Published in Bioinformatics on November 10, 2006
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol (2014) 8.13
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet (2009) 5.99
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell (2010) 4.50
Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature (2010) 4.23
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Melanomas resist T-cell therapy through inflammation-induced reversible dedifferentiation. Nature (2012) 3.83
Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med (2010) 3.81
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet (2012) 3.08
Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc (2009) 2.80
clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS (2012) 2.46
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (2009) 2.37
Intra-graft expression of genes involved in iron homeostasis predicts the development of operational tolerance in human liver transplantation. J Clin Invest (2011) 2.36
Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics (2011) 2.31
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. Nat Neurosci (2015) 2.31
Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Mol Cell Proteomics (2008) 2.29
PINA v2.0: mining interactome modules. Nucleic Acids Res (2011) 2.23
The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network. Cell Stem Cell (2012) 2.17
DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell (2011) 2.17
Transcriptomic dissection of tongue squamous cell carcinoma. BMC Genomics (2008) 2.09
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection. Nat Med (2013) 2.06
Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics (2009) 2.02
Effects of atherogenic diet on hepatic gene expression across mouse strains. Physiol Genomics (2009) 2.00
Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol (2008) 1.95
A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res (2012) 1.92
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics (2008) 1.81
Gene set enrichment analysis made simple. Stat Methods Med Res (2009) 1.79
Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis. Dev Cell (2015) 1.75
IL-33 amplifies an innate immune response in the degenerating retina. J Exp Med (2016) 1.74
Salmonella Typhimurium type III secretion effectors stimulate innate immune responses in cultured epithelial cells. PLoS Pathog (2009) 1.73
The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res (2012) 1.72
Extensive copy-number variation of the human olfactory receptor gene family. Am J Hum Genet (2008) 1.71
Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res (2010) 1.67
Stepwise DNA methylation changes are linked to escape from defined proliferation barriers and mammary epithelial cell immortalization. Cancer Res (2009) 1.65
A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome Res (2012) 1.63
Adult somatic stem cells in the human parasite Schistosoma mansoni. Nature (2013) 1.61
Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One (2011) 1.60
Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res (2010) 1.59
Foxf genes integrate tbx5 and hedgehog pathways in the second heart field for cardiac septation. PLoS Genet (2014) 1.59
A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. Genetics (2008) 1.58
Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics (2009) 1.55
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics (2007) 1.54
Gene expression profiling differentiates autism case-controls and phenotypic variants of autism spectrum disorders: evidence for circadian rhythm dysfunction in severe autism. Autism Res (2009) 1.53
Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet (2015) 1.53
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One (2008) 1.53
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52
Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD. PLoS Genet (2015) 1.52
Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics (2009) 1.52
PPARgamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells. J Cell Biochem (2009) 1.51
Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage. Mol Biol Cell (2010) 1.49
MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis. PLoS Genet (2015) 1.49
Functional genomics unique to week 20 post wounding in the deep cone/fat dome of the Duroc/Yorkshire porcine model of fibroproliferative scarring. PLoS One (2011) 1.48
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
Statistical methods for gene set co-expression analysis. Bioinformatics (2009) 1.47
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res (2010) 1.45
Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res (2009) 1.44
Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PLoS Pathog (2013) 1.43
The Genome of the "Great Speciator" Provides Insights into Bird Diversification. Genome Biol Evol (2015) 1.43
Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development. Genomics (2008) 1.42
Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis. PLoS One (2011) 1.41
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PLoS One (2013) 1.41
Merging transcriptomics and metabolomics--advances in breast cancer profiling. BMC Cancer (2010) 1.41
Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use. Clin Epigenetics (2016) 1.39
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics (2010) 1.38
Global transcriptome analysis in influenza-infected mouse lungs reveals the kinetics of innate and adaptive host immune responses. PLoS One (2012) 1.37
Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages. PLoS Genet (2012) 1.37
Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet (2008) 1.37
Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma. Mol Syst Biol (2012) 1.36
Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice. G3 (Bethesda) (2012) 1.35
A comparative analysis of biclustering algorithms for gene expression data. Brief Bioinform (2012) 1.33
Genomic alterations indicate tumor origin and varied metastatic potential of disseminated cells from prostate cancer patients. Cancer Res (2008) 1.32
Combination of chemical genetics and phosphoproteomics for kinase signaling analysis enables confident identification of cellular downstream targets. Mol Cell Proteomics (2011) 1.32
g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res (2016) 1.31
Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus. J Virol (2011) 1.30
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res (2014) 1.29
Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics (2012) 1.28
Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos. PLoS One (2010) 1.27
Variable DNA methylation is associated with chronic obstructive pulmonary disease and lung function. Am J Respir Crit Care Med (2011) 1.26
Discovering transcriptional modules by Bayesian data integration. Bioinformatics (2010) 1.25
Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions. Nucleic Acids Res (2012) 1.24
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biol (2012) 1.23
Culture of human mesenchymal stem cells at low oxygen tension improves growth and genetic stability by activating glycolysis. Cell Death Differ (2011) 1.23
The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol (2010) 1.23
Comparative analysis of microarray data identifies common responses to caloric restriction among mouse tissues. Mech Ageing Dev (2007) 1.22
CORNA: testing gene lists for regulation by microRNAs. Bioinformatics (2009) 1.21
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res (2013) 1.20
Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. BMC Proc (2009) 1.19
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions. PLoS Comput Biol (2012) 1.18
Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia. Genome Med (2010) 1.18
Combined deletion of Fxr and Shp in mice induces Cyp17a1 and results in juvenile onset cholestasis. J Clin Invest (2010) 1.17
MicroRNAs coordinately regulate protein complexes. BMC Syst Biol (2011) 1.17
DFLAT: functional annotation for human development. BMC Bioinformatics (2014) 1.17
Novel insights into DNA methylation features in spermatozoa: stability and peculiarities. PLoS One (2012) 1.16
Single sample expression-anchored mechanisms predict survival in head and neck cancer. PLoS Comput Biol (2012) 1.16
Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol (2007) 1.15
Gene expression profiling of long-lived dwarf mice: longevity-associated genes and relationships with diet, gender and aging. BMC Genomics (2007) 1.14
Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci U S A (2012) 1.14
Global expression changes of constitutive and hormonally regulated genes during endometrial neoplastic transformation. Gynecol Oncol (2001) 2.20
Using flowViz to visualize flow cytometry data. Bioinformatics (2008) 1.79
Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res (2008) 1.17
Identification of aberrant pathway and network activity from high-throughput data. Pac Symp Biocomput (2011) 0.77
Interpreting genetics of gene expression: integrative architecture in Bioconductor. Pac Symp Biocomput (2009) 0.76