Cross-platform prediction of gene expression signatures.

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

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol (1996) 72.84

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08

GenePattern 2.0. Nat Genet (2006) 29.07

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56

The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24

Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci U S A (2001) 13.30

Latent bone metastasis in breast cancer tied to Src-dependent survival signals. Cancer Cell (2009) 5.24

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41

A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32

Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet (2003) 3.78

A pathway-based classification of human breast cancer. Proc Natl Acad Sci U S A (2010) 3.30

A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell (2009) 2.22

A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech (2004) 1.73

Prediction and uncertainty in the analysis of gene expression profiles. In Silico Biol (2002) 1.27

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo. Genome Biol (2008) 0.95

SIGNATURE: a workbench for gene expression signature analysis. BMC Bioinformatics (2011) 0.94

A methodology for utilization of predictive genomic signatures in FFPE samples. BMC Med Genomics (2011) 0.80

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56

Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (2009) 16.52

A signalling pathway controlling c-Myc degradation that impacts oncogenic transformation of human cells. Nat Cell Biol (2004) 6.61

Functional genomic analysis of phagocytosis and identification of a Drosophila receptor for E. coli. Nature (2002) 4.33

Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res (2002) 3.77

A pathway-based classification of human breast cancer. Proc Natl Acad Sci U S A (2010) 3.30

Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nat Methods (2006) 3.29

Signaling role of hemocytes in Drosophila JAK/STAT-dependent response to septic injury. Dev Cell (2003) 3.05

FlyRNAi: the Drosophila RNAi screening center database. Nucleic Acids Res (2006) 2.43

Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. Nat Protoc (2007) 2.05

High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymol (2005) 1.83

Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics (2007) 1.82

FOXC2 expression links epithelial-mesenchymal transition and stem cell properties in breast cancer. Cancer Res (2013) 1.76

A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment. Am J Respir Crit Care Med (2013) 1.73

SOCS36E, a novel Drosophila SOCS protein, suppresses JAK/STAT and EGF-R signalling in the imaginal wing disc. Oncogene (2002) 1.71

Increased expression of Drosophila tetraspanin, Tsp68C, suppresses the abnormal proliferation of ytr-deficient and Ras/Raf-activated hemocytes. Oncogene (2004) 1.46

The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res (2003) 1.44

Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer. EMBO Mol Med (2013) 1.38

Biomedical term mapping databases. Nucleic Acids Res (2005) 1.29

Genetic heterogeneity of Myc-induced mammary tumors reflecting diverse phenotypes including metastatic potential. Proc Natl Acad Sci U S A (2009) 1.26

Network calisthenics: control of E2F dynamics in cell cycle entry. Cell Cycle (2011) 1.25

Using a stem cell-based signature to guide therapeutic selection in cancer. Cancer Res (2010) 1.24

Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma. Cancer Res (2008) 1.19

A pharmacogenomic method for individualized prediction of drug sensitivity. Mol Syst Biol (2011) 1.15

Epigenetic silencing of microRNA-203 is required for EMT and cancer stem cell properties. Sci Rep (2013) 1.13

Utilization of genomic signatures to identify phenotype-specific drugs. PLoS One (2009) 1.12

FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res (2011) 1.11

Amplification and high-level expression of heat shock protein 90 marks aggressive phenotypes of human epidermal growth factor receptor 2 negative breast cancer. Breast Cancer Res (2012) 1.09

A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila. Genome Biol (2007) 1.05

Patterns of cell signaling pathway activation that characterize mammary development. Development (2008) 1.02

Differential requirement for STAT by gain-of-function and wild-type receptor tyrosine kinase Torso in Drosophila. Development (2002) 1.00

Yantar, a conserved arginine-rich protein is involved in Drosophila hemocyte development. Dev Biol (2004) 0.96

Yin yang 1 modulates taxane response in epithelial ovarian cancer. Mol Cancer Res (2009) 0.95

Drug-target identification in Drosophila cells: combining high-throughout RNAi and small-molecule screens. Drug Discov Today (2006) 0.90

A signature of epithelial-mesenchymal plasticity and stromal activation in primary tumor modulates late recurrence in breast cancer independent of disease subtype. Breast Cancer Res (2014) 0.90

Matter arising: off-targets and genome-scale RNAi screens in Drosophila. Fly (Austin) (2008) 0.89

p38 MAPK inhibits breast cancer metastasis through regulation of stromal expansion. Int J Cancer (2014) 0.82

DIG--a system for gene annotation and functional discovery. Bioinformatics (2005) 0.77

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data. Biochemistry (2014) 0.76

Do-it-yourself RNAi made easy? Nat Methods (2007) 0.75