A comprehensive transcriptional portrait of human cancer cell lines

[1]  O. Griffith,et al.  Mitelman Database (Chromosome Aberrations and Gene Fusions in Cancer) , 2014 .

[2]  Benjamin Haibe-Kains,et al.  Inconsistency in large pharmacogenomic studies , 2013, Nature.

[3]  Matheus C. Bürger,et al.  Brief Report: The lincRNA Hotair Is Required for Epithelial‐to‐Mesenchymal Transition and Stemness Maintenance of Cancer Cell Lines , 2013, Stem cells.

[4]  N. Shah,et al.  Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data , 2013, BMC Genomics.

[5]  P. Meltzer,et al.  The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. , 2013, Cancer research.

[6]  Nickolay A. Khazanov,et al.  Identification of targetable FGFR gene fusions in diverse cancers. , 2013, Cancer discovery.

[7]  C. Croce,et al.  Cross-talk between MET and EGFR in non-small cell lung cancer involves miR-27a and Sprouty2 , 2013, Proceedings of the National Academy of Sciences.

[8]  E. Lander,et al.  Lessons from the Cancer Genome , 2013, Cell.

[9]  S. Gabriel,et al.  Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.

[10]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[11]  Thomas D. Wu,et al.  Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events , 2012, Genome research.

[12]  D. Brat,et al.  Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma , 2012, Science.

[13]  Melanie A. Huntley,et al.  Recurrent R-spondin fusions in colon cancer , 2012, Nature.

[14]  S. Ramaswamy,et al.  Systematic identification of genomic markers of drug sensitivity in cancer cells , 2012, Nature.

[15]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[16]  Thomas D. Wu,et al.  The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. , 2012, Genome research.

[17]  Joseph Coco,et al.  Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES , 2012, Journal of Virology.

[18]  Mark Merchant,et al.  Intermittent administration of MEK inhibitor GDC-0973 plus PI3K inhibitor GDC-0941 triggers robust apoptosis and tumor growth inhibition. , 2012, Cancer research.

[19]  A. Chinnaiyan,et al.  Functionally Recurrent Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer , 2011, Nature Medicine.

[20]  BinQing Wei,et al.  Discovery of a potent, selective, and orally available class I phosphatidylinositol 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) kinase inhibitor (GDC-0980) for the treatment of cancer. , 2011, Journal of medicinal chemistry.

[21]  Süleyman Cenk Sahinalp,et al.  deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data , 2011, PLoS Comput. Biol..

[22]  G. Getz,et al.  GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.

[23]  A. Gonzalez-Perez,et al.  Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. , 2011, American journal of human genetics.

[24]  A. Børresen-Dale,et al.  Identification of fusion genes in breast cancer by paired-end RNA-sequencing , 2011, Genome Biology.

[25]  Kakajan Komurov,et al.  Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes , 2010, Proceedings of the National Academy of Sciences.

[26]  Masters,et al.  Cell line misidentification: the beginning of the end , 2010 .

[27]  J. Maguire,et al.  Integrative analysis of the melanoma transcriptome. , 2010, Genome research.

[28]  D. Haber,et al.  Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents , 2010, Nature Reviews Cancer.

[29]  H. Parkinson,et al.  A global map of human gene expression , 2010, Nature Biotechnology.

[30]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[31]  P. Deloukas,et al.  Signatures of mutation and selection in the cancer genome , 2010, Nature.

[32]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[33]  N. Turner,et al.  Fibroblast growth factor signalling: from development to cancer , 2010, Nature Reviews Cancer.

[34]  Derek Y. Chiang,et al.  The landscape of somatic copy-number alteration across human cancers , 2010, Nature.

[35]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[36]  S. Swamy,et al.  PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data , 2009, Biostatistics.

[37]  American Type Culture Collection Standards Development Orga ASN-0002.  Cell line misidentification: the beginning of the end , 2010, Nature Reviews Cancer.

[38]  Morag Park,et al.  Crosstalk in Met receptor oncogenesis. , 2009, Trends in cell biology.

[39]  J. Warmus,et al.  The Discovery of the Benzhydroxamate MEK Inhibitors CI‐1040 and PD 0325901. , 2009 .

[40]  Gary Box,et al.  The identification of 2-(1H-indazol-4-yl)-6-(4-methanesulfonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (GDC-0941) as a potent, selective, orally bioavailable inhibitor of class I PI3 kinase for the treatment of cancer . , 2008, Journal of medicinal chemistry.

[41]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[42]  A. Iafrate,et al.  Genomic alterations of anaplastic lymphoma kinase may sensitize tumors to anaplastic lymphoma kinase inhibitors. , 2008, Cancer research.

[43]  Wen-Lin Kuo,et al.  A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. , 2006, Cancer cell.

[44]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[45]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[46]  C. Sawyers,et al.  Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. , 2001, The New England journal of medicine.

[47]  Christian A. Rees,et al.  Systematic variation in gene expression patterns in human cancer cell lines , 2000, Nature Genetics.

[48]  D. Botstein,et al.  A gene expression database for the molecular pharmacology of cancer , 2000, Nature Genetics.

[49]  S. Hubbard,et al.  Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain , 1998, The EMBO journal.

[50]  G. S. Johnson,et al.  An Information-Intensive Approach to the Molecular Pharmacology of Cancer , 1997, Science.

[51]  L. Penland,et al.  Use of a cDNA microarray to analyse gene expression patterns in human cancer , 1996, Nature Genetics.

[52]  J. Ford.  A beginning or an end? , 1987, Nature.

[53]  H. S. Greene.  On the development of cancer. , 1948, Scientific American.