Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Authors
Keywords
-
Journal
PROTEOMICS
Volume -, Issue -, Pages 1900147
Publisher
Wiley
Online
2019-10-28
DOI
10.1002/pmic.201900147
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45,810 Computational Analysis Runs
- (2019) Sean Peters et al. JOURNAL OF PROTEOME RESEARCH
- mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
- (2019) Nils Hoffmann et al. ANALYTICAL CHEMISTRY
- Advances in computational metabolomics and databases deepen the understanding of metabolisms
- (2018) Hiroshi Tsugawa CURRENT OPINION IN BIOTECHNOLOGY
- Bioconda: sustainable and comprehensive software distribution for the life sciences
- (2018) Björn Grüning et al. NATURE METHODS
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
- (2018) Enis Afgan et al. NUCLEIC ACIDS RESEARCH
- Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA
- (2018) Frank Koopmans et al. PROTEOMICS
- Practical Computational Reproducibility in the Life Sciences
- (2018) Björn Grüning et al. Cell Systems
- Protein Inference Using PIA Workflows and PSI Standard File Formats
- (2018) Julian Uszkoreit et al. JOURNAL OF PROTEOME RESEARCH
- PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
- (2018) Kristian Peters et al. GigaScience
- Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
- (2017) Sarah Cohen-Boulakia et al. Future Generation Computer Systems-The International Journal of eScience
- OpenMS – A platform for reproducible analysis of mass spectrometry data
- (2017) Julianus Pfeuffer et al. JOURNAL OF BIOTECHNOLOGY
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
- (2017) Eric W. Deutsch et al. JOURNAL OF PROTEOME RESEARCH
- In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
- (2017) Enrique Audain et al. Journal of Proteomics
- Navigating freely-available software tools for metabolomics analysis
- (2017) Rachel Spicer et al. Metabolomics
- The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
- (2017) Juan Antonio Vizcaíno et al. MOLECULAR & CELLULAR PROTEOMICS
- Discovering and linking public omics data sets using the Omics Discovery Index
- (2017) Yasset Perez-Riverol et al. NATURE BIOTECHNOLOGY
- Nextflow enables reproducible computational workflows
- (2017) Paolo Di Tommaso et al. NATURE BIOTECHNOLOGY
- Toil enables reproducible, open source, big biomedical data analyses
- (2017) John Vivian et al. NATURE BIOTECHNOLOGY
- MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
- (2017) Andy T Kong et al. NATURE METHODS
- Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy
- (2016) Ralf J. M. Weber et al. Metabolomics
- Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
- (2016) Johannes Griss et al. NATURE METHODS
- The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
- (2016) Stefka Tyanova et al. Nature Protocols
- Ten Simple Rules for Taking Advantage of Git and GitHub
- (2016) Yasset Perez-Riverol et al. PLoS Computational Biology
- Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data
- (2016) Robert L. Davidson et al. GigaScience
- PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface
- (2015) Julian Uszkoreit et al. JOURNAL OF PROTEOME RESEARCH
- Open source libraries and frameworks for biological data visualisation: A guide for developers
- (2015) Rui Wang et al. PROTEOMICS
- Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics
- (2014) F. Giacomoni et al. BIOINFORMATICS
- Bioinformatic analysis of proteomics data
- (2014) Andreas Schmidt et al. BMC Systems Biology
- The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
- (2014) Johannes Griss et al. MOLECULAR & CELLULAR PROTEOMICS
- OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
- (2014) Hannes L Röst et al. NATURE BIOTECHNOLOGY
- MS-GF+ makes progress towards a universal database search tool for proteomics
- (2014) Sangtae Kim et al. Nature Communications
- Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
- (2013) Yasset Perez-Riverol et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Effectively addressing complex proteomic search spaces with peptide spectrum matching
- (2013) Diogo Borges et al. BIOINFORMATICS
- High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome
- (2013) Nadin Neuhauser et al. JOURNAL OF PROTEOME RESEARCH
- Two birds with one stone: Doing metabolomics with your proteomics kit
- (2013) Roman Fischer et al. PROTEOMICS
- Ten Simple Rules for Reproducible Computational Research
- (2013) Geir Kjetil Sandve et al. PLoS Computational Biology
- Snakemake--a scalable bioinformatics workflow engine
- (2012) J. Koster et al. BIOINFORMATICS
- Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
- (2011) Jürgen Cox et al. JOURNAL OF PROTEOME RESEARCH
- Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
- (2010) Brendan MacLean et al. BIOINFORMATICS
- MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
- (2010) Tomáš Pluskal et al. BMC BIOINFORMATICS
- mzML—a Community Standard for Mass Spectrometry Data
- (2010) Lennart Martens et al. MOLECULAR & CELLULAR PROTEOMICS
- A guided tour of the Trans-Proteomic Pipeline
- (2010) Eric W. Deutsch et al. PROTEOMICS
- Mass spectrometry: from proteomics to metabolomics and lipidomics
- (2009) William J. Griffiths et al. CHEMICAL SOCIETY REVIEWS
- XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization
- (2008) H. P. Benton et al. ANALYTICAL CHEMISTRY
- How do your data grow?
- (2008) Clifford Lynch NATURE
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now