Proteogenomic characterization of human colon and rectal cancer

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

EMT is the dominant program in human colon cancer

(2013) Andre Loboda et al.   BMC Medical Genomics

Proteogenomic Analysis Reveals Unanticipated Adaptations of Colorectal Tumor Cells to Deficiencies in DNA Mismatch Repair

(2013) P. J. Halvey et al.   CANCER RESEARCH

Identification and Selective Degradation of Neopeptide-Containing Truncated Mutant Proteins in the Tumors with High Microsatellite Instability

(2013) W. K. Kim et al.   CLINICAL CANCER RESEARCH

Integrative Omics Analysis Reveals the Importance and Scope of Translational Repression in microRNA-mediated Regulation

(2013) Qi Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

(2013) Felipe De Sousa E Melo et al.   NATURE MEDICINE

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

(2013) Anguraj Sadanandam et al.   NATURE MEDICINE

NetGestalt: integrating multidimensional omics data over biological networks

(2013) Zhiao Shi et al.   NATURE METHODS

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts

(2013) Shunqiang Li et al.   Cell Reports

HNF4α: a new biomarker in colon cancer?

(2012) Karthikeyani Chellappa et al.   Biomarkers in Medicine

Proteomic analysis of oropharyngeal carcinomas reveals novel HPV-associated biological pathways

(2012) Robbert J.C. Slebos et al.   INTERNATIONAL JOURNAL OF CANCER

Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

(2012) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

(2012) Kang Ning et al.   JOURNAL OF PROTEOME RESEARCH

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Regulation of the tumor suppressor homeogene Cdx2 by HNF4α in intestinal cancer

(2012) T Saandi et al.   ONCOGENE

Src tyrosine kinase phosphorylation of nuclear receptor HNF4  correlates with isoform-specific loss of HNF4  in human colon cancer

(2012) K. Chellappa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Molecular Genetics of Colorectal Cancer

(2011) Eric R. Fearon   Annual Review of Pathology-Mechanisms of Disease

Supporting tool suite for production proteomics

(2011) Z.-Q. Ma et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

GO-function: deriving biologically relevant functions from statistically significant functions

(2011) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Proteomic Consequences of a Single Gene Mutation in a Colorectal Cancer Model

(2011) Patrick J. Halvey et al.   JOURNAL OF PROTEOME RESEARCH

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer

(2010) Jie Peng et al.   Annals of Applied Statistics

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Hepatocyte Nuclear Factor-4  Promotes Gut Neoplasia in Mice and Protects against the Production of Reactive Oxygen Species

(2010) M. Darsigny et al.   CANCER RESEARCH

Improved LC−MS/MS Spectral Counting Statistics by Recovering Low-Scoring Spectra Matched to Confidently Identified Peptide Sequences

(2010) Jian-Ying Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling

(2010) Ming Li et al.   JOURNAL OF PROTEOME RESEARCH

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Correlations between RNA and protein expression profiles in 23 human cell lines

(2009) Marcus Gry et al.   BMC GENOMICS

Biomarkers for epithelial-mesenchymal transitions

(2009) Michael Zeisberg et al.   JOURNAL OF CLINICAL INVESTIGATION

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

System-wide molecular evidence for phenotypic buffering in Arabidopsis

(2009) Jingyuan Fu et al.   NATURE GENETICS

Inhibition of colorectal cancer by targeting hepatocyte nuclear factor-4α

(2008) Betty Schwartz et al.   INTERNATIONAL JOURNAL OF CANCER

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Anomalous Features of EMT during Keratinocyte Transformation

(2008) Tamar Geiger et al.   PLoS One