proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

(2015) Nathan J. Edwards et al.   JOURNAL OF PROTEOME RESEARCH

CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets

(2015) Shuai Yang et al.   JOURNAL OF PROTEOME RESEARCH

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

(2015) Shivashankar H. Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics

(2014) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Onco-proteogenomics: cancer proteomics joins forces with genomics

(2014) Javier A Alfaro et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards

(2014) Fawaz Ghali et al.   PROTEOMICS

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

(2014) Xiaojing Wang et al.   PROTEOMICS

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

(2013) Xiaojing Wang et al.   BIOINFORMATICS

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

(2013) Jainab Khatun et al.   BMC GENOMICS

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

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

Tools to Covisualize and Coanalyze Proteomic Data with Genomes and Transcriptomes: Validation of Genes and Alternative mRNA Splicing

(2013) Chi Nam Ignatius Pang et al.   JOURNAL OF PROTEOME RESEARCH

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

(2013) Teck Yew Low et al.   Cell Reports

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Visualizing next-generation sequencing data with JBrowse

(2012) O. Westesson et al.   BRIEFINGS IN BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides

(2012) Banu Dost et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A First Step Toward Completion of a Genome-Wide Characterization of the Human Proteome

(2012) Gyorgy Marko-Varga et al.   JOURNAL OF PROTEOME RESEARCH

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

(2012) Young-Ki Paik et al.   NATURE BIOTECHNOLOGY

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations

(2012) Mathias Kuhring et al.   PLoS One

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

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

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

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY