Published in Proc Natl Acad Sci U S A on September 08, 2005
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
A systems biology approach for pathway level analysis. Genome Res (2007) 6.95
Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol (2012) 6.38
A novel signaling pathway impact analysis. Bioinformatics (2008) 5.06
A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res (2007) 4.09
A general modular framework for gene set enrichment analysis. BMC Bioinformatics (2009) 3.92
GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics (2009) 3.86
Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics (2007) 3.68
Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics (2010) 2.86
Feature Screening via Distance Correlation Learning. J Am Stat Assoc (2012) 2.64
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LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics (2008) 2.53
Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data. Am J Hum Genet (2010) 2.50
A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics (2006) 2.42
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A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30
GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics (2013) 2.29
Comparative evaluation of gene-set analysis methods. BMC Bioinformatics (2007) 2.19
Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics (2008) 2.14
Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells. PLoS One (2008) 2.10
Microarray-based gene set analysis: a comparison of current methods. BMC Bioinformatics (2008) 2.06
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res (2013) 2.05
Small molecule activation of PKM2 in cancer cells induces serine auxotrophy. Chem Biol (2012) 1.96
Pathway analysis of primary central nervous system lymphoma. Blood (2008) 1.85
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Gene set enrichment analysis made simple. Stat Methods Med Res (2009) 1.79
Penalized model-based clustering with cluster-specific diagonal covariance matrices and grouped variables. Electron J Stat (2008) 1.76
Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics (2011) 1.76
Gene set enrichment analysis using linear models and diagnostics. Bioinformatics (2008) 1.75
Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer (2007) 1.75
Development of resistance to targeted therapies transforms the clinically associated molecular profile subtype of breast tumor xenografts. Cancer Res (2008) 1.75
Comparative study of gene set enrichment methods. BMC Bioinformatics (2009) 1.74
Gene-set analysis and reduction. Brief Bioinform (2008) 1.71
Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS One (2010) 1.70
Analysis of gene sets based on the underlying regulatory network. J Comput Biol (2009) 1.67
Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics (2010) 1.59
Preclinical model of organotypic culture for pharmacodynamic profiling of human tumors. Proc Natl Acad Sci U S A (2010) 1.55
Analysis of microarray experiments of gene expression profiling. Am J Obstet Gynecol (2006) 1.53
Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol (2011) 1.52
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics (2009) 1.48
Meta-analysis for pathway enrichment analysis when combining multiple genomic studies. Bioinformatics (2010) 1.47
Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics (2010) 1.47
Multiple oncogenic pathway signatures show coordinate expression patterns in human prostate tumors. PLoS One (2008) 1.46
Identification and Functional Validation of Reciprocal microRNA-mRNA Pairings in African American Prostate Cancer Disparities. Clin Cancer Res (2015) 1.46
Network enrichment analysis in complex experiments. Stat Appl Genet Mol Biol (2010) 1.44
A simple and robust method for connecting small-molecule drugs using gene-expression signatures. BMC Bioinformatics (2008) 1.42
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PLoS One (2013) 1.41
A computational screen for mouse signaling pathways targeted by microRNA clusters. RNA (2008) 1.41
An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet (2008) 1.40
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLoS Comput Biol (2015) 1.39
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinformatics (2010) 1.36
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics (2007) 1.35
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics (2009) 1.35
Accurate and reliable cancer classification based on probabilistic inference of pathway activity. PLoS One (2009) 1.33
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics (2010) 1.33
Detecting intergene correlation changes in microarray analysis: a new approach to gene selection. BMC Bioinformatics (2009) 1.32
Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection. Bioinformatics (2009) 1.32
Gene set analysis methods: statistical models and methodological differences. Brief Bioinform (2014) 1.30
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol (2006) 1.29
Gene module level analysis: identification to networks and dynamics. Curr Opin Biotechnol (2008) 1.29
Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data. BMC Bioinformatics (2009) 1.26
Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16. BMC Proc (2009) 1.26
Along signal paths: an empirical gene set approach exploiting pathway topology. Nucleic Acids Res (2012) 1.22
sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures. BMC Bioinformatics (2009) 1.20
Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PLoS One (2011) 1.19
Utility of correlation measures in analysis of gene expression. NeuroRx (2006) 1.19
A method for computing the overall statistical significance of a treatment effect among a group of genes. BMC Bioinformatics (2006) 1.18
Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy. PLoS One (2009) 1.17
Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet (2007) 1.17
DFLAT: functional annotation for human development. BMC Bioinformatics (2014) 1.17
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood (2012) 1.16
A novel significance score for gene selection and ranking. Bioinformatics (2012) 1.14
Graphite Web: Web tool for gene set analysis exploiting pathway topology. Nucleic Acids Res (2013) 1.13
Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure. Genome Biol (2009) 1.13
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. BMC Bioinformatics (2008) 1.11
Differential expression analysis for pathways. PLoS Comput Biol (2013) 1.11
A biological evaluation of six gene set analysis methods for identification of differentially expressed pathways in microarray data. Cancer Inform (2008) 1.09
Rebuilding pluripotency from primordial germ cells. Stem Cell Reports (2013) 1.09
Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics (2012) 1.09
The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol Ther (2009) 1.09
Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet (2016) 1.08
Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol (2009) 1.08
Genome-wide expression profiling deciphers host responses altered during dengue shock syndrome and reveals the role of innate immunity in severe dengue. PLoS One (2010) 1.08
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. Bioinformatics (2013) 1.06
A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PLoS One (2012) 1.06
Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors. Mol Cancer (2007) 1.06
A regularized Hotelling's T(2) test for pathway analysis in proteomic studies. J Am Stat Assoc (2011) 1.05
HD CAG-correlated gene expression changes support a simple dominant gain of function. Hum Mol Genet (2011) 1.04
Gene set internal coherence in the context of functional profiling. BMC Genomics (2009) 1.04
Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics (2008) 1.03
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer (2009) 1.03
Analysis of DNA microarray expression data. Best Pract Res Clin Haematol (2009) 1.03
Characterizing human stem cell-derived sensory neurons at the single-cell level reveals their ion channel expression and utility in pain research. Mol Ther (2014) 1.01
Identification of differentially expressed subnetworks based on multivariate ANOVA. BMC Bioinformatics (2009) 1.01
R-based software for the integration of pathway data into bioinformatic algorithms. Biology (Basel) (2014) 1.01
Gene expression module-based chemical function similarity search. Nucleic Acids Res (2008) 1.01
Distinct early molecular responses to mutations causing vLINCL and JNCL presage ATP synthase subunit C accumulation in cerebellar cells. PLoS One (2011) 1.01
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics (2008) 1.00
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet (2002) 14.69
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res (2003) 9.30
Polymyositis and dermatomyositis. Lancet (2003) 7.24
Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci U S A (2004) 5.65
Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res (2004) 4.33
Calcium dyshomeostasis and intracellular signalling in Alzheimer's disease. Nat Rev Neurosci (2002) 3.84
Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinformatics (2004) 3.57
Exploring gene expression data with class scores. Pac Symp Biocomput (2002) 3.51
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res (2003) 3.31
Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis. Ann Neurol (2005) 3.07
The effect of replication on gene expression microarray experiments. Bioinformatics (2003) 2.49
Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48
Statistical concerns about the GSEA procedure. Nat Genet (2004) 1.91
Synthesis rate of muscle proteins, muscle functions, and amino acid kinetics in type 2 diabetes. Diabetes (2002) 1.82
Measurement of gelatinase B (MMP-9) in the cerebrospinal fluid of patients with vascular dementia and Alzheimer disease. Stroke (2004) 1.63
Modeling mitochondrial function in aging neurons. Trends Neurosci (2004) 1.56
Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol (2004) 1.27
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10
Managing incidental findings and research results in genomic research involving biobanks and archived data sets. Genet Med (2012) 9.65
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet (2006) 7.16
Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (2002) 7.07
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc (2009) 6.49
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics (2005) 6.44
A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry (2012) 6.34
Creation and implications of a phenome-genome network. Nat Biotechnol (2006) 5.79
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Altered microRNA expression in human heart disease. Physiol Genomics (2007) 5.64
Tectonic shifts in the health information economy. N Engl J Med (2008) 5.42
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res (2004) 4.43
Landscape of somatic retrotransposition in human cancers. Science (2012) 4.37
Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature (2013) 4.03
Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A (2002) 3.83
Taxonomizing, sizing, and overcoming the incidentalome. Genet Med (2012) 3.82
Postmeiotic sex chromatin in the male germline of mice. Curr Biol (2006) 3.80
An assessment of histone-modification antibody quality. Nat Struct Mol Biol (2010) 3.72
Distinctive patterns of microRNA expression in primary muscular disorders. Proc Natl Acad Sci U S A (2007) 3.72
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics (2005) 3.66
The Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature (2010) 3.55
Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J Exp Med (2003) 3.46
High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev (2006) 3.30
A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell (2010) 3.27
Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell (2013) 3.26
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics (2005) 3.23
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A (2011) 3.18
Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell (2012) 3.13
A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell (2008) 3.10
The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat Genet (2008) 2.95
No small change for the health information economy. N Engl J Med (2009) 2.92
MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell (2007) 2.87
CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell (2010) 2.86
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics (2005) 2.83
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A (2011) 2.72
Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proc Natl Acad Sci U S A (2002) 2.60
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54
The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarction. PLoS One (2007) 2.52
Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics (2004) 2.51
The SMART Platform: early experience enabling substitutable applications for electronic health records. J Am Med Inform Assoc (2012) 2.48
Immune-mediated necrotizing myopathy associated with statins. Muscle Nerve (2010) 2.48
Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev (2005) 2.46
X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature (2011) 2.44
A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics (2006) 2.42
Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet (2012) 2.35
Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J (2003) 2.30
A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens. Stud Health Technol Inform (2004) 2.28
Minimal haplotype tagging. Proc Natl Acad Sci U S A (2003) 2.28
Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics (2003) 2.20
Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records. J Am Med Inform Assoc (2009) 2.20
MicroRNA-1 negatively regulates expression of the hypertrophy-associated calmodulin and Mef2a genes. Mol Cell Biol (2009) 2.18
Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev (2004) 2.16
Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells. PLoS One (2008) 2.10
Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell (2011) 2.09
Normalization and experimental design for ChIP-chip data. BMC Bioinformatics (2007) 2.08
Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metab (2011) 2.08
Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship. Proc Natl Acad Sci U S A (2010) 2.07
Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res (2011) 2.05
The PING personally controlled electronic medical record system: technical architecture. J Am Med Inform Assoc (2004) 2.01
Diverse mechanisms of somatic structural variations in human cancer genomes. Cell (2013) 2.00
Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records. Diabetes Care (2009) 2.00
Escaping the EHR trap--the future of health IT. N Engl J Med (2012) 1.96
Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform (2011) 1.96
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell (2013) 1.91
Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway. Ann Rheum Dis (2011) 1.91
Finding the missing link for big biomedical data. JAMA (2014) 1.90
Development of heart valves requires Gata4 expression in endothelial-derived cells. Development (2006) 1.90
A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res (2011) 1.89
Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell (2008) 1.89
A self-scaling, distributed information architecture for public health, research, and clinical care. J Am Med Inform Assoc (2007) 1.88
Transcriptomic analysis of human lung development. Am J Respir Crit Care Med (2009) 1.87
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res (2010) 1.87
Pathway analysis of primary central nervous system lymphoma. Blood (2008) 1.85
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80
SHRINE: enabling nationally scalable multi-site disease studies. PLoS One (2013) 1.80
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res (2005) 1.80
Does collocation inform the impact of collaboration? PLoS One (2010) 1.78
Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med (2010) 1.77
Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol (2012) 1.77
Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res (2012) 1.77
Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res (2009) 1.74
Gata4 is required for maintenance of postnatal cardiac function and protection from pressure overload-induced heart failure. Proc Natl Acad Sci U S A (2006) 1.73
Type I interferon-inducible gene expression in blood is present and reflects disease activity in dermatomyositis and polymyositis. Arthritis Rheum (2007) 1.72
The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department. J Am Med Inform Assoc (2004) 1.70
A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data. Stat Med (2012) 1.70
The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell (2013) 1.68
Parents as partners in obtaining the medication history. J Am Med Inform Assoc (2005) 1.67
Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol (2009) 1.63
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials (2014) 1.62
Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A (2013) 1.60