scott SA
Quantifying influenza virus diversity and transmission in humans.
Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E
Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.
Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, Walker AS, Peto TE, Crook DW, Mathers AJ
Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
Pereira E, Camacho-Vanegas O, Anand S, Sebra R, Catalina Camacho S, Garnar-Wortzel L, Nair N, Moshier E, Wooten M, Uzilov A, Chen R, Prasad-Hayes M, Zakashansky K, Beddoe AM, Schadt E, Dottino P, Martignetti JA
Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.
Planet PJ, Diaz L, Kolokotronis SO, Narechania A, Reyes J, Xing G, Rincon S, Smith H, Panesso D, Ryan C, Smith DP, Guzman M, Zurita J, Sebra R, Deikus G, Nolan RL, Tenover FC, Weinstock GM, Robinson DA, Arias CA
The PsychENCODE project.
PsychENCODE Consortium., Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N
The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.
Tufariello JM, Kerantzas CA, Vilchèze C, Calder RB, Nordberg EK, Fischer JA, Hartman TE, Yang E, Driscoll T, Cole LE, Sebra R, Maqbool SB, Wattam AR, Jacobs WR Jr
Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A
Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.
Panesso D, Planet PJ, Diaz L, Hugonnet JE, Tran TT, Narechania A, Munita JM, Rincon S, Carvajal LP, Reyes J, Londoño A, Smith H, Sebra R, Deikus G, Weinstock GM, Murray BE, Rossi F, Arthur M, Arias CA
Single molecule real-time sequencing of <i>Xanthomonas oryzae</i> genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.
Booher NJ, Carpenter SC, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ
An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium., Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO
Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G
Characterizing and Overriding the Structural Mechanism of the Quizartinib-Resistant FLT3 “Gatekeeper” F691L Mutation with PLX3397.
Smith CC, Zhang C, Lin KC, Lasater EA, Zhang Y, Massi E, Damon LE, Pendleton M, Bashir A, Sebra R, Perl A, Kasarskis A, Shellooe R, Tsang G, Carias H, Powell B, Burton EA, Matusow B, Zhang J, Spevak W, Ibrahim PN, Le MH, Hsu HH, Habets G, West BL, Bollag G, Shah NP
Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS).
Yang Y, Sebra R, Pullman BS, Qiao W, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA
Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection.
Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin ME, Fitch A, Twaddle A, Cui L, Holmes EC, Boivin G, Ghedin E
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.
Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF
Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.
Benson MA, Ohneck EA, Ryan C, Alonzo F 3rd, Smith H, Narechania A, Kolokotronis SO, Satola SW, Uhlemann AC, Sebra R, Deikus G, Shopsin B, Planet PJ, Torres VJ
HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes.
Brinzevich D, Young GR, Sebra R, Ayllon J, Maio SM, Deikus G, Chen BK, Fernandez-Sesma A, Simon V, Mulder LC
Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.
Parker D, Narechania A, Sebra R, Deikus G, Larussa S, Ryan C, Smith H, Prince A, Mathema B, Ratner AJ, Kreiswirth B, Planet PJ
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW
A hybrid approach for the automated finishing of bacterial genomes.
Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK
Real-time DNA sequencing from single polymerase molecules.
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S
Controlled polymerization chemistry to graft architectures that influence cell-material interactions.
Sebra RP, Reddy SK, Masters KS, Bowman CN, Anseth KS
Detection of antigens in biologically complex fluids with photografted whole antibodies.
Sebra RP, Masters KS, Cheung CY, Bowman CN, Anseth KS
Surface grafted antibodies: controlled architecture permits enhanced antigen detection.
Sebra RP, Masters KS, Bowman CN, Anseth KS
Robust polymer microfluidic device fabrication via contact liquid photolithographic polymerization (CLiPP).
Hutchison JB, Haraldsson KT, Good BT, Sebra RP, Luo N, Anseth KS, Bowman CN

Erick Scott’s Articles

The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit.
Chan YY, Wang P, Rogers L, Tignor N, Zweig M, Hershman SG, Genes N, Scott ER, Krock E, Badgeley M, Edgar R, Violante S, Wright R, Powell CA, Dudley JT, Schadt EE
Whole-Genome Sequencing of a Healthy Aging Cohort.
Erikson GA, Bodian DL, Rueda M, Molparia B, Scott ER, Scott-Van Zeeland AA, Topol SE, Wineinger NE, Niederhuber JE, Topol EJ, Torkamani A
METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS.
Tignor N, Wang P, Genes N, Rogers L, Hershman SG, Scott ER, Zweig M, Yvonne Chan YF, Schadt EE
A genome sequencing program for novel undiagnosed diseases.
Bloss CS, Zeeland AA, Topol SE, Darst BF, Boeldt DL, Erikson GA, Bethel KJ, Bjork RL, Friedman JR, Hwynn N, Patay BA, Pockros PJ, Scott ER, Simon RA, Williams GW, Schork NJ, Topol EJ, Torkamani A
An Examination of the Relationship between Lipid Levels and Associated Genetic Markers across Racial/Ethnic Populations in the Multi-Ethnic Study of Atherosclerosis.
Johnson L, Zhu J, Scott ER, Wineinger NE
Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay.
Larman HB, Scott ER, Wogan M, Oliveira G, Torkamani A, Schultz PG
Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia.
Chen YZ, Friedman JR, Chen DH, Chan GC, Bloss CS, Hisama FM, Topol SE, Carson AR, Pham PH, Bonkowski ES, Scott ER, Lee JK, Zhang G, Oliveira G, Xu J, Scott-Van Zeeland AA, Chen Q, Levy S, Topol EJ, Storm D, Swanson PD, Bird TD, Schork NJ, Raskind WH, Torkamani A
Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease.
Cruchaga C, Karch CM, Jin SC, Benitez BA, Cai Y, Guerreiro R, Harari O, Norton J, Budde J, Bertelsen S, Jeng AT, Cooper B, Skorupa T, Carrell D, Levitch D, Hsu S, Choi J, Ryten M, UK Brain Expression Consortium., Hardy J, Ryten M, Trabzuni D, Weale ME, Ramasamy A, Smith C, Sassi C, Bras J, Gibbs JR, Hernandez DG, Lupton MK, Powell J, Forabosco P, Ridge PG, Corcoran CD, Tschanz JT, Norton MC, Munger RG, Schmutz C, Leary M, Demirci FY, Bamne MN, Wang X, Lopez OL, Ganguli M, Medway C, Turton J, Lord J, Braae A, Barber I, Brown K, Alzheimer’s Research UK Consortium., Passmore P, Craig D, Johnston J, McGuinness B, Todd S, Heun R, Kölsch H, Kehoe PG, Hooper NM, Vardy ER, Mann DM, Pickering-Brown S, Brown K, Kalsheker N, Lowe J, Morgan K, David Smith A, Wilcock G, Warden D, Holmes C, Pastor P, Lorenzo-Betancor O, Brkanac Z, Scott E, Topol E, Morgan K, Rogaeva E, Singleton AB, Hardy J, Kamboh MI, St George-Hyslop P, Cairns N, Morris JC, Kauwe JS, Goate AM
Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases.
Tatro ET, Scott ER, Nguyen TB, Salaria S, Banerjee S, Moore DJ, Masliah E, Achim CL, Everall IP
IL-6 induces regionally selective spinal cord injury in patients with the neuroinflammatory disorder transverse myelitis.
Kaplin AI, Deshpande DM, Scott E, Krishnan C, Carmen JS, Shats I, Martinez T, Drummond J, Dike S, Pletnikov M, Keswani SC, Moran TH, Pardo CA, Calabresi PA, Kerr DA

Research

Our breakthrough insights and products arise out of decades of real-world clinical knowledge and academic research.

RESEARCH HIGHLIGHTS

Putting Genomes Together to Understand the Complexity of Life

Assembly and diploid architecture of an individual human genome via single-molecule technologies

Pioneering a Novel Genome Assembly Approach

A hybrid approach for the automated finishing of bacterial genomes

The Clinical Utility of Understanding Complex Genomes

Development and clinical application of an integrative genomic approach to personalized cancer therapy

Modeling the Complexity of Human Disease