Harald
Barsnes
Researcher
Visit Address:
Jonas Lies vei 91
5020 Bergen
Postal Address:
Postboks 7804
5020 Bergen
Phone:
+47 55 58 63 78
E-mail:
Dr. Barsnes (PhD) is employed as a bioinformatician at the Proteomics Unit at the University of Bergen, and is also associated with the Computational Biology Unit (CBU) at the Bergen Center for Computational Science (BCCS).
PhD and Master degrees were both obtained at the Department of Informatics at the University of Bergen.
His main research area is the development of tools and infrastructure for analyzing quantitative mass spectrometry data.
Books
- 2013. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry. John Wiley & Sons. 334 pages. ISBN: 978-1-119-96400-1.
Journal articles
- 2014. Machine learning applications in proteomics research: How the past can boost the future. Proteomics. 14: 353-366. doi: 10.1002/pmic.201300289
- 2014. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. Journal of Proteome Research. 13: 1143-1146. doi: 10.1021/pr4008078
- 2014. Shedding light on black boxes in protein identification. Proteomics. 14: 1001-1005. doi: 10.1002/pmic.201300488
- 2013. Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids. 44: 1129-1137. doi: 10.1007/s00726-012-1455-z
- 2013. Pride-asap: automatic fragment ion annotation of identified PRIDE spectra. Journal of Proteomics. 95: 89-92. doi: 10.1016/j.jprot.2013.04.011
- 2013. Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. Journal of Proteomics. 78: 312-325. doi: 10.1016/j.jprot.2012.09.037
- 2013. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. doi: 10.1002/pmic.201300288
- 2012. Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins. Analytical Chemistry. 84: 4999-5006. doi: 10.1021/ac300596r
- 2012. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium. Molecular & Cellular Proteomics. 11: 1682-1689. doi: 10.1074/mcp.O112.021543
- 2011. IsobariQ: Software for Isobaric Quantitative Proteomics using IPTL, iTRAQ, and TMT. Journal of Proteome Research. 10: 913-920. doi: 10.1021/pr1009977
- 2011. A global analysis of peptide fragmentation variability. Proteomics. 11: 1181-1188. doi: 10.1002/pmic.201000640
- 2011. compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics. 12. 5 pages. doi: 10.1186/1471-2105-12-70
- 2011. Submitting proteomics data to PRIDE using PRIDE Converter. Methods in Molecular Biology. 694: 237-253. doi: 10.1007/978-1-60761-977-2_16
- 2011. thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files. Journal of Proteome Research. 10: 3840-3843. doi: 10.1021/pr2005154
- 2011. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 11: 996-999. doi: 10.1002/pmic.201000595
- 2010. OLS Dialog: An open-source front end to the Ontology Lookup Service. BMC Bioinformatics. 11. doi: 10.1186/1471-2105-11-34
- 2010. Fragmentation Analyzer: An open-source tool to analyze MS/MS fragmentation data. Proteomics. 10: 1087-1090. doi: 10.1002/pmic.200900681
- 2010. The Ontology Lookup Service: bigger and better. Nucleic Acids Research. 38: W155-W160. doi: 10.1093/nar/gkq331
- 2010. ms_lims, a simple yet powerful open source LIMS for mass spectrometry-driven proteomics. Proteomics. 10: 1261-1264. doi: 10.1002/pmic.200900409
- 2010. XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 10: 1522-1524. doi: 10.1002/pmic.200900759
- 2010. The Proteomics Identifications database: 2010 update. Nucleic Acids Research. 38: D736-D742. doi: 10.1093/nar/gkp964
- 2009. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics. 9: 3772-3774. doi: 10.1002/pmic.200900037
- 2009. PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology. 27: 598-599. doi: 10.1038/nbt0709-598
- 2009. Proteomics data collection - 4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics. 9: 218-222. doi: 10.1002/pmic.200800732
- 2009. Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics. 9: 3626-3629. doi: 10.1002/pmic.200900205
- 2009. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-3933. doi: 10.1002/pmic.200900247
- 2008. Protease-dependent fractional mass and peptide properties. European journal of mass spectrometry. 14: 311-317. doi: 10.1255/ejms.934
- 2008. Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases. BMC Research Notes. 1.
- 2006. MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. BMC Bioinformatics. 7. 9 pages. doi: 10.1186/1471-2105-7-42
Book sections
- 2008. MassSorter: Peptide Mass Fingerprinting Data Analysis. 23, pages 345-359. In:
- 2008. Functional proteomics: Methods and protocols. Humana Press. 595 pages. ISBN: 978-1-58829-971-0.
More information in national current research information system (CRIStin)
PhD thesis:
Development of Tools for Analyzing and Sharing Proteomics Data
(Bergen Open Research Archive)
Books:
Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (details)
Research groups
Current projects
Various tools related to mass spectrometry data have been developed: