Published in Science on September 29, 2006
Genetic mapping in human disease. Science (2008) 15.12
Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet (2007) 12.08
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Mapping complex disease traits with global gene expression. Nat Rev Genet (2009) 7.44
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Targeting microRNAs in cancer: rationale, strategies and challenges. Nat Rev Drug Discov (2010) 6.07
Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med (2011) 5.77
Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med (2011) 5.30
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Direct inhibition of the NOTCH transcription factor complex. Nature (2009) 4.82
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics (2013) 4.73
Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A (2010) 4.35
Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics (2013) 4.30
Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19
Inhibition of proteasome deubiquitinating activity as a new cancer therapy. Nat Med (2011) 4.09
Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85
Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol (2008) 3.74
Human tissues contain CD141hi cross-presenting dendritic cells with functional homology to mouse CD103+ nonlymphoid dendritic cells. Immunity (2012) 3.58
Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55
Proteomic and transcriptomic profiling reveals a link between the PI3K pathway and lower estrogen-receptor (ER) levels and activity in ER+ breast cancer. Breast Cancer Res (2010) 3.53
Hyperactivation of phosphatidylinositol-3 kinase promotes escape from hormone dependence in estrogen receptor-positive human breast cancer. J Clin Invest (2010) 3.53
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci U S A (2008) 3.41
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol (2011) 3.22
Target profiling of small molecules by chemical proteomics. Nat Chem Biol (2009) 3.20
HOXA9 is required for survival in human MLL-rearranged acute leukemias. Blood (2008) 3.12
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Natural products version 2.0: connecting genes to molecules. J Am Chem Soc (2010) 3.06
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia (2007) 3.06
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol (2008) 2.99
Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc Natl Acad Sci U S A (2009) 2.94
Large-scale chemical dissection of mitochondrial function. Nat Biotechnol (2008) 2.91
A network view of disease and compound screening. Nat Rev Drug Discov (2009) 2.90
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One (2011) 2.89
TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental program. PLoS Genet (2007) 2.84
PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc Natl Acad Sci U S A (2010) 2.79
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science (2013) 2.79
Reuse of public genome-wide gene expression data. Nat Rev Genet (2012) 2.79
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation. Proc Natl Acad Sci U S A (2009) 2.72
Ontology-based meta-analysis of global collections of high-throughput public data. PLoS One (2010) 2.67
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Unravelling the complexity of metastasis - molecular understanding and targeted therapies. Nat Rev Cancer (2011) 2.64
Human disease-drug network based on genomic expression profiles. PLoS One (2009) 2.62
Histone deacetylase inhibitors induce growth arrest and differentiation in uveal melanoma. Clin Cancer Res (2011) 2.54
Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform (2011) 2.52
Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. Semin Liver Dis (2010) 2.46
Treatment of obesity with celastrol. Cell (2015) 2.45
DNA-encoded antibody libraries: a unified platform for multiplexed cell sorting and detection of genes and proteins. J Am Chem Soc (2007) 2.42
Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci U S A (2009) 2.40
Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell (2009) 2.39
High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell (2016) 2.31
Effects of cigarette smoke on the human oral mucosal transcriptome. Cancer Prev Res (Phila) (2010) 2.30
A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program. Neuron (2016) 2.26
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood (2008) 2.26
DGIdb: mining the druggable genome. Nat Methods (2013) 2.26
Nanotechnology and cancer. Annu Rev Med (2008) 2.25
Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics (2009) 2.24
A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell (2009) 2.22
Heat shock protein 70 (hsp70) as an emerging drug target. J Med Chem (2010) 2.21
Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell (2009) 2.16
Small-molecule inhibitors of HIF-2a translation link its 5'UTR iron-responsive element to oxygen sensing. Mol Cell (2008) 2.15
An animal model of MYC-driven medulloblastoma. Cancer Cell (2012) 2.12
Chromosomal instability determines taxane response. Proc Natl Acad Sci U S A (2009) 2.12
A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol (2014) 2.12
mRNA expression signatures of human skeletal muscle atrophy identify a natural compound that increases muscle mass. Cell Metab (2011) 2.11
Probing the probes: fitness factors for small molecule tools. Chem Biol (2010) 2.08
Post-transcriptional regulons coordinate the initiation and resolution of inflammation. Nat Rev Immunol (2010) 2.08
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
Heat shock proteins and heat shock factor 1 in carcinogenesis and tumor development: an update. Arch Toxicol (2012) 2.04
Pharmacogenomic modeling of circulating tumor and invasive cells for prediction of chemotherapy response and resistance in pancreatic cancer. Clin Cancer Res (2014) 2.04
Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet (2012) 2.02
Target identification and mechanism of action in chemical biology and drug discovery. Nat Chem Biol (2013) 2.01
Combination chemical genetics. Nat Chem Biol (2008) 1.98
Oncogenic pathway combinations predict clinical prognosis in gastric cancer. PLoS Genet (2009) 1.96
Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nat Rev Drug Discov (2009) 1.95
Transforming growth factor beta engages TACE and ErbB3 to activate phosphatidylinositol-3 kinase/Akt in ErbB2-overexpressing breast cancer and desensitizes cells to trastuzumab. Mol Cell Biol (2008) 1.95
Disease signatures are robust across tissues and experiments. Mol Syst Biol (2009) 1.93
Topoisomerases facilitate transcription of long genes linked to autism. Nature (2013) 1.93
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol (2009) 1.90
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A (2010) 1.84
A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics. Clin Exp Metastasis (2010) 1.83
Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Proc Natl Acad Sci U S A (2009) 1.81
Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput Biol (2009) 1.80
ERα-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer. Cancer Discov (2011) 1.76
Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA). PLoS One (2010) 1.75
Differences in the tumor microenvironment between African-American and European-American breast cancer patients. PLoS One (2009) 1.72
Targeting breast cancer stem cells. Mol Oncol (2010) 1.72
Drug discovery: Cell lines battle cancer. Nature (2012) 1.70
Learning therapeutic lessons from metastasis suppressor proteins. Nat Rev Cancer (2009) 1.69
Retracted A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proc Natl Acad Sci U S A (2008) 1.69
MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase inhibition in microsatellite unstable colorectal cancers. Cancer Res (2011) 1.68
Network-based relating pharmacological and genomic spaces for drug target identification. PLoS One (2010) 1.68
Selective killing of K-ras mutant cancer cells by small molecule inducers of oxidative stress. Proc Natl Acad Sci U S A (2011) 1.68
Drug-induced regulation of target expression. PLoS Comput Biol (2010) 1.65
Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. Nat Chem Biol (2016) 1.65
Network analysis of FDA approved drugs and their targets. Mt Sinai J Med (2007) 1.65
Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment. PLoS One (2010) 1.65
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
MicroRNA expression profiles classify human cancers. Nature (2005) 69.12
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
GenePattern 2.0. Nat Genet (2006) 29.07
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature (2008) 18.20
The mammalian epigenome. Cell (2007) 18.13
Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis. Cancer Cell (2005) 17.41
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
BRAF mutation predicts sensitivity to MEK inhibition. Nature (2005) 17.14
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet (2007) 15.46
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature (2005) 15.28
Genetic mapping in human disease. Science (2008) 15.12
COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature (2010) 14.62
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways. Nat Med (2004) 13.57
A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 13.51
High-throughput oncogene mutation profiling in human cancer. Nat Genet (2007) 12.68
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell (2007) 12.33
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature (2006) 11.90
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood (2004) 11.07
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet (2004) 10.92