Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

(2014) Pratik D. Jagtap et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

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

(2014) Sangtae Kim et al.   Nature Communications

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

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

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

(2012) Faviel F. Gonzalez-Galarza et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS