Harald Barsnes

发表

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

Lennart Martens, Harald Barsnes, Yasset Perez-Riverol, 2019, bioRxiv.

Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results.

Eystein Oveland, Frode S Berven, Harald Barsnes, 2016, Advances in experimental medicine and biology.

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra☆

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2013, Journal of proteomics.

Standards and Databases

Lennart Martens, Harald Barsnes, Ingvar Eidhammer, 2013 .

Submitting proteomics data to PRIDE using PRIDE Converter.

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2011, Methods in molecular biology.

Interpretation of Quantitative Shotgun Proteomic Data.

Frode S Berven, Harald Barsnes, Marc Vaudel, 2016, Methods in molecular biology.

Distributed computing and data storage in proteomics: Many hands make light work, and a stronger memory

Lennart Martens, Harald Barsnes, Kenneth Verheggen, 2014, Proteomics.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics*

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2017, Molecular & Cellular Proteomics.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

Thilo Muth, Erdmann Rapp, Frode S Berven, 2016, Advances in experimental medicine and biology.

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

Harald Barsnes, Henning Hermjakob, Stefan Johansson, 2018, bioRxiv.

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Eystein Oveland, Lennart Martens, Frode S Berven, 2015, Nature Biotechnology.

The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

Lennart Martens, Harald Barsnes, Johannes Griss, 2012, Molecular & Cellular Proteomics.

Machine learning applications in proteomics research: How the past can boost the future

Lennart Martens, Harald Barsnes, Wout Bittremieux, 2014, Proteomics.

BioContainers: an open-source and community-driven framework for software standardization

Harald Barsnes, Johannes Griss, Rafael C. Jimenez, 2017, Bioinform..

The Ontology Lookup Service: bigger and better

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2010, Nucleic Acids Res..

Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam, The Netherlands

Lennart Martens, Harald Barsnes, Helmut E Meyer, 2009, Proteomics.

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

Lennart Martens, Harald Barsnes, Marc Vaudel, 2010, Proteomics.

The Proteomics Identifications database: 2010 update

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2009, Nucleic Acids Res..

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion.

Lennart Martens, Harald Barsnes, Yasset Perez-Riverol, 2019, Journal of proteome research.

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences

Harald Barsnes, Ingvar Eidhammer, Svein-Ole Mikalsen, 2005, BMC Bioinformatics.

PRIDE Converter: making proteomics data-sharing easy

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2009, Nature Biotechnology.

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

Lennart Martens, Harald Barsnes, Niels Hulstaert, 2016, Journal of proteome research.

compomics-utilities: an open-source Java library for computational proteomics

Lennart Martens, Harald Barsnes, Marc Vaudel, 2011, BMC Bioinformatics.

JSparklines: Making tabular proteomics data come alive

Lennart Martens, Harald Barsnes, Marc Vaudel, 2015, Proteomics.

Shedding light on black boxes in protein identification

Lennart Martens, Frode S Berven, Harald Barsnes, 2014, Proteomics.

Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, Greece

Lennart Martens, Harald Barsnes, Helmut E Meyer, 2009, Proteomics.

Analysing the structure of pathways and its influence on the interpretation of biomedical datasets

Harald Barsnes, Marc Vaudel, Bram Burger, 2018, bioRxiv.

PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping

Harald Barsnes, Henning Hermjakob, Marc Vaudel, 2018 .

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.

Harald Barsnes, Marc Vaudel, Harald Barsnes, 2018, Journal of proteome research.

CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders*

Eystein Oveland, Harald Barsnes, Frode S. Berven, 2016, Molecular & Cellular Proteomics.

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

Lennart Martens, Frode S Berven, Harald Barsnes, 2011, Proteomics.

OLS Dialog: An open-source front end to the Ontology Lookup Service

Lennart Martens, Harald Barsnes, Richard G. Côté, 2010, BMC Bioinformatics.

Crowdsourcing in proteomics: public resources lead to better experiments

Lennart Martens, Harald Barsnes, L. Martens, 2013, Amino Acids.

Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets.

Harald Barsnes, Marc Vaudel, Bram Burger, 2018, Journal of proteome research.

Label Based Quantification

Lennart Martens, Harald Barsnes, Ingvar Eidhammer, 2013 .

PathwayMatcher: multi-omics pathway mapping and proteoform network generation

Harald Barsnes, Henning Hermjakob, Stefan Johansson, 2018 .

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

Harald Barsnes, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2017, Proteomics.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Lennart Martens, Harald Barsnes, Praveen Kumar, 2017, Cancer research.

Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community.

Lennart Martens, Frode S Berven, Harald Barsnes, 2014, Methods in molecular biology.

On the importance of block randomisation when designing proteomics experiments.

Harald Barsnes, Marc Vaudel, Bram Burger, 2020, Journal of proteome research.

Distributed and interactive visual analysis of omics data.

Frode S Berven, Harald Barsnes, Kjell Petersen, 2015, Journal of proteomics.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

Lennart Martens, Harald Barsnes, Marc Vaudel, 2011, Journal of proteome research.

Database Search Engines: Paradigms, Challenges and Solutions.

Lennart Martens, Frode S Berven, Harald Barsnes, 2016, Advances in experimental medicine and biology.

Development of Tools for Analyzing and Sharing Proteomics Data

Harald Barsnes, Harald Barsnes, 2010 .

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

Thilo Muth, Erdmann Rapp, Lennart Martens, 2013, Journal of proteome research.

ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics

Lennart Martens, Harald Barsnes, An Staes, 2010, Proteomics.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results

Lennart Martens, Harald Barsnes, Albert Sickmann, 2009, Proteomics.

PeptideMapper: efficient and versatile amino acid sequence and tag mapping

Harald Barsnes, Marc Vaudel, Albert Sickmann, 2017, Bioinform..

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

Lennart Martens, Harald Barsnes, Ingvar Eidhammer, 2013 .

Proteomics Data Visualisation

Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob, 2015, Proteomics.

FragmentationAnalyzer: An open‐source tool to analyze MS/MS fragmentation data

Lennart Martens, Harald Barsnes, Ingvar Eidhammer, 2010, Proteomics.

Practical Considerations for Omics Experiments in Biomedical Sciences.

Frode S Berven, Harald Barsnes, Marc Vaudel, 2016, Current pharmaceutical biotechnology.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

Lennart Martens, Frode S Berven, Harald Barsnes, 2020, Mass spectrometry reviews.

Protease-Dependent Fractional Mass and Peptide Properties

Harald Barsnes, Ingvar Eidhammer, Svein-Ole Mikalsen, 2008, European journal of mass spectrometry.

Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins.

Frode S Berven, Harald Barsnes, Albert J R Heck, 2012, Analytical chemistry.

A global analysis of peptide fragmentation variability

Lennart Martens, Harald Barsnes, Ingvar Eidhammer, 2011, Proteomics.

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

Lennart Martens, Harald Barsnes, Martin Eisenacher, 2009, Proteomics.