Publications
Lisa Edelmann’s Articles
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Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA.
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Development and clinical application of an integrative genomic approach to personalized cancer therapy.
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Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
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A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects.
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Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment.
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Setleis syndrome due to inheritance of the 1p36.22p36.21 duplication: evidence for lack of penetrance.
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Myeloid Dysregulation in a Human Induced Pluripotent Stem Cell Model of PTPN11-Associated Juvenile Myelomonocytic Leukemia.
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ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
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Chromosome 1p36.22p36.21 duplications/triplication causes Setleis syndrome (focal facial dermal dysplasia type III).
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Evaluation of the Affymetrix CytoScan(®) Dx Assay for developmental delay.
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A PTPN11 allele encoding a catalytically impaired SHP2 protein in a patient with a Noonan syndrome phenotype.
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Analytical validation of whole exome and whole genome sequencing for clinical applications.
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Setleis syndrome: genetic and clinical findings in a new case with epilepsy.
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An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy.
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Phelan-McDermid syndrome: a review of the literature and practice parameters for medical assessment and monitoring.
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46,XY disorder of sex development and developmental delay associated with a novel 9q33.3 microdeletion encompassing NR5A1.
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Effect of copy number variants on outcomes for infants with single ventricle heart defects.
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Localization of BRCA1 protein in breast cancer tissue and cell lines with mutations.
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Phenotypic heterogeneity in a family with a small atypical microduplication of chromosome 22q11.2 involving TBX1.
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Complex autism spectrum disorder in a patient with a 17q12 microduplication.
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Role of copy number variants in structural birth defects.
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Copy number variation and warfarin dosing: evaluation of CYP2C9, VKORC1, CYP4F2, GGCX and CALU.
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Experience with carrier screening and prenatal diagnosis for 16 Ashkenazi Jewish genetic diseases.
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Type 1 Gaucher disease: significant disease manifestations in “asymptomatic” homozygotes.
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Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome.
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Genes essential for cell viability that are linked to tumor suppressor genes play a role in cancer susceptibility.
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Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome.
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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.
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Amniotic fluid cells are more efficiently reprogrammed to pluripotency than adult cells.
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Cis lethal genetic interactions attenuate and alter p53 tumorigenesis.
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A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region.
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Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization.
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Development of genomic DNA reference materials for genetic testing of disorders common in people of ashkenazi jewish descent.
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Clinical utility of array CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies.
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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.
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Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations.
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Multiple hemangiomas in a patient with a t(3q;4p) translocation: an infrequent association with Wolf-Hirschhorn syndrome.
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CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population.
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An atypical deletion of the Williams-Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism.
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Mutation in Rpa1 results in defective DNA double-strand break repair, chromosomal instability and cancer in mice.
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Cystic fibrosis carrier screening: validation of a novel method using BeadChip technology.
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Premarital and prenatal screening for cystic fibrosis: experience in the Ashkenazi Jewish population.
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Loss of DNA mismatch repair function and cancer predisposition in the mouse: animal models for human hereditary nonpolyposis colorectal cancer.
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Familial dysautonomia: detection of the IKBKAP IVS20(+6T –> C) and R696P mutations and frequencies among Ashkenazi Jews.
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Carrier screening for mucolipidosis type IV in the American Ashkenazi Jewish population.
Jun Zhu’s Articles
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Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy.
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Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition.
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Gene expression elucidates functional impact of polygenic risk for schizophrenia.
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EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer.
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Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression.
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Impact of non-neoplastic vs intratumoural hepatitis B viral DNA and replication on hepatocellular carcinoma recurrence.
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Disease-specific classification using deconvoluted whole blood gene expression.
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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.
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Discover the network mechanisms underlying the connections between aging and age-related diseases.
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Meditation and vacation effects have an impact on disease-associated molecular phenotypes.
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Development and clinical application of an integrative genomic approach to personalized cancer therapy.
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Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders.
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Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease.
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Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage.
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Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.
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A Next Generation Multiscale View of Inborn Errors of Metabolism.
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Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.
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Characterization of Genetic Networks Associated with Alzheimer’s Disease.
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Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.
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Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer.
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Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
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A robust blood gene expression-based prognostic model for castration-resistant prostate cancer.
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KRAS as a predictor of poor prognosis and benefit from postoperative FOLFOX chemotherapy in patients with stage II and III colorectal cancer.
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Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
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Molecular portraits of epithelial, mesenchymal, and hybrid States in lung adenocarcinoma and their relevance to survival.
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Integrative network analysis reveals molecular mechanisms of blood pressure regulation.
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Integrative network analysis reveals molecular mechanisms of blood pressure regulation.
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A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits.
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Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.
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MODMatcher: multi-omics data matcher for integrative genomic analysis.
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Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.
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Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease.
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An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy.
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Biomarkers for bladder cancer management: present and future.
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Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains.
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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.
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A systems biology framework identifies molecular underpinnings of coronary heart disease.
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The Genotype-Tissue Expression (GTEx) project.
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Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease.
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Modeling causality for pairs of phenotypes in system genetics.
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Cancer-Specific requirement for BUB1B/BUBR1 in human brain tumor isolates and genetically transformed cells.
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11β-HSD1 inhibition reduces atherosclerosis in mice by altering proinflammatory gene expression in the vasculature.
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Functional genomics- and network-driven systems biology approaches for pharmacogenomics and toxicogenomics.
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Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.
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Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.
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Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers.
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Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.
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Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.
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Construction of regulatory networks using expression time-series data of a genotyped population.
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Inferring causal genomic alterations in breast cancer using gene expression data.
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A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.
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Forkhead transcription factor foxq1 promotes epithelial-mesenchymal transition and breast cancer metastasis.
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Bayesian models for detecting epistatic interactions from genetic data.
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Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.
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An integrative multi-network and multi-classifier approach to predict genetic interactions.
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Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
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Identification and validation of genes affecting aortic lesions in mice.
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Simultaneous clustering of multiple gene expression and physical interaction datasets.
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Characterizing dynamic changes in the human blood transcriptional network.
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A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.
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The effect of food intake on gene expression in human peripheral blood.
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Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
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Ppargamma2 is a key driver of longevity in the mouse.
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Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments.
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Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.
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Disentangling molecular relationships with a causal inference test.
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Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks.
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Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.
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Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
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Mapping the genetic architecture of gene expression in human liver.
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Variations in DNA elucidate molecular networks that cause disease.
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Genetics of gene expression and its effect on disease.
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A systems biology approach to drug discovery.
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Statistical power of phylo-HMM for evolutionarily conserved element detection.
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Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations.
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Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes.
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Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels.
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An integrative genomics approach to infer causal associations between gene expression and disease.
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An integrative genomics approach to the reconstruction of gene networks in segregating populations.
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Database search based on Bayesian alignment.
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Bayesian adaptive sequence alignment algorithms.
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Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome.
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Bayesian adaptive alignment and inference.
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Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice.
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A common-lines based method for determining orientations for N > 3 particle projections simultaneously.
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SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
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A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome.
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A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome.
Eric Schadt’s Articles
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Rationale and Design of Family-Based Approach in a Minority Community Integrating Systems-Biology for Promotion of Health (FAMILIA).
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Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
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Heterozygous Pathogenic Variant in DACT1 Causes an Autosomal-Dominant Syndrome with Features Overlapping Townes-Brocks Syndrome.
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The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit.
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Genomic profiling reveals mutational landscape in parathyroid carcinomas.
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Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease.
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Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks.
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Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project.
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High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors.
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Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.
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Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.
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variancePartition: interpreting drivers of variation in complex gene expression studies.
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Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease.
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Gene expression elucidates functional impact of polygenic risk for schizophrenia.
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Corrigendum: Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).
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Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project.
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Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).
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Discover the network mechanisms underlying the connections between aging and age-related diseases.
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Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.
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CD47-blocking antibodies restore phagocytosis and prevent atherosclerosis.
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The Self-Directed Biological Transformation Initiative and Well-Being.
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Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.
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Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
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Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn’s Disease Cohort Inform IBD Genetic Association Loci.
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A new molecular signature method for prediction of driver cancer pathways from transcriptional data.
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Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
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Extensive sequencing of seven human genomes to characterize benchmark reference materials.
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Development and clinical application of an integrative genomic approach to personalized cancer therapy.
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Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
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Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease.
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Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
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Family-Based Approaches to Cardiovascular Health Promotion.
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Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease.
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In utero exposures to environmental organic pollutants disrupt epigenetic marks linked to fetoplacental development.
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New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.
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Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
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A Next Generation Multiscale View of Inborn Errors of Metabolism.
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Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.
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Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.
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Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.
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Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.
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IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS.
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METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS.
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EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.
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Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
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Correction: A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen.
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A Cytosine Methyltransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen [corrected].
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Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
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How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study.
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Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis.
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Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.
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Prediction of Causal Candidate Genes in Coronary Artery Disease Loci.
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An integrated map of structural variation in 2,504 human genomes.
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A robust blood gene expression-based prognostic model for castration-resistant prostate cancer.
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Preparing the next generation of genomicists: a laboratory-style course in medical genomics.
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Assembly and diploid architecture of an individual human genome via single-molecule technologies.
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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
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Modern Methods for Delineating Metagenomic Complexity.
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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
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Improved integrative framework combining association data with gene expression features to prioritize Crohn’s disease genes.
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Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
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Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss.
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Prothymosin α variants isolated from CD8+ T cells and cervicovaginal fluid suppress HIV-1 replication through type I interferon induction.
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Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.
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Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease.
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Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.
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Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans.
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Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders.
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Genetic studies of body mass index yield new insights for obesity biology.
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New genetic loci link adipose and insulin biology to body fat distribution.
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Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma.
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Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.
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Exploring the associations between microRNA expression profiles and environmental pollutants in human placenta from the National Children’s Study (NCS).
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Systems biology of asthma and allergic diseases: a multiscale approach.
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Causal inference in biology networks with integrated belief propagation.
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Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders.
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TGFβ receptor 1: an immune susceptibility gene in HPV-associated cancer.
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iPSC-derived dopamine neurons reveal differences between monozygotic twins discordant for Parkinson’s disease.
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A role for noncoding variation in schizophrenia.
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Geroscience: linking aging to chronic disease.
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lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R.
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Downregulation of carnitine acyl-carnitine translocase by miRNAs 132 and 212 amplifies glucose-stimulated insulin secretion.
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Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.
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Biomarkers for combat-related PTSD: focus on molecular networks from high-dimensional data.
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MODMatcher: multi-omics data matcher for integrative genomic analysis.
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Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis.
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Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease.
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Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.
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The role of macromolecular damage in aging and age-related disease.
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Translational genomics. Clues from the resilient.
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Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.
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Analytical validation of whole exome and whole genome sequencing for clinical applications.
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Mutations in tetratricopeptide repeat domain 7A result in a severe form of very early onset inflammatory bowel disease.
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Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci.
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Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis.
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Causal effects of body mass index on cardiometabolic traits and events: a Mendelian randomization analysis.
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Unifying immunology with informatics and multiscale biology.
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Autotransporters but not pAA are critical for rabbit colonization by Shiga toxin-producing Escherichia coli O104:H4.
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Personalized ovarian cancer disease surveillance and detection of candidate therapeutic drug target in circulating tumor DNA.
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Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study.
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Characterization of the human ESC transcriptome by hybrid sequencing.
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Fine-mapping, gene expression and splicing analysis of the disease associated LRRK2 locus.
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A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry.
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
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Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease.
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Loci influencing blood pressure identified using a cardiovascular gene-centric array.
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CR1 and the “vanishing amyloid” hypothesis of Alzheimer’s disease.
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Loss of CDKN2B promotes p53-dependent smooth muscle cell apoptosis and aneurysm formation.
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Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
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Large-scale association analysis identifies new risk loci for coronary artery disease.
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Improving breast cancer survival analysis through competition-based multidimensional modeling.
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Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
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Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.
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Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.
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Seventy-five genetic loci influencing the human red blood cell.
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A systematic approach to multifactorial cardiovascular disease: causal analysis.
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Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
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Non-O1 Vibrio cholerae unlinked to cholera in Haiti.
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Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
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Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.
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Mapping cis- and trans-regulatory effects across multiple tissues in twins.
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Genetics. A GPS for navigating DNA.
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Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.
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Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis.
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Eric Schadt. Interview by H. Craig Mak.
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This I believe: gaining new insights through integrating “old” data.
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Leveraging models of cell regulation and GWAS data in integrative network-based association studies.
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Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers.
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A hybrid approach for the automated finishing of bacterial genomes.
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The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.
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Genome scans for transmission ratio distortion regions in mice.
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Bayesian method to predict individual SNP genotypes from gene expression data.
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Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia.
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Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.
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A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models.
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Systems genetics of susceptibility to obesity-induced diabetes in mice.
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NEW: network-enabled wisdom in biology, medicine, and health care.
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Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
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The changing privacy landscape in the era of big data.
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Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.
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Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.
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Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
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Integrative genomics strategies to elucidate the complexity of drug response.
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Construction of regulatory networks using expression time-series data of a genotyped population.
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Clinicopathologic and gene expression parameters predict liver cancer prognosis.
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The arrestin domain-containing 3 protein regulates body mass and energy expenditure.
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Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake.
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Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
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Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
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Inferring causal genomic alterations in breast cancer using gene expression data.
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A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.
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Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.
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Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques.
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COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
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Identification of a common variant in the TFR2 gene implicated in the physiological regulation of serum iron levels.
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Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
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Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology.
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Systematic detection of polygenic cis-regulatory evolution.
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Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.
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Genome-sequencing anniversary. First steps on a long road.
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A model selection approach for expression quantitative trait loci (eQTL) mapping.
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Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height.
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The origin of the Haitian cholera outbreak strain.
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Dissecting cis regulation of gene expression in human metabolic tissues.
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Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.
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Identification of genes and networks driving cardiovascular and metabolic phenotypes in a mouse F2 intercross.
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Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
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Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
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A window into third-generation sequencing.
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Hundreds of variants clustered in genomic loci and biological pathways affect human height.
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In the absence of HCV infection, interferon stimulated gene expression in liver is not associated with IL28B genotype.
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Drug discovery in a multidimensional world: systems, patterns, and networks.
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Correction for hidden confounders in the genetic analysis of gene expression.
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An integrative multi-network and multi-classifier approach to predict genetic interactions.
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FoxM1 is up-regulated by obesity and stimulates beta-cell proliferation.
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Computational solutions to large-scale data management and analysis.
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Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.
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From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus.
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Biological, clinical and population relevance of 95 loci for blood lipids.
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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.
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Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
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Gene bionetwork analysis of ovarian primordial follicle development.
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Expression quantitative trait loci: replication, tissue- and sex-specificity in mice.
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Identification and validation of genes affecting aortic lesions in mice.
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An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
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Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes.
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Simultaneous clustering of multiple gene expression and physical interaction datasets.
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Integrating pathway analysis and genetics of gene expression for genome-wide association studies.
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Assessing the prospects of genome-wide association studies performed in inbred mice.
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Evidence for widespread adaptive evolution of gene expression in budding yeast.
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Characterizing dynamic changes in the human blood transcriptional network.
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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.
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A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.
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Magnitude of stratification in human populations and impacts on genome wide association studies.
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The quantitative genetics of phenotypic robustness.
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The effect of food intake on gene expression in human peripheral blood.
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Disruption of the aortic elastic lamina and medial calcification share genetic determinants in mice.
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Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
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Ppargamma2 is a key driver of longevity in the mouse.
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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.
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Alternative splicing of TCF7L2 gene in omental and subcutaneous adipose tissue and risk of type 2 diabetes.
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Common body mass index-associated variants confer risk of extreme obesity.
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Molecular networks as sensors and drivers of common human diseases.
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The C3a anaphylatoxin receptor is a key mediator of insulin resistance and functions by modulating adipose tissue macrophage infiltration and activation.
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Obesity and genetics regulate microRNAs in islets, liver, and adipose of diabetic mice.
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On the adjustment for covariates in genetic association analysis: a novel, simple principle to infer direct causal effects.
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Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.
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Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments.
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Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.
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Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history.
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Disentangling molecular relationships with a causal inference test.
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Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks.
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A network view of disease and compound screening.
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Something wiki this way comes. Interview by Bryn Nelson.
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Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks.
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Diurnal variation of the human adipose transcriptome and the link to metabolic disease.
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Integrative genomics and drug development.
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The Pro12Ala PPARgamma2 variant determines metabolism at the gene-environment interface.
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Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.
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An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association.
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Common variants at 30 loci contribute to polygenic dyslipidemia.
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Uncovering the genetic landscape for multiple sleep-wake traits.
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Genomics and genome-wide association studies: an integrative approach to expression QTL mapping.
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Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
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Calibrating the performance of SNP arrays for whole-genome association studies.
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Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences.
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Mapping the genetic architecture of gene expression in human liver.
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A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.
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On the replication of genetic associations: timing can be everything!
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Variations in DNA elucidate molecular networks that cause disease.
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Genetics of gene expression and its effect on disease.
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Systems biology and its potential role in radiobiology.
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A systems biology approach to drug discovery.
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Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.
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Statistical power of phylo-HMM for evolutionarily conserved element detection.
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A genome-wide set of congenic mouse strains derived from CAST/Ei on a C57BL/6 background.
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Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data.
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Linkage disequilibrium in wild mice.
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Moving toward a system genetics view of disease.
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Pharmacogenetics of metformin response: a step in the path toward personalized medicine.
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Evidence for novel susceptibility genes for late-onset Alzheimer’s disease from a genome-wide association study of putative functional variants.
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Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations.
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Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics.
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DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies.
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Dosage compensation is less effective in birds than in mammals.
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Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes.
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Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.
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Integrating genetic and network analysis to characterize genes related to mouse weight.
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Tissue-specific expression and regulation of sexually dimorphic genes in mice.
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Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice.
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Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes.
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Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity.
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Exploiting naturally occurring DNA variation and molecular profiling data to dissect disease and drug response traits.
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Sequence variation in NPC1L1 and association with improved LDL-cholesterol lowering in response to ezetimibe treatment.
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Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice.
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Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice.
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Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels.
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Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits.
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A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background.
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Embracing complexity, inching closer to reality.
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An integrative genomics approach to infer causal associations between gene expression and disease.
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Cis-acting expression quantitative trait loci in mice.
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Ultrafine mapping of SNPs from mouse strains C57BL/6J, DBA/2J, and C57BLKS/J for loci contributing to diabetes and atherosclerosis susceptibility.
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Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
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Genomic analysis of metabolic pathway gene expression in mice.
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The Collaborative Cross, a community resource for the genetic analysis of complex traits.
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A comprehensive transcript index of the human genome generated using microarrays and computational approaches.
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Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.
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Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice.
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Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.
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A family-based test for correlation between gene expression and trait values.
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Genetics of gene expression surveyed in maize, mouse and man.
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Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.
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Applications of codon and rate variation models in molecular phylogeny.
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Codon and rate variation models in molecular phylogeny.
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Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis.
Rui Chang’s Articles
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Using chiral tactoids as optical probes to study the aggregation behavior of chromonics.
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Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
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Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer binding protein alpha.
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Metabolic network failures in Alzheimer’s disease-A biochemical road map.
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Snail acetylation by histone acetyltransferase p300 in lung cancer.
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Piezo2 senses airway stretch and mediates lung inflation-induced apnoea.
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Wetting of Inkjet Polymer Droplets on Porous Alumina Substrates.
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Sensory Neurons that Detect Stretch and Nutrients in the Digestive System.
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Nm23-H1 was involved in regulation of KAI1 expression in high-metastatic lung cancer cells L9981.
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The K+ channel KIR2.1 functions in tandem with proton influx to mediate sour taste transduction.
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EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.
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Immune biomarkers are more accurate in prediction of survival in ulcerated than in non-ulcerated primary melanomas.
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Spontaneous emergence of chirality in achiral lyotropic chromonic liquid crystals confined to cylinders.
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Design and performance of the APPLE-Knot undulator.
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Using “Tender” X-ray Ambient Pressure X-Ray Photoelectron Spectroscopy as A Direct Probe of Solid-Liquid Interface.
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Vagal Sensory Neuron Subtypes that Differentially Control Breathing.
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Causal inference in biology networks with integrated belief propagation.
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A near ambient pressure XPS study of subnanometer silver clusters on Al2O3 and TiO2 ultrathin film supports.
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Arbuscular mycorrhizae improve low temperature tolerance in cucumber via alterations in H2O2 accumulation and ATPase activity.
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Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease.
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CO2 activation and carbonate intermediates: an operando AP-XPS study of CO2 electrolysis reactions on solid oxide electrochemical cells.
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Defining the role of CD2 in disease progression and overall survival among patients with completely resected stage-II to -III cutaneous melanoma.
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MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.
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Overexpression of mitochondrial uncoupling protein conferred resistance to heat stress and Botrytis cinerea infection in tomato.
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Vasonatrin peptide, a novel protector of dopaminergic neurons against the injuries induced by n-methyl-4-phenylpyridiniums.
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The suppressive role and aberrent promoter methylation of BTG3 in the progression of hepatocellular carcinoma.
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SPAG9 is overexpressed in human astrocytoma and promotes cell proliferation and invasion.
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Hyperphosphorylation of tau protein by calpain regulation in retina of Alzheimer’s disease transgenic mouse.
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Ozone-induced band bending on metal-oxide surfaces studied under environmental conditions.
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Oxidation and reduction of size-selected subnanometer Pd clusters on Al2O3 surface.
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The top cited articles on glioma stem cells in Web of Science.
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Importance of the metal-oxide interface in catalysis: in situ studies of the water-gas shift reaction by ambient-pressure X-ray photoelectron spectroscopy.
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[Research advance on mechanism and application of HATs and HDACs in epithelial-mesenchymal transition of lung cancer].
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Elevated rates of transaminitis during ipilimumab therapy for metastatic melanoma.
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Synchronous evolution of an odor biosynthesis pathway and behavioral response.
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Association between obesity and dental caries in Chinese children.
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Immunoreactivity of Pluripotent Markers SSEA-5 and L1CAM in Human Tumors, Teratomas, and Induced Pluripotent Stem Cells.
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Direct work function measurement by gas phase photoelectron spectroscopy and its application on PbS nanoparticles.
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Genetics. A GPS for navigating DNA.
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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.
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Systematic search for recipes to generate induced pluripotent stem cells.
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[Effects of negative pressure on osteogenesis in human bone marrow-derived stroma cells cultured in vitro].
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Lysine acetylation sites in bovine foamy virus transactivator BTas are important for its DNA binding activity.
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A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention.
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A TRPA1-dependent mechanism for the pungent sensation of weak acids.
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A proton current drives action potentials in genetically identified sour taste cells.
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TRPA1 is a component of the nociceptive response to CO2.
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A requirement for cyclin-dependent kinase 6 in thymocyte development and tumorigenesis.
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The nociceptor ion channel TRPA1 is potentiated and inactivated by permeating calcium ions.
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Secreted APP regulates the function of full-length APP in neurite outgrowth through interaction with integrin beta1.
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[Application of proteomic technology in virological research].
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Modeling semantics of inconsistent qualitative knowledge for quantitative Bayesian network inference.
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A critical function for beta-amyloid precursor protein in neuronal migration revealed by in utero RNA interference.
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Beta-catenin stabilization stalls the transition from double-positive to single-positive stage and predisposes thymocytes to malignant transformation.
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Effects of insulin-like growth factor 1 on synaptic excitability in cultured rat hippocampal neurons.
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Potential polyphenol markers of phase change in apple (Malus domestica).
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Effects of insulin-like growth factor-1 on okadaic acid-induced apoptosis in SH-SY5Y cells.
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A role of insulin-like growth factor 1 in beta amyloid-induced disinhibition of hippocampal neurons.
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Loss of adenomatous polyposis coli gene function disrupts thymic development.
-
[Using chemical methods to crosslink xenogeneic heart valves: the progress of bioprosthetic heart valves].
Li Li’s Articles
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Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis.
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Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.
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Replicating Cardiovascular Condition-Birth Month Associations.
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Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
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Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
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Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.
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Evaluation of direct-to-consumer low-volume lab tests in healthy adults.
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Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer.
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Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center.
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PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT.
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Identification of type 2 diabetes subgroups through topological analysis of patient similarity.
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A Three-Gene Assay for Monitoring Immune Quiescence in Kidney Transplantation.
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Age-stratified risk of unexpected uterine sarcoma following surgery for presumed benign leiomyoma.
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Inhibition of intracellular clusterin attenuates cell death in nephropathic cystinosis.
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Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis.
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An integrative pipeline for multi-modal discovery of disease relationships.
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Disease risk factors identified through shared genetic architecture and electronic medical records.
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Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation.
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Immune response profiling identifies autoantibodies specific to Moyamoya patients.
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Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection.
-
Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records.
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Complete steroid avoidance is effective and safe in children with renal transplants: a multicenter randomized trial with three-year follow-up.
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A peripheral blood diagnostic test for acute rejection in renal transplantation.
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Stanniocalcin supports the functional adaptation of adult-sized kidneys transplanted into the pediatric recipients.
-
A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation.
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Non-HLA antibodies to immunogenic epitopes predict the evolution of chronic renal allograft injury.
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Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach.
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Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.
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The dual role of epithelial-to-mesenchymal transition in chronic allograft injury in pediatric renal transplantation.
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Soluble human leukocyte antigen-G in pediatric renal transplantation.
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Phenotypic evaluation of B-cell subsets after rituximab for treatment of acute renal allograft rejection in pediatric recipients.
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Efficacy and safety of thymoglobulin induction as an alternative approach for steroid-free maintenance immunosuppression in pediatric renal transplantation.
-
Differential immunogenicity and clinical relevance of kidney compartment specific antigens after renal transplantation.
-
Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis.
-
Expression of soluble HLA-G identifies favorable outcomes in liver transplant recipients.
-
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
-
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
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Compartmental localization and clinical relevance of MICA antibodies after renal transplantation.
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Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients.
-
BAFF may modulate the rate of B-cell repopulation after rituximab therapy for acute renal transplant rejection.
-
Expression of complement components differs between kidney allografts from living and deceased donors.
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Steroid-free immunosuppression in pediatric renal transplantation: rationale for and [corrected] outcomes following conversion to steroid based therapy.
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Steroid-free immunosuppression since 1999: 129 pediatric renal transplants with sustained graft and patient benefits.
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Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures.
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A randomized, prospective trial of rituximab for acute rejection in pediatric renal transplantation.
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Potential influence of tacrolimus and steroid avoidance on early graft function in pediatric renal transplantation.
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Characterization of intra-graft B cells during renal allograft rejection.
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Patient selection critical for calcineurin inhibitor withdrawal in pediatric kidney transplantation.
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“To B or not to B?” B-cells and graft rejection.
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Maturation of dose-corrected tacrolimus predose trough levels in pediatric kidney allograft recipients.
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Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.
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FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
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AILUN: reannotating gene expression data automatically.
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Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance.
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Transplant reno-vascular stenoses associated with early erythropoietin use.
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Optimizing outcomes for neonatal ARPKD.
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Subclinical cytomegalovirus and Epstein-Barr virus viremia are associated with adverse outcomes in pediatric renal transplantation.
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A novel, semiquantitative, clinically correlated calcineurin inhibitor toxicity score for renal allograft biopsies.
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Designer genes: Filling the gap in transplantation.
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Computational prediction of binding hotspots.
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RDOCK: refinement of rigid-body protein docking predictions.
-
ZDOCK predictions for the CAPRI challenge.
-
ZDOCK: an initial-stage protein-docking algorithm.
Rong Chen’s Articles
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Genomic profiling reveals mutational landscape in parathyroid carcinomas.
-
Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer.
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Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.
-
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.
-
Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease.
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A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers.
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Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
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Development and clinical application of an integrative genomic approach to personalized cancer therapy.
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Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.
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Anabolic actions of Notch on mature bone.
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The CYP2D6 VCF Translator.
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Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases.
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Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.
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IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS.
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DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts.
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Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing.
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Identification of type 2 diabetes subgroups through topological analysis of patient similarity.
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ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
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Shared genetic etiology underlying Alzheimer’s disease and type 2 diabetes.
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Disease-associated variants in different categories of disease located in distinct regulatory elements.
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An integrative pipeline for multi-modal discovery of disease relationships.
-
Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis.
-
Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
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Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway.
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
-
Disease risk factors identified through shared genetic architecture and electronic medical records.
-
Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS).
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Systematic functional regulatory assessment of disease-associated variants.
-
Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.
-
Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus.
-
Immune response profiling identifies autoantibodies specific to Moyamoya patients.
-
Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records.
-
Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus.
-
Whole genome sequencing in support of wellness and health maintenance.
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Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.
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A peripheral blood diagnostic test for acute rejection in renal transplantation.
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Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery.
-
Sequencing and analysis of a South Asian-Indian personal genome.
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Human genomic disease variants: a neutral evolutionary explanation.
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Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes.
-
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
-
Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
-
A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation.
-
Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes.
-
Therapeutic effects of systemic administration of chaperone αB-crystallin associated with binding proinflammatory plasma proteins.
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Personal omics profiling reveals dynamic molecular and medical phenotypes.
-
Integrative approach to pain genetics identifies pain sensitivity loci across diseases.
-
Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.
-
Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
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Quantifying multi-ethnic representation in genetic studies of high mortality diseases.
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Performance comparison of whole-genome sequencing platforms.
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ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
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Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.
-
Performance comparison of exome DNA sequencing technologies.
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Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
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Matching cancer genomes to established cell lines for personalized oncology.
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The reference human genome demonstrates high risk of type 1 diabetes and other disorders.
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Content-based microarray search using differential expression profiles.
-
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association.
-
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
-
Translational bioinformatics in the cloud: an affordable alternative.
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Likelihood ratios for genome medicine.
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Clinical assessment incorporating a personal genome.
-
Compartmental localization and clinical relevance of MICA antibodies after renal transplantation.
-
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets.
-
Similarly strong purifying selection acts on human disease genes of all evolutionary ages.
-
Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures.
-
Ontology-driven indexing of public datasets for translational bioinformatics.
-
GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed.
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Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.
-
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
-
Integrating statistical pair potentials into protein complex prediction.
-
AILUN: reannotating gene expression data automatically.
-
Methodologies for extracting functional pharmacogenomic experiments from international repository.
-
Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.
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ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
-
Protein-Protein Docking Benchmark 2.0: an update.
-
RDOCK: refinement of rigid-body protein docking predictions.
-
A protein-protein docking benchmark.
-
ZDOCK: an initial-stage protein-docking algorithm.
-
ZDOCK predictions for the CAPRI challenge.
-
A novel shape complementarity scoring function for protein-protein docking.
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics.
-
Purification and characterization of trichomaglin–a novel ribosome-inactivating protein with abortifacient activity.
Robert Sebra’s Articles
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Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in Chromosome.
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Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR<sup>+</sup> Populations with Stem Cell Properties.
-
Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography.
-
Genomic profiling reveals mutational landscape in parathyroid carcinomas.
-
Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.
-
Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer.
-
Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, blaKPC, in Klebsiella Species Is Elusive but Not Rare.
-
Sequence Type 631 Vibrio parahaemolyticus, an Emerging Foodborne Pathogen in North America.
-
Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri.
-
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.
-
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.
-
Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.
-
First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.
-
Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
-
Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans, the Causative Agent of Bat White-Nose Syndrome.
-
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
-
Development and clinical application of an integrative genomic approach to personalized cancer therapy.
-
Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.
-
Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131.
-
Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6.
-
Quantifying influenza virus diversity and transmission in humans.
-
Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.
-
Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.
-
Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.
-
The PsychENCODE project.
-
The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.
-
Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
-
Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.
-
Single molecule real-time sequencing of <i>Xanthomonas oryzae</i> genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.
-
An integrated map of structural variation in 2,504 human genomes.
-
Assembly and diploid architecture of an individual human genome via single-molecule technologies.
-
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
-
Characterizing and Overriding the Structural Mechanism of the Quizartinib-Resistant FLT3 “Gatekeeper” F691L Mutation with PLX3397.
-
Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS).
-
Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection.
-
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.
-
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
-
Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.
-
HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes.
-
Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.
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Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
-
A hybrid approach for the automated finishing of bacterial genomes.
-
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
-
Real-time DNA sequencing from single polymerase molecules.
-
Controlled polymerization chemistry to graft architectures that influence cell-material interactions.
-
Detection of antigens in biologically complex fluids with photografted whole antibodies.
-
Surface grafted antibodies: controlled architecture permits enhanced antigen detection.
-
Robust polymer microfluidic device fabrication via contact liquid photolithographic polymerization (CLiPP).
Erick Scott’s Articles
-
The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit.
-
Whole-Genome Sequencing of a Healthy Aging Cohort.
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METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS.
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A genome sequencing program for novel undiagnosed diseases.
-
An Examination of the Relationship between Lipid Levels and Associated Genetic Markers across Racial/Ethnic Populations in the Multi-Ethnic Study of Atherosclerosis.
-
Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay.
-
Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia.
-
Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease.
-
Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases.
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IL-6 induces regionally selective spinal cord injury in patients with the neuroinflammatory disorder transverse myelitis.