Published in Genome Biol on December 30, 2009
Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet (2016) 1.08
Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. Genome Biol (2015) 0.81
A measure of the signal-to-noise ratio of microarray samples and studies using gene correlations. PLoS One (2012) 0.77
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (2001) 414.27
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res (2001) 45.29
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
ZOOM! Zillions of oligos mapped. Bioinformatics (2008) 29.78
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell (2006) 21.66
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med (2008) 9.20
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome. Clin Cancer Res (2008) 8.17
Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell (2006) 8.09
Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med (2004) 6.91
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A (2000) 6.87
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
Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature (2008) 4.24
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics (2007) 2.93
Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat (2007) 2.49
Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model. Am J Pathol (2005) 2.39
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics (2008) 2.29
Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res (2007) 1.83
Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood (2009) 1.64
Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41
G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics (2008) 1.30
Overexpression of E2F-5 correlates with a pathological basal phenotype and a worse clinical outcome. Br J Cancer (2009) 0.99
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. Int J Plant Genomics (2008) 0.78
Temporal lobectomy: a promising alternative. J Neurosci Nurs (1991) 0.77
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44
Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature (2009) 7.37
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A (2006) 6.80
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell (2011) 5.75
The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell (2010) 4.71
Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci (2007) 3.89
Reverse engineering cellular networks. Nat Protoc (2006) 3.67
Transcriptional analysis of the B cell germinal center reaction. Proc Natl Acad Sci U S A (2003) 3.45
Lessons from the DREAM2 Challenges. Ann N Y Acad Sci (2009) 3.44
Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol (2008) 2.99
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity. Nat Cell Biol (2013) 2.90
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol (2009) 2.79
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A (2005) 2.36
iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18
Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension. Circ Cardiovasc Genet (2012) 2.16
The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell (2009) 2.04
geWorkbench: an open source platform for integrative genomics. Bioinformatics (2010) 2.03
Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets. J Clin Invest (2007) 1.97
The TLX1 oncogene drives aneuploidy in T cell transformation. Nat Med (2010) 1.93
Identification of the human mature B cell miRNome. Immunity (2009) 1.82
Tracking CD40 signaling during germinal center development. Blood (2004) 1.81
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A (2013) 1.66
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A (2008) 1.65
Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood (2009) 1.64
Towards patient-based cancer therapeutics. Nat Biotechnol (2010) 1.63
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling. J Clin Invest (2003) 1.63
BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A (2009) 1.62
Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med (2012) 1.56
Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci (2007) 1.51
Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41
Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes. Blood (2011) 1.40
Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. J Exp Med (2004) 1.37
Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol (2004) 1.35
A molecular signature predictive of indolent prostate cancer. Sci Transl Med (2013) 1.32
Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput (2009) 1.32
Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation. Cancer Res (2007) 1.28
Verification of systems biology research in the age of collaborative competition. Nat Biotechnol (2011) 1.28
Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput (2009) 1.28
ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. Proc Natl Acad Sci U S A (2013) 1.26
Motif-based construction of a functional map for mammalian olfactory receptors. Genomics (2003) 1.23
Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. Cancer Res (2012) 1.20
MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol (2013) 1.17
B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. Cancer Res (2012) 1.15
Rewiring makes the difference. Mol Syst Biol (2011) 1.13
A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. Plant J (2009) 1.10
PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. Plant J (2011) 1.07
Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol (2014) 1.05
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A (2007) 1.01
Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med (2012) 0.98
The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev (2014) 0.98
Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas. Haematologica (2008) 0.96
Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. BMC Proc (2007) 0.93
Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc (2011) 0.92
Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol Biol (2012) 0.92
Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. J Cell Mol Med (2011) 0.89
Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. Mol Neurodegener (2014) 0.87
Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development (2011) 0.86
Pharmacogenetics: ethical issues and policy options. Kennedy Inst Ethics J (2002) 0.86
A systems biology approach to transcription factor binding site prediction. PLoS One (2010) 0.85
Influencing women's actions on cervical cancer screening and treatment in Karawang District, Indonesia. Asian Pac J Cancer Prev (2012) 0.84
Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol (2008) 0.84
Survival factor NFIL3 restricts FOXO-induced gene expression in cancer. Genes Dev (2013) 0.83
Gene expression dynamics during germinal center transit in B cells. Ann N Y Acad Sci (2003) 0.83
Pooled shRNA screenings: computational analysis. Methods Mol Biol (2013) 0.82
Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells (2015) 0.81
T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses. Genes Chromosomes Cancer (2011) 0.81
Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci U S A (2012) 0.80
Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme. J Neurooncol (2014) 0.80
Report: workshop on mediastinal grey zone lymphoma. Eur J Haematol Suppl (2005) 0.80
The challenges of systems biology. Preface. Ann N Y Acad Sci (2009) 0.79
Evaluation of a 5-year cervical cancer prevention project in Indonesia: opportunities, issues, and challenges. J Obstet Gynaecol Res (2013) 0.79
CASTOR: clustering algorithm for sequence taxonomical organization and relationships. J Comput Biol (2003) 0.79
Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor. Nat Commun (2013) 0.78
Management of complicated gallstones: results of an alternative approach to difficult cholecystectomies. Minim Invasive Ther Allied Technol (2010) 0.78
A systems approach to drug discovery in Alzheimer's disease. Neurotherapeutics (2015) 0.77