Published in PLoS One on September 11, 2008
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol (2011) 9.60
Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science (2013) 4.42
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res (2010) 3.24
Making sense of cancer genomic data. Genes Dev (2011) 3.01
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet (2009) 2.51
Advances in sarcoma genomics and new therapeutic targets. Nat Rev Cancer (2011) 2.34
Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF. Oncogene (2011) 2.10
Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol (2013) 1.92
A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A (2010) 1.81
Integrative, multimodal analysis of glioblastoma using TCGA molecular data, pathology images, and clinical outcomes. IEEE Trans Biomed Eng (2011) 1.63
Liposarcoma: molecular genetics and therapeutics. Sarcoma (2010) 1.55
JISTIC: identification of significant targets in cancer. BMC Bioinformatics (2010) 1.47
Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A (2014) 1.38
Integrative subtype discovery in glioblastoma using iCluster. PLoS One (2012) 1.29
Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med Genomics (2011) 1.29
Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol (2011) 1.26
Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One (2011) 1.25
Soft tissue sarcomas with complex genomic profiles. Virchows Arch (2010) 1.24
Genomic dissection of the epidermal growth factor receptor (EGFR)/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers. Proc Natl Acad Sci U S A (2011) 1.21
Candidate pathways for promoting differentiation or quiescence of oligodendrocyte progenitor-like cells in glioma. Cancer Res (2012) 1.15
Molecular classification of soft tissue sarcomas and its clinical applications. Int J Clin Exp Pathol (2010) 1.15
Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. Sci Signal (2013) 1.08
miR-34a functions as a tumor suppressor modulating EGFR in glioblastoma multiforme. Oncogene (2012) 1.08
Genomic dissection of Hurthle cell carcinoma reveals a unique class of thyroid malignancy. J Clin Endocrinol Metab (2013) 1.07
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol (2012) 1.07
MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. Oncotarget (2015) 1.05
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics (2014) 0.99
Copy number losses define subgroups of dedifferentiated liposarcoma with poor prognosis and genomic instability. Clin Cancer Res (2012) 0.98
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS One (2013) 0.97
Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome. PLoS One (2011) 0.92
TRIM3, a tumor suppressor linked to regulation of p21(Waf1/Cip1.). Oncogene (2013) 0.88
Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One (2012) 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
NF2 Loss Promotes Oncogenic RAS-Induced Thyroid Cancers via YAP-Dependent Transactivation of RAS Proteins and Sensitizes Them to MEK Inhibition. Cancer Discov (2015) 0.86
Pleomorphic liposarcoma: clinical observations and molecular variables. Cancer (2011) 0.85
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. BMC Bioinformatics (2009) 0.85
Precision medicine for metastatic breast cancer-limitations and solutions. Nat Rev Clin Oncol (2015) 0.85
Establishment of highly tumorigenic human colorectal cancer cell line (CR4) with properties of putative cancer stem cells. PLoS One (2014) 0.83
Discovering tumor suppressor genes through genome-wide copy number analysis. Curr Genomics (2010) 0.83
Collection, integration and analysis of cancer genomic profiles: from data to insight. Curr Opin Genet Dev (2014) 0.82
Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics (2013) 0.81
Determining frequent patterns of copy number alterations in cancer. PLoS One (2010) 0.81
Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. Breast Cancer Res (2014) 0.79
Soft tissue sarcoma subtypes exhibit distinct patterns of acquired uniparental disomy. BMC Med Genomics (2012) 0.78
Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma. Proc Natl Acad Sci U S A (2016) 0.78
Comparative analysis of copy number variations in ulcerative colitis associated and sporadic colorectal neoplasia. BMC Cancer (2016) 0.77
Interactive analysis of large cancer copy number studies with Copy Number Explorer. Bioinformatics (2015) 0.76
Correlation between EGFR amplification and the expression of microRNA-200c in primary glioblastoma multiforme. PLoS One (2014) 0.76
Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. PLoS Genet (2014) 0.76
Voting-based cancer module identification by combining topological and data-driven properties. PLoS One (2013) 0.76
Copy Number Gains at 8q24 and 20q11-q13 in Gastric Cancer Are More Common in Intestinal-Type than Diffuse-Type. PLoS One (2015) 0.75
Emerging technologies in paediatric leukaemia. Transl Pediatr (2015) 0.75
Systematic analysis of gene expression alterations and clinical outcomes of adenylate cyclase-associated protein in cancer. Oncotarget (2017) 0.75
Laminin-binding integrin gene copy number alterations in distinct epithelial-type cancers. Am J Transl Res (2016) 0.75
Steady-state levels of phosphorylated mitogen-activated protein kinase kinase 1/2 determined by mortalin/HSPA9 and protein phosphatase 1 alpha in KRAS and BRAF tumor cells. Mol Cell Biol (2017) 0.75
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med (2004) 71.08
EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science (2004) 61.56
The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02
Global variation in copy number in the human genome. Nature (2006) 57.50
Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science (1987) 49.88
Detection of large-scale variation in the human genome. Nat Genet (2004) 49.18
Patterns of somatic mutation in human cancer genomes. Nature (2007) 38.41
The genomic landscapes of human breast and colorectal cancers. Science (2007) 38.12
A census of human cancer genes. Nat Rev Cancer (2004) 36.20
Large-scale copy number polymorphism in the human genome. Science (2004) 34.64
EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A (2004) 33.85
MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science (2007) 32.68
A fine-scale map of recombination rates and hotspots across the human genome. Science (2005) 26.82
Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med (2001) 24.51
Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics (2004) 24.18
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
The fine-scale structure of recombination rate variation in the human genome. Science (2004) 17.05
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer (2004) 12.35
Adipocyte differentiation from the inside out. Nat Rev Mol Cell Biol (2006) 11.36
Copy number variation: new insights in genome diversity. Genome Res (2006) 8.66
Chromosome aberrations in solid tumors. Nat Genet (2003) 7.01
Array comparative genomic hybridization and its applications in cancer. Nat Genet (2005) 6.69
High-resolution genomic profiles of human lung cancer. Proc Natl Acad Sci U S A (2005) 6.52
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics (2005) 6.44
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88
The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet (2008) 5.08
High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science (2008) 5.02
High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell (2006) 5.01
A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics (2005) 4.57
Molecular mechanisms for genomic disorders. Annu Rev Genomics Hum Genet (2002) 4.51
Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol (2000) 4.10
High-resolution characterization of the pancreatic adenocarcinoma genome. Proc Natl Acad Sci U S A (2004) 3.75
Allelotype of pancreatic adenocarcinoma using xenograft enrichment. Cancer Res (1995) 3.33
Subtype specific prognostic nomogram for patients with primary liposarcoma of the retroperitoneum, extremity, or trunk. Ann Surg (2006) 3.23
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res (2006) 3.21
Cancer incidence after retinoblastoma. Radiation dose and sarcoma risk. JAMA (1997) 3.00
Mechanisms of sarcoma development. Nat Rev Cancer (2003) 2.78
Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res (2007) 2.44
Sarcomas and other malignancies of soft tissue, retroperitoneum, peritoneum, pleura, heart, mediastinum, and spleen. Cancer (1995) 2.25
Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet (2007) 1.95
Mouse double minute antagonist Nutlin-3a enhances chemotherapy-induced apoptosis in cancer cells with mutant p53 by activating E2F1. Oncogene (2006) 1.78
Malignant peripheral nerve sheath tumors in neurofibromatosis 1. Am J Med Genet (2000) 1.76
Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma. Cancer Res (2002) 1.64
Adenoviral E1A-associated protein p300 is involved in acute myeloid leukemia with t(11;22)(q23;q13). Blood (1997) 1.63
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 1.62
JUN oncogene amplification and overexpression block adipocytic differentiation in highly aggressive sarcomas. Cancer Cell (2007) 1.56
Increased expression of delta-catenin/neural plakophilin-related armadillo protein is associated with the down-regulation and redistribution of E-cadherin and p120ctn in human prostate cancer. Hum Pathol (2005) 1.54
Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics (2007) 1.52
Hotspots of homologous recombination in the human genome: not all homologous sequences are equal. Genome Biol (2004) 1.51
Genomic mutation consequence calculator. Bioinformatics (2007) 1.48
From microscopes to microarrays: dissecting recurrent chromosomal rearrangements. Nat Rev Genet (2007) 1.37
Wnt5b partially inhibits canonical Wnt/beta-catenin signaling pathway and promotes adipogenesis in 3T3-L1 preadipocytes. Biochem Biophys Res Commun (2005) 1.37
Epigenetic versus genetic alterations in the inactivation of E-cadherin. Semin Cancer Biol (2002) 1.36
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 1.35
Distinct chromosomal imbalances in pleomorphic and in high-grade dedifferentiated liposarcomas. Int J Cancer (2002) 0.94
HFM1, the human homologue of yeast Mer3, encodes a putative DNA helicase expressed specifically in germ-line cells. DNA Seq (2006) 0.89
EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science (2004) 61.56
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med (2005) 26.35
Efficacy and safety of imatinib mesylate in advanced gastrointestinal stromal tumors. N Engl J Med (2002) 24.88
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Signatures of mutational processes in human cancer. Nature (2013) 21.63
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis. Cancer Cell (2005) 17.41
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature (2010) 14.62
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
KRAS mutations and primary resistance of lung adenocarcinomas to gefitinib or erlotinib. PLoS Med (2005) 13.40
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
High-throughput oncogene mutation profiling in human cancer. Nat Genet (2007) 12.68
A landscape of driver mutations in melanoma. Cell (2012) 12.61
Identification of virus-encoded microRNAs. Science (2004) 12.56
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib. Proc Natl Acad Sci U S A (2007) 11.85
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
Kinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumor. J Clin Oncol (2003) 11.33
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
PDGFRA activating mutations in gastrointestinal stromal tumors. Science (2003) 11.11
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med (2012) 10.20
Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med (2008) 10.12
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer. Clin Cancer Res (2008) 9.29
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res (2004) 8.86
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. J Clin Oncol (2011) 8.37
The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. Proc Natl Acad Sci U S A (2008) 8.08
Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature (2011) 8.03
LKB1 modulates lung cancer differentiation and metastasis. Nature (2007) 7.80
Melanoma genome sequencing reveals frequent PREX2 mutations. Nature (2012) 7.77
Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76
Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73
TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res (2006) 7.61
Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell (2007) 7.60
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet (2009) 6.99
Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med (2006) 6.96
Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res (2005) 6.93
Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors. Clin Cancer Res (2006) 6.91
Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet (2011) 6.89
Computational identification of microRNA targets. Dev Biol (2004) 6.84
Activating mutations in ALK provide a therapeutic target in neuroblastoma. Nature (2008) 6.80
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet (2009) 6.35
Crizotinib in ALK-rearranged inflammatory myofibroblastic tumor. N Engl J Med (2010) 6.28
CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature (2008) 6.24
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10