Published in PLoS Comput Biol on January 15, 2010
Computational solutions to large-scale data management and analysis. Nat Rev Genet (2010) 6.58
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc (2012) 2.14
Genomewide multiple-loci mapping in experimental crosses by iterative adaptive penalized regression. Genetics (2010) 1.83
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol (2012) 1.82
Detecting epistasis in human complex traits. Nat Rev Genet (2014) 1.61
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res (2012) 1.46
Joint genetic analysis of gene expression data with inferred cellular phenotypes. PLoS Genet (2011) 1.26
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics (2012) 1.11
GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm. PLoS Genet (2013) 1.03
Simultaneous grouping pursuit and feature selection over an undirected graph. J Am Stat Assoc (2013) 1.01
Bayesian detection of expression quantitative trait loci hot spots. Genetics (2011) 1.00
High-order SNP combinations associated with complex diseases: efficient discovery, statistical power and functional interactions. PLoS One (2012) 1.00
Use of pleiotropy to model genetic interactions in a population. PLoS Genet (2012) 0.95
A new mapping method for quantitative trait loci of silkworm. BMC Genet (2011) 0.94
Simulating systems genetics data with SysGenSIM. Bioinformatics (2011) 0.93
Statistical analysis reveals co-expression patterns of many pairs of genes in yeast are jointly regulated by interacting loci. PLoS Genet (2013) 0.90
eQTL Epistasis - Challenges and Computational Approaches. Front Genet (2013) 0.89
Bridging the Gap between Genotype and Phenotype via Network Approaches. Front Genet (2013) 0.88
Module cover - a new approach to genotype-phenotype studies. Pac Symp Biocomput (2013) 0.87
Robust prediction of expression differences among human individuals using only genotype information. PLoS Genet (2013) 0.86
A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics (2015) 0.82
Molecular network analysis enhances understanding of the biology of mental disorders. Bioessays (2014) 0.82
Integrative multi-omics module network inference with Lemon-Tree. PLoS Comput Biol (2015) 0.81
Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics (2013) 0.80
Expression QTL modules as functional components underlying higher-order phenotypes. PLoS One (2010) 0.80
Biomarkers for combat-related PTSD: focus on molecular networks from high-dimensional data. Eur J Psychotraumatol (2014) 0.79
Statistical Methods in Integrative Genomics. Annu Rev Stat Appl (2016) 0.78
Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum. Mol Biosyst (2012) 0.76
Two-stage genome-wide search for epistasis with implementation to Recombinant Inbred Lines (RIL) populations. PLoS One (2014) 0.75
Exploring dependence between categorical variables: Benefits and limitations of using variable selection within Bayesian clustering in relation to log-linear modelling with interaction terms. J Stat Plan Inference (2016) 0.75
POEM: Identifying Joint Additive Effects on Regulatory Circuits. Front Genet (2016) 0.75
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. Bioinformatics (2015) 0.75
Using stochastic causal trees to augment Bayesian networks for modeling eQTL datasets. BMC Bioinformatics (2011) 0.75
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics (1989) 79.44
Functional discovery via a compendium of expression profiles. Cell (2000) 31.39
Genetic analysis of genome-wide variation in human gene expression. Nature (2004) 27.28
Genetic dissection of transcriptional regulation in budding yeast. Science (2002) 25.01
Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17
Genetics of gene expression and its effect on disease. Nature (2008) 21.35
Mapping the genetic architecture of gene expression in human liver. PLoS Biol (2008) 19.44
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet (2003) 11.84
An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet (2005) 11.40
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A (2005) 9.66
Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics (1995) 8.84
Genetic interactions between polymorphisms that affect gene expression in yeast. Nature (2005) 6.42
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80
Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol (2005) 5.61
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68
Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet (2005) 3.23
Yeast Cbk1 and Mob2 activate daughter-specific genetic programs to induce asymmetric cell fates. Cell (2001) 2.76
Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Genomics (2005) 2.61
Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics (2003) 2.55
A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics (2008) 1.91
Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics (2006) 1.85
An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics (2007) 1.82
Regulation of the yeast TSA1 peroxiredoxin by ZAP1 is an adaptive response to the oxidative stress of zinc deficiency. J Biol Chem (2006) 1.17
Multiple interval mapping for gene expression QTL analysis. Genetica (2009) 1.00
Dabigatran versus warfarin in patients with atrial fibrillation. N Engl J Med (2009) 39.97
Biological, clinical and population relevance of 95 loci for blood lipids. Nature (2010) 28.21
Apixaban versus warfarin in patients with atrial fibrillation. N Engl J Med (2011) 23.50
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet (2010) 23.08
Genetics of gene expression and its effect on disease. Nature (2008) 21.35
Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet (2008) 20.66
Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature (2010) 20.01
Mapping the genetic architecture of gene expression in human liver. PLoS Biol (2008) 19.44
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature (2010) 12.07
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet (2005) 11.40
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12
Apixaban in patients with atrial fibrillation. N Engl J Med (2011) 9.97
The origin of the Haitian cholera outbreak strain. N Engl J Med (2010) 9.85
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med (2011) 9.37
The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet (2004) 9.37
Dronedarone in high-risk permanent atrial fibrillation. N Engl J Med (2011) 8.93
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet (2010) 7.94
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet (2012) 6.97
Cis-acting expression quantitative trait loci in mice. Genome Res (2005) 6.66
Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res (2006) 6.45
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell (2007) 5.67
Early versus delayed invasive intervention in acute coronary syndromes. N Engl J Med (2009) 4.83
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Arsenic degrades PML or PML-RARalpha through a SUMO-triggered RNF4/ubiquitin-mediated pathway. Nat Cell Biol (2008) 4.68
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet (2005) 4.56
A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence. Am J Hum Genet (2007) 4.46
Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell (2013) 4.45
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res (2008) 4.33
Bayesian inference of epistatic interactions in case-control studies. Nat Genet (2007) 4.31
The Spo0A regulon of Bacillus subtilis. Mol Microbiol (2003) 4.19
Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature (2012) 4.01
Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits. PLoS Genet (2011) 3.92
Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet (2010) 3.75
Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet (2005) 3.74
Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet (2010) 3.63
Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet (2006) 3.51
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Comput Biol (2007) 3.37
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics (2003) 3.33
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet (2013) 3.25
Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A (2013) 3.25
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet (2011) 3.18
Bortezomib-based therapy for newly diagnosed mantle-cell lymphoma. N Engl J Med (2015) 3.18
Glucose-insulin-potassium therapy in patients with ST-segment elevation myocardial infarction. JAMA (2007) 3.09
Correction for hidden confounders in the genetic analysis of gene expression. Proc Natl Acad Sci U S A (2010) 3.08
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res (2011) 3.00
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet (2009) 2.97
Eradication of acute promyelocytic leukemia-initiating cells through PML-RARA degradation. Nat Med (2008) 2.85
BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR (2003) 2.74
The Long-Term Multicenter Observational Study of Dabigatran Treatment in Patients With Atrial Fibrillation (RELY-ABLE) Study. Circulation (2013) 2.64
China's facility-based birth strategy and neonatal mortality: a population-based epidemiological study. Lancet (2011) 2.64
Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Genomics (2005) 2.61
The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. J Mol Biol (2003) 2.59
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics (2008) 2.57
CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol (2005) 2.56
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
CD47-blocking antibodies restore phagocytosis and prevent atherosclerosis. Nature (2016) 2.53
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet (2012) 2.53
Dabigatran versus warfarin: effects on ischemic and hemorrhagic strokes and bleeding in Asians and non-Asians with atrial fibrillation. Stroke (2013) 2.52
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genet (2010) 2.43
Association analyses identify six new psoriasis susceptibility loci in the Chinese population. Nat Genet (2010) 2.41
Moving toward a system genetics view of disease. Mamm Genome (2007) 2.38
Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice. Nature (2005) 2.29
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
ToxR regulon of Vibrio cholerae and its expression in vibrios shed by cholera patients. Proc Natl Acad Sci U S A (2003) 2.29
Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics (2007) 2.27
Prevalence of and risk factors for fatty liver in a general population of Shanghai, China. J Hepatol (2005) 2.21
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics (2012) 2.21
De novo cis-regulatory module elicitation for eukaryotic genomes. Proc Natl Acad Sci U S A (2005) 2.20
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet (2009) 2.16
Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood (2010) 2.15
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet (2010) 2.15
A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods (2010) 2.14
Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. Proc Natl Acad Sci U S A (2007) 2.13
Detection of minor drug-resistant populations by parallel allele-specific sequencing. Nat Methods (2007) 2.09
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A (2007) 2.09