Published in Genes Chromosomes Cancer on November 01, 2006
Comprehensive molecular portraits of human breast tumours. Nature (2012) 47.39
Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature (2009) 13.45
Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A (2010) 7.70
Inferring tumor progression from genomic heterogeneity. Genome Res (2009) 6.09
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One (2009) 4.62
MTDH activation by 8q22 genomic gain promotes chemoresistance and metastasis of poor-prognosis breast cancer. Cancer Cell (2009) 4.47
Evidence that inositol polyphosphate 4-phosphatase type II is a tumor suppressor that inhibits PI3K signaling. Cancer Cell (2009) 4.30
Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer. Ann Appl Stat (2010) 3.94
Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med (2010) 3.43
A pathway-based classification of human breast cancer. Proc Natl Acad Sci U S A (2010) 3.30
Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. Oncogene (2008) 2.83
TBCRC 001: randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer. J Clin Oncol (2012) 2.45
Phosphoinositide signalling in cancer: beyond PI3K and PTEN. Nat Rev Cancer (2010) 2.35
Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat (2011) 2.23
Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics (2008) 2.11
Comparative oncogenomics identifies breast tumors enriched in functional tumor-initiating cells. Proc Natl Acad Sci U S A (2011) 2.01
Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res (2010) 1.94
The multifaceted role of MTDH/AEG-1 in cancer progression. Clin Cancer Res (2009) 1.89
Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol (2010) 1.80
Expression of the embryonic stem cell marker SOX2 in early-stage breast carcinoma. BMC Cancer (2011) 1.74
Breast cancer - one term, many entities? J Clin Invest (2011) 1.72
RCP is a human breast cancer-promoting gene with Ras-activating function. J Clin Invest (2009) 1.71
High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer. Breast Cancer Res (2010) 1.62
Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Biomed Res Int (2013) 1.61
The polarity protein Par6 induces cell proliferation and is overexpressed in breast cancer. Cancer Res (2008) 1.59
Systems biology and genomics of breast cancer. Cold Spring Harb Perspect Biol (2011) 1.59
Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes. Breast Cancer Res (2009) 1.59
Tracing the tumor lineage. Mol Oncol (2010) 1.56
Flexible and accurate detection of genomic copy-number changes from aCGH. PLoS Comput Biol (2007) 1.54
Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic Acids Res (2008) 1.52
Genomic instability in breast cancer: pathogenesis and clinical implications. Mol Oncol (2010) 1.43
Basal breast cancer: a complex and deadly molecular subtype. Curr Mol Med (2012) 1.43
The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis. BMC Med Genomics (2008) 1.41
Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer. PLoS Genet (2008) 1.39
Astrocyte elevated gene-1 (AEG-1): A multifunctional regulator of normal and abnormal physiology. Pharmacol Ther (2011) 1.37
18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Res (2011) 1.36
The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome. Int J Cancer (2009) 1.34
Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer. Clin Proteomics (2011) 1.32
Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes. Breast Cancer Res (2009) 1.32
Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation. Bioinformatics (2010) 1.28
RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells. Breast Cancer Res (2010) 1.25
Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup. PLoS One (2009) 1.25
Minireview: Basal-like breast cancer: from molecular profiles to targeted therapies. Mol Endocrinol (2010) 1.24
Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules. BMC Cancer (2010) 1.22
Demystifying basal-like breast carcinomas. J Clin Pathol (2007) 1.22
Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China. Cancer Res (2009) 1.20
Relevance of PTEN loss in brain metastasis formation in breast cancer patients. Breast Cancer Res (2012) 1.20
Frequent aberrant DNA methylation of ABCB1, FOXC1, PPP2R2B and PTEN in ductal carcinoma in situ and early invasive breast cancer. Breast Cancer Res (2010) 1.18
FGFR1 is amplified during the progression of in situ to invasive breast carcinoma. Breast Cancer Res (2012) 1.18
Synthetic lethal approaches to breast cancer therapy. Nat Rev Clin Oncol (2010) 1.17
CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer. Mol Oncol (2008) 1.16
Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers. Breast Cancer Res (2007) 1.15
The complex genetic landscape of familial breast cancer. Hum Genet (2013) 1.14
High-resolution comparative genomic hybridization of inflammatory breast cancer and identification of candidate genes. PLoS One (2011) 1.14
8p22 MTUS1 gene product ATIP3 is a novel anti-mitotic protein underexpressed in invasive breast carcinoma of poor prognosis. PLoS One (2009) 1.14
In vitro and in vivo analysis of B-Myb in basal-like breast cancer. Oncogene (2008) 1.13
Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer. Oncogene (2009) 1.11
A perspective on DNA microarrays in pathology research and practice. Am J Pathol (2007) 1.11
Reversal of endocrine resistance in breast cancer: interrelationships among 14-3-3ζ, FOXM1, and a gene signature associated with mitosis. Breast Cancer Res (2011) 1.10
Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression. Am J Pathol (2012) 1.09
Altered-function p53 missense mutations identified in breast cancers can have subtle effects on transactivation. Mol Cancer Res (2010) 1.07
Inferring causal genomic alterations in breast cancer using gene expression data. BMC Syst Biol (2011) 1.06
bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses. Database (Oxford) (2013) 1.05
A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. Br J Cancer (2012) 1.05
DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response. Mol Cancer (2010) 1.05
Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer. PLoS One (2011) 1.02
Expression profiling of familial breast cancers demonstrates higher expression of FGFR2 in BRCA2-associated tumors. Breast Cancer Res Treat (2008) 1.00
Syndecan-1 and syndecan-4 are independent indicators in breast carcinoma. J Histochem Cytochem (2011) 1.00
Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues. PLoS One (2014) 0.98
Genome-wide copy number alterations in subtypes of invasive breast cancers in young white and African American women. Breast Cancer Res Treat (2011) 0.98
The consequences of chromosomal aneuploidy on the transcriptome of cancer cells. Biochim Biophys Acta (2012) 0.97
Phosphatases: the new brakes for cancer development? Enzyme Res (2011) 0.97
Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol (2013) 0.97
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BRCA1-mutated and basal-like breast cancers have similar aCGH profiles and a high incidence of protein truncating TP53 mutations. BMC Cancer (2010) 0.95
Drug resistance mediated by AEG-1/MTDH/LYRIC. Adv Cancer Res (2013) 0.95
The expression of ERCC1, RRM1, and BRCA1 in breast cancer according to the immunohistochemical phenotypes. J Korean Med Sci (2011) 0.94
Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models. Breast Cancer Res (2008) 0.93
Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach. J Cancer Res Clin Oncol (2010) 0.93
Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes. PLoS One (2014) 0.92
Chromosomal changes in aggressive breast cancers with basal-like features. Cancer Genet Cytogenet (2009) 0.92
Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling. PLoS One (2013) 0.92
Clinicopathological features and treatment strategy for triple-negative breast cancer. Int J Clin Oncol (2010) 0.92
The gene expression landscape of breast cancer is shaped by tumor protein p53 status and epithelial-mesenchymal transition. Breast Cancer Res (2012) 0.91
DNA repair protein biomarkers associated with time to recurrence in triple-negative breast cancer. Clin Cancer Res (2010) 0.90
Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition. PLoS One (2014) 0.90
Genomic profiling of prostate cancers from African American men. Neoplasia (2009) 0.90
Breast and ovarian cancers: a survey and possible roles for the cell surface heparan sulfate proteoglycans. J Histochem Cytochem (2012) 0.89
Distinct patterns of DNA copy number alterations associate with BRAF mutations in melanomas and melanoma-derived cell lines. Genes Chromosomes Cancer (2009) 0.89
Genomic and phenotypic analysis of BRCA2 mutated breast cancers reveals co-occurring changes linked to progression. Breast Cancer Res (2011) 0.88
Concurrent gene signatures for han chinese breast cancers. PLoS One (2013) 0.88
Proteomic characterization of breast cancer xenografts identifies early and late bevacizumab-induced responses and predicts effective drug combinations. Clin Cancer Res (2013) 0.88
A systems approach to analysis of molecular complexity in breast cancer. Clin Cancer Res (2009) 0.88
Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Res Treat (2015) 0.88
Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. PLoS One (2014) 0.87
Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer. BMC Syst Biol (2010) 0.87
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer. Breast Cancer Res (2011) 0.87
Chemotherapy of metastatic triple negative breast cancer: Experience of using platinum-based chemotherapy. Oncotarget (2015) 0.86
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
Sparse inverse covariance estimation with the graphical lasso. Biostatistics (2007) 24.38
Signatures of mutational processes in human cancer. Nature (2013) 21.63
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47
International network of cancer genome projects. Nature (2010) 20.35
Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res (2004) 16.51
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature (2009) 13.45
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
The landscape of cancer genes and mutational processes in breast cancer. Nature (2012) 11.24
Mutational processes molding the genomes of 21 breast cancers. Cell (2012) 11.22
Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol (2005) 11.00
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85
The life history of 21 breast cancers. Cell (2012) 10.59
Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol (2002) 10.56
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med (2004) 9.81
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics (2009) 9.40
Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A (2010) 7.70
Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol (2004) 7.68
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05
Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med (2007) 6.80
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet (2006) 5.92
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet (2011) 5.62
Partial Correlation Estimation by Joint Sparse Regression Models. J Am Stat Assoc (2009) 5.41
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One (2009) 4.62
Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J Clin Oncol (2006) 4.49
Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol (2003) 4.28
Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res (2006) 4.25
The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res (2005) 4.17
Mutant p53 disrupts mammary tissue architecture via the mevalonate pathway. Cell (2012) 4.09
Aberrant epidermal growth factor receptor signaling and enhanced sensitivity to EGFR inhibitors in lung cancer. Cancer Res (2005) 3.98
Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer. Ann Appl Stat (2010) 3.94
Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92
Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics (2007) 3.80
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell (2004) 3.73
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66
Regularized linear discriminant analysis and its application in microarrays. Biostatistics (2006) 3.66
Development of FuGO: an ontology for functional genomics investigations. OMICS (2006) 3.59
Overlapping meta-analyses on the same topic: survey of published studies. BMJ (2013) 3.57
Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 3.48
A framework for feature selection in clustering. J Am Stat Assoc (2010) 3.46
Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol (2004) 3.45
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res (2011) 3.44
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics (2006) 3.32
Covariance-regularized regression and classification for high-dimensional problems. J R Stat Soc Series B Stat Methodol (2009) 3.31
Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res (2007) 3.13
A transcriptional response to Wnt protein in human embryonic carcinoma cells. BMC Dev Biol (2002) 3.09
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res (2010) 3.08
MYC stimulates EZH2 expression by repression of its negative regulator miR-26a. Blood (2008) 3.03
4-1BB-mediated immunotherapy of rheumatoid arthritis. Nat Med (2004) 3.01
TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Res (2007) 3.01
Ghrelin stimulation of growth hormone release and appetite is mediated through the growth hormone secretagogue receptor. Proc Natl Acad Sci U S A (2004) 2.99
A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol (2011) 2.91
A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90
Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87
A method for calling gains and losses in array CGH data. Biostatistics (2005) 2.86
A network model of a cooperative genetic landscape in brain tumors. JAMA (2009) 2.86
Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms. BMC Genomics (2006) 2.86
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Determination of stromal signatures in breast carcinoma. PLoS Biol (2005) 2.84
Massive transfusion protocols: the role of aggressive resuscitation versus product ratio in mortality reduction. J Am Coll Surg (2009) 2.80
The clinical value of somatic TP53 gene mutations in 1,794 patients with breast cancer. Clin Cancer Res (2006) 2.76
Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: findings from the Breast Cancer Association Consortium. Hum Mol Genet (2011) 2.72
miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One (2011) 2.70
CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics (2004) 2.65
Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray. Am J Pathol (2003) 2.59
Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med (2005) 2.56
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis. Mod Pathol (2007) 2.47
Spectral Regularization Algorithms for Learning Large Incomplete Matrices. J Mach Learn Res (2010) 2.45
Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics (2002) 2.42
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics (2009) 2.39
Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics (2011) 2.36
Differentiation stage-specific expression of microRNAs in B lymphocytes and diffuse large B-cell lymphomas. Blood (2008) 2.36