PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data

(2015) Aidan P. Tay et al.   JOURNAL OF PROTEOME RESEARCH

IPeak: An open source tool to combine results from multiple MS/MS search engines

(2015) Bo Wen et al.   PROTEOMICS

rTANDEM, an R/Bioconductor package for MS/MS protein identification

(2014) Frédéric Fournier et al.   BIOINFORMATICS

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments

(2014) Bo Wen et al.   BIOINFORMATICS

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

(2014) Gloria M Sheynkman et al.   BMC GENOMICS

Exome-Driven Characterization of the Cancer Cell Lines at the Proteome Level: The NCI-60 Case Study

(2014) Maria A. Karpova et al.   JOURNAL OF PROTEOME RESEARCH

Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver

(2014) Peng Wu et al.   JOURNAL OF PROTEOME RESEARCH

The OMSSAPercolator: An automated tool to validate OMSSA results

(2014) Bo Wen et al.   PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Nozzle: a report generation toolkit for data analysis pipelines

(2013) Nils Gehlenborg et al.   BIOINFORMATICS

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

(2013) Xiaojing Wang et al.   BIOINFORMATICS

Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences

(2013) Gloria M. Sheynkman et al.   JOURNAL OF PROTEOME RESEARCH

Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

(2013) Fawaz Ghali et al.   MOLECULAR & CELLULAR PROTEOMICS

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley 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

De novo derivation of proteomes from transcriptomes for transcript and protein identification

(2012) Vanessa C Evans et al.   NATURE METHODS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

(2012) Florian Reisinger et al.   PROTEOMICS

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

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

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics

(2011) Jing Li et al.   MOLECULAR & CELLULAR PROTEOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results

(2010) Thilo Muth et al.   PROTEOMICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

(2008) Fan Mo et al.   BMC BIOINFORMATICS