Published in Proc Natl Acad Sci U S A on October 14, 2011
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med (2013) 6.09
Inconsistency in large pharmacogenomic studies. Nature (2013) 3.46
ERBB receptors: from oncogene discovery to basic science to mechanism-based cancer therapeutics. Cancer Cell (2014) 2.44
Modeling precision treatment of breast cancer. Genome Biol (2013) 2.42
An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell (2013) 2.30
Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Sci Rep (2013) 2.19
The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res (2012) 2.18
A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol (2014) 2.12
Critical research gaps and translational priorities for the successful prevention and treatment of breast cancer. Breast Cancer Res (2013) 1.92
Aurora A kinase (AURKA) in normal and pathological cell division. Cell Mol Life Sci (2012) 1.84
Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol (2013) 1.75
A comprehensive review of the preclinical efficacy profile of the ErbB family blocker afatinib in cancer. Naunyn Schmiedebergs Arch Pharmacol (2014) 1.63
Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents. Cancer Discov (2012) 1.59
Computational solutions for omics data. Nat Rev Genet (2013) 1.58
PI3K regulates MEK/ERK signaling in breast cancer via the Rac-GEF, P-Rex1. Proc Natl Acad Sci U S A (2013) 1.57
MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways. Front Oncol (2013) 1.53
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One (2013) 1.50
The Basis of Oncoimmunology. Cell (2016) 1.47
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics (2012) 1.43
Matricellular protein SPARCL1 regulates tumor microenvironment-dependent endothelial cell heterogeneity in colorectal carcinoma. J Clin Invest (2016) 1.43
Cancer pharmacogenomics: strategies and challenges. Nat Rev Genet (2012) 1.41
Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes. Breast Cancer Res Treat (2013) 1.27
Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Sci Rep (2014) 1.25
Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer. Proc Natl Acad Sci U S A (2012) 1.25
Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer. Proc Natl Acad Sci U S A (2014) 1.25
Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines. Sci Signal (2013) 1.17
Unifying immunology with informatics and multiscale biology. Nat Immunol (2014) 1.15
What are we learning from the cancer genome? Nat Rev Clin Oncol (2012) 1.13
Metasignatures identify two major subtypes of breast cancer. CPT Pharmacometrics Syst Pharmacol (2013) 1.13
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics (2013) 1.09
Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity. Br J Cancer (2013) 1.09
Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell (2013) 1.09
Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol Sci (2014) 1.05
High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells. PLoS One (2013) 1.04
The major reverse transcriptase-incompetent splice variant of the human telomerase protein inhibits telomerase activity but protects from apoptosis. Cancer Res (2013) 1.04
Calpain system protein expression in basal-like and triple-negative invasive breast cancer. Ann Oncol (2012) 1.02
Cancer Systems Biology: a peek into the future of patient care? Nat Rev Clin Oncol (2014) 1.01
Recurrent ESR1-CCDC170 rearrangements in an aggressive subset of oestrogen receptor-positive breast cancers. Nat Commun (2014) 1.00
Comparison of gene expression patterns across 12 tumor types identifies a cancer supercluster characterized by TP53 mutations and cell cycle defects. Oncogene (2014) 0.99
The DNA methylation-regulated miR-193a-3p dictates the multi-chemoresistance of bladder cancer via repression of SRSF2/PLAU/HIC2 expression. Cell Death Dis (2014) 0.98
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. BMC Bioinformatics (2012) 0.98
Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods (2016) 0.97
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discov (2014) 0.96
A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Cell (2016) 0.96
Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Res Treat (2012) 0.96
Metabolite profiling stratifies pancreatic ductal adenocarcinomas into subtypes with distinct sensitivities to metabolic inhibitors. Proc Natl Acad Sci U S A (2015) 0.96
Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay. Mol Cell Proteomics (2013) 0.95
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics (2013) 0.95
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford) (2016) 0.95
Linking signaling pathways to transcriptional programs in breast cancer. Genome Res (2014) 0.95
mTORC1/C2 and pan-HDAC inhibitors synergistically impair breast cancer growth by convergent AKT and polysome inhibiting mechanisms. Breast Cancer Res Treat (2014) 0.94
Expression of VEGF and semaphorin genes define subgroups of triple negative breast cancer. PLoS One (2013) 0.94
Targeting the adaptability of heterogeneous aneuploids. Cell (2015) 0.93
Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. Mol Cancer Res (2015) 0.93
Models and Mechanisms of Acquired Antihormone Resistance in Breast Cancer: Significant Clinical Progress Despite Limitations. Horm Mol Biol Clin Investig (2012) 0.92
Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes Dev (2015) 0.91
Genomics: the breast cancer landscape. Nature (2012) 0.91
Pharmacogene regulatory elements: from discovery to applications. Genome Med (2012) 0.91
Targeting uPAR with antagonistic recombinant human antibodies in aggressive breast cancer. Cancer Res (2013) 0.91
Kinome profiling reveals breast cancer heterogeneity and identifies targeted therapeutic opportunities for triple negative breast cancer. Oncotarget (2014) 0.91
The differential susceptibilities of MCF-7 and MDA-MB-231 cells to the cytotoxic effects of curcumin are associated with the PI3K/Akt-SKP2-Cip/Kips pathway. Cancer Cell Int (2014) 0.88
Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. Cell Commun Signal (2015) 0.88
Molecular pathways: extracting medical knowledge from high-throughput genomic data. Clin Cancer Res (2013) 0.88
The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res (2013) 0.88
FOXO transcription factors control E2F1 transcriptional specificity and apoptotic function. Cancer Res (2013) 0.87
A New Drug Combinatory Effect Prediction Algorithm on the Cancer Cell Based on Gene Expression and Dose-Response Curve. CPT Pharmacometrics Syst Pharmacol (2015) 0.87
Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer. BMC Genomics (2016) 0.87
KAT6A, a chromatin modifier from the 8p11-p12 amplicon is a candidate oncogene in luminal breast cancer. Neoplasia (2014) 0.86
Pathway Analysis: State of the Art. Front Physiol (2015) 0.86
Mass spectrometry based method to increase throughput for kinome analyses using ATP probes. Anal Chem (2013) 0.86
Metabolic reprogramming in triple-negative breast cancer through Myc suppression of TXNIP. Proc Natl Acad Sci U S A (2015) 0.85
Computation as the mechanistic bridge between precision medicine and systems therapeutics. Clin Pharmacol Ther (2012) 0.85
Quantitative high-throughput efficacy profiling of approved oncology drugs in inflammatory breast cancer models of acquired drug resistance and re-sensitization. Cancer Lett (2013) 0.85
Metalloproteinase-disintegrin ADAM12 is associated with a breast tumor-initiating cell phenotype. Breast Cancer Res Treat (2013) 0.84
A novel double-negative feedback loop between miR-489 and the HER2-SHP2-MAPK signaling axis regulates breast cancer cell proliferation and tumor growth. Oncotarget (2016) 0.84
Computational prediction of microRNA networks incorporating environmental toxicity and disease etiology. Sci Rep (2014) 0.84
Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther (2016) 0.84
Histone deacetylase inhibitor, suberoylanilide hydroxamic acid (SAHA), enhances anti-tumor effects of the poly (ADP-ribose) polymerase (PARP) inhibitor olaparib in triple-negative breast cancer cells. Breast Cancer Res (2015) 0.84
The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors. Mol Oncol (2013) 0.83
Progress in breast cancer research. Proc Natl Acad Sci U S A (2012) 0.82
Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance. Pac Symp Biocomput (2014) 0.82
Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype. EBioMedicine (2017) 0.82
Pharmacological profiling of kinase dependency in cell lines across triple-negative breast cancer subtypes. Mol Cancer Ther (2014) 0.81
A personalized committee classification approach to improving prediction of breast cancer metastasis. Bioinformatics (2014) 0.81
Amplification and over-expression of MAP3K3 gene in human breast cancer promotes formation and survival of breast cancer cells. J Pathol (2014) 0.81
Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy. Oncotarget (2015) 0.81
MiR-34a-5p promotes the multi-drug resistance of osteosarcoma by targeting the CD117 gene. Oncotarget (2016) 0.81
Rab25 acts as an oncogene in luminal B breast cancer and is causally associated with Snail driven EMT. Oncotarget (2016) 0.81
Systemic alteration of cell-surface and secreted glycoprotein expression in malignant breast cancer cell lines. Glycobiology (2013) 0.80
Multi-Scale Genomic, Transcriptomic and Proteomic Analysis of Colorectal Cancer Cell Lines to Identify Novel Biomarkers. PLoS One (2015) 0.80
Anti-protozoal and anti-bacterial antibiotics that inhibit protein synthesis kill cancer subtypes enriched for stem cell-like properties. Cell Cycle (2015) 0.80
From drug response profiling to target addiction scoring in cancer cell models. Dis Model Mech (2015) 0.80
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput Biol (2015) 0.79
dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data. Front Genet (2015) 0.79
In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics (2015) 0.79
Omics and therapy - a basis for precision medicine. Mol Oncol (2012) 0.79
Prolactin-induced protein is required for cell cycle progression in breast cancer. Neoplasia (2014) 0.79
miRNA - Therapeutic tool in breast cancer? Where are we now? Rep Pract Oncol Radiother (2014) 0.78
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science (2004) 61.56
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell (2006) 27.36
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics (2007) 14.25
Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene (2007) 11.85
The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res (2007) 11.56
Cisplatin: mode of cytotoxic action and molecular basis of resistance. Oncogene (2003) 10.74
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol (2007) 10.49
Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. J Natl Cancer Inst (1991) 9.39
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (2010) 8.44
Targeted cancer therapy. Nature (2004) 7.81
Activity of the dual kinase inhibitor lapatinib (GW572016) against HER-2-overexpressing and trastuzumab-treated breast cancer cells. Cancer Res (2006) 7.18
Novel anticancer targets: revisiting ERBB2 and discovering ERBB3. Nat Rev Cancer (2009) 6.28
Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res (2009) 5.68
Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol (2010) 5.50
Beta-catenin, a novel prognostic marker for breast cancer: its roles in cyclin D1 expression and cancer progression. Proc Natl Acad Sci U S A (2000) 4.71
Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics (2008) 3.62
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics (2009) 2.90
FOXA1 expression in breast cancer--correlation with luminal subtype A and survival. Clin Cancer Res (2007) 2.22
Overexpression of ErbB2 blocks Taxol-induced apoptosis by upregulation of p21Cip1, which inhibits p34Cdc2 kinase. Mol Cell (1998) 2.00
Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A (2011) 1.78
Changes associated with the development of resistance to imatinib (STI571) in two leukemia cell lines expressing p210 Bcr/Abl protein. Cancer (2004) 1.75
Spotlight on molecular profiling: "Integromic" analysis of the NCI-60 cancer cell lines. Mol Cancer Ther (2006) 1.73
Hsp-90-associated oncoproteins: multiple targets of geldanamycin and its analogs. Leukemia (2002) 1.70
Phosphorylation on tyrosine-15 of p34(Cdc2) by ErbB2 inhibits p34(Cdc2) activation and is involved in resistance to taxol-induced apoptosis. Mol Cell (2002) 1.67
beta-catenin is a downstream effector of Wnt-mediated tumorigenesis in the mammary gland. Oncogene (2001) 1.52
Transcriptional switch by activating transcription factor 2-derived peptide sensitizes melanoma cells to apoptosis and inhibits their tumorigenicity. Proc Natl Acad Sci U S A (2004) 1.46
GSK1070916, a potent Aurora B/C kinase inhibitor with broad antitumor activity in tissue culture cells and human tumor xenograft models. Mol Cancer Ther (2009) 1.27
Forkhead-box A1 (FOXA1) expression in breast cancer and its prognostic significance. Eur J Cancer (2008) 1.24
A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. BMC Med (2009) 1.22
Key signalling nodes in mammary gland development and cancer: Myc. Breast Cancer Res (2009) 1.19
Gene expression profile of metastatic colon cancer cells resistant to cisplatin-induced apoptosis. Int J Oncol (2003) 1.14
The effect of cyclin D1 overexpression in human head and neck cancer cells. Eur Arch Otorhinolaryngol (2004) 0.90
The human genome browser at UCSC. Genome Res (2002) 168.23
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
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
The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
Diversity of the human intestinal microbial flora. Science (2005) 49.64
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell (2006) 27.36
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
International network of cancer genome projects. Nature (2010) 20.35
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
mTOR inhibition induces upstream receptor tyrosine kinase signaling and activates Akt. Cancer Res (2006) 18.44
Ultraconserved elements in the human genome. Science (2004) 17.14
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A (2003) 16.58
Use of proteomic patterns in serum to identify ovarian cancer. Lancet (2002) 16.38
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell (2006) 16.05
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
The UCSC Known Genes. Bioinformatics (2006) 14.67
Integrated genomic characterization of endometrial carcinoma. Nature (2013) 14.29
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
Exploiting the PI3K/AKT pathway for cancer drug discovery. Nat Rev Drug Discov (2005) 11.46
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell (2007) 11.21
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics (2005) 10.43
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature (2002) 9.40
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02
The biology of ovarian cancer: new opportunities for translation. Nat Rev Cancer (2009) 9.01
Induction of tumors in mice by genomic hypomethylation. Science (2003) 8.86
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res (2004) 8.86
Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med (2008) 8.77
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat Genet (2004) 8.55
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (2010) 8.44
An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature (2009) 8.44
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature (2002) 8.32
microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A (2006) 8.24
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res (2008) 8.12
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature (2012) 8.03
Reconstruction of functionally normal and malignant human breast tissues in mice. Proc Natl Acad Sci U S A (2004) 7.96
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol Cancer Ther (2006) 7.73
End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A (2003) 7.70
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
An RNA gene expressed during cortical development evolved rapidly in humans. Nature (2006) 7.23
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05