Harald Barsness bilde
Harald
Barsnes
Forsker
Besøksadresse: 
Jonas Lies vei 91
5020 Bergen
Postadresse: 
Postboks 7804
5020 Bergen
Telefon: 
+47 55 58 63 78
Last ned visittkort

Dr. Barsnes (PhD) er ansatt som bioinformatiker ved proteomikkenheten (PROBE) ved Universitetet i Bergen, og er også knyttet til Computational Biology Unit (CBU) ved Bergen Center for Computational Science (BCCS).

PhD og Master grader ble begge tatt ved Institutt for informatikk ved Universitetet i Bergen.

Hovedforskningsfeltet er utvikling av verktøy og infrastruktur for analyse av kvantitative massespektrometridata.

Bøker
  • Eidhammer, Ingvar; Barsnes, Harald; Eide, Geir Egil; Martens, Lennart. 2013. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry. John Wiley & Sons. 334 sider. ISBN: 978-1-119-96400-1.
Tidsskriftartikler
  • Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, S; Ramon, Jan; Laukens, Kris; Valkenborg, Dirk; Barsnes, Harald; Martens, Lennart. 2014. Machine learning applications in proteomics research: How the past can boost the future. Proteomics. 14: 353-366. doi: 10.1002/pmic.201300289
  • Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald. 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
  • Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald. 2014. Shedding light on black boxes in protein identification. Proteomics. 14: 1001-1005. doi: 10.1002/pmic.201300488
  • Barsnes, Harald; Martens, Lennart. 2013. Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids. 44: 1129-1137. doi: 10.1007/s00726-012-1455-z
  • Hulstaert, Niels; Reisinger, Florian; Rameseder, Jonathan; Barsnes, Harald; Vizcaíno, Juan Antonio; Martens, Lennart. 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
  • Kroksveen, Ann Cathrine; Aasebø, Elise; Vethe, Heidrun; van Pesch, Vincent; Franciotta, Diego; Teunissen, Charlotte E.; Ulvik, Rune Johan; Vedeler, Christian A.; Myhr, Kjell-Morten; Barsnes, Harald; Berven, Frode. 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
  • Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart. 2013. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. doi: 10.1002/pmic.201300288
  • Aye, Thin Thin; Low, Teck Yew; Bjørlykke, Yngvild; Barsnes, Harald; Heck, Albert J.R.; Berven, Frode. 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
  • Côté, Richard G.; Griss, Johannes; Dianes, José A.; Wang, Rui; Wright, James C.; van den Toorn, Henk W.P.; van Breukelen, Bas; Heck, Albert J. R.; Hulstaert, Niels; Martens, Lennart; Reisinger, Florian; Csordas, Attila; Ovelleiro, David; Perez-Rivevol, Yasset; Barsnes, Harald; Hermjakob, Henning; Vizcaíno, Juan Antonio. 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
  • Arntzen, Magnus; Koehler, Christian; Barsnes, Harald; Berven, Frode; Treumann, Achim; Thiede, Bernd. 2011. IsobariQ: Software for Isobaric Quantitative Proteomics using IPTL, iTRAQ, and TMT. Journal of Proteome Research. 10: 913-920. doi: 10.1021/pr1009977
  • Barsnes, Harald; Eidhammer, Ingvar; Martens, Lennart. 2011. A global analysis of peptide fragmentation variability. Proteomics. 11: 1181-1188. doi: 10.1002/pmic.201000640
  • Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode; Martens, Lennart. 2011. compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics. 12. 5 sider. doi: 10.1186/1471-2105-12-70
  • Barsnes, Harald; Vizcaíno, Juan Antonio; Reisinger, Florian; Eidhammer, Ingvar; Martens, Lennart. 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
  • Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart. 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
  • Vaudel, Marc; Barsnes, Harald; Berven, Frode; Sickmann, Albert; Martens, Lennart Martens. 2011. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 11: 996-999. doi: 10.1002/pmic.201000595
  • Barsnes, Harald; Côté, Richard G.; Eidhammer, Ingvar; Martens, Lennart. 2010. OLS Dialog: An open-source front end to the Ontology Lookup Service. BMC Bioinformatics. 11. doi: 10.1186/1471-2105-11-34
  • Barsnes, Harald; Eidhammer, Ingvar; Martens, Lennart. 2010. Fragmentation Analyzer: An open-source tool to analyze MS/MS fragmentation data. Proteomics. 10: 1087-1090. doi: 10.1002/pmic.200900681
  • Côté, Richard G.; Reisinger, Florian; Martens, Lennart; Barsnes, Harald; Vizcaíno, Juan Antonio; Hermjakob, Henning. 2010. The Ontology Lookup Service: bigger and better. Nucleic Acids Research. 38: W155-W160. doi: 10.1093/nar/gkq331
  • Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joel; Gevaert, Kris; Martens, Lennart. 2010. ms_lims, a simple yet powerful open source LIMS for mass spectrometry-driven proteomics. Proteomics. 10: 1261-1264. doi: 10.1002/pmic.200900409
  • Muth, Thilo; Vaudel, Marc; Barsnes, Harald; Martens, Lennart; Sickmann, Albert. 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
  • Vizcaíno, Juan Antonio; Côté, Richard G.; Reisinger, Florian; Barsnes, Harald; Foster, JM; Rameseder, Jonathan; Hermjakob, Henning; Martens, Lennart. 2010. The Proteomics Identifications database: 2010 update. Nucleic Acids Research. 38: D736-D742. doi: 10.1093/nar/gkp964
  • Barsnes, Harald; Huber, Steffen; Sickmann, Albert; Eidhammer, Ingvar; Martens, Lennart. 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
  • Barsnes, Harald; Vizcaíno, Juan Antonio; Eidhammer, Ingvar; Martens, Lennart. 2009. PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology. 27: 598-599. doi: 10.1038/nbt0709-598
  • Eisenacher, Martin; Kohl, Michael; Martens, Lennart; Barsnes, Harald; Hardt, Tanja; Levander, Fredrik; Häkkinen, Jari; Rolf, Apweiler; Meyer, Helmut E.; Stephan, Christian. 2009. Proteomics data collection - 4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics. 9: 218-222. doi: 10.1002/pmic.200800732
  • Eisenacher, Martin; Martens, Lennart; Barsnes, Harald; Hardt, Tanja; Kohl, Michael; Häkkinen, Jari; Apweiler, Rolf; Meyer, Helmut E.; Stephan, Christian. 2009. Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics. 9: 3626-3629. doi: 10.1002/pmic.200900205
  • Eisenacher, Martin; Martens, Lennart; Hardt, Tanja; Kohl, Michael; Barsnes, Harald; Helsens, Kenny; Häkkinen, Jari; Levander, Fredrik; Aebersold, Ruedi; Vandekerckhove, Joel; Dunn, Michael J.; Frederique, Lisacek; Siepen, Jennifer A.; Hubbard, Simon J.; Pierre-Alain, Binz; Blüggel, Martin; Thiele, Herbert; Cottrell, John; Meyer, Helmut E.; Apweiler, Rolf; Stephan, Christian. 2009. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-3933. doi: 10.1002/pmic.200900247
  • Barsnes, Harald; Eidhammer, Ingvar; Cruciani, Véronique; Mikalsen, Svein-Ole. 2008. Protease-dependent fractional mass and peptide properties. European journal of mass spectrometry. 14: 311-317. doi: 10.1255/ejms.934
  • Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar. 2008. Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases. BMC Research Notes. 1.
  • Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar. 2006. MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. BMC Bioinformatics. 7. 9 sider. doi: 10.1186/1471-2105-7-42
Bokkapitler
  • Eidhammer, Ingvar; Barsnes, Harald; Mikalsen, Svein-Ole. 2008. MassSorter: Peptide Mass Fingerprinting Data Analysis. 23, sider 345-359. I:
    • Thompson, Julie D.; Schaeffer-Reiss, Christine; Ueffing, Marius. 2008. Functional proteomics: Methods and protocols. Humana Press. 595 sider. ISBN: 978-1-58829-971-0.

Se fullstendig oversikt over publikasjoner i CRIStin.

Publikasjoner i PubMed

PhD avhandling:
Development of Tools for Analyzing and Sharing Proteomics Data
(Bergen Open Research Archive)

Bøker:
Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (details)

Forskergrupper

Prosjekter