Harald Barsness bilde
Harald
Barsnes
Forsker
Besøksadresse: 
Haukeland universitetssykehus, Laboratoriebygget
5020 Bergen
Postadresse: 
Postboks 7804
5020 Bergen
Telefon: 
+47 55 58 63 78
Last ned visittkort

Harald Barsnes har en PhD fra Institutt for informatikk ved Universitetet i Bergen i 2010, med et fokus på bioinformatikk og proteomikk. Etter PhD'en har han jobbet ved PROBE ved Institutt for biomedisin, først som senioringeniør og deretter som postdoc finansiert via NFR. Han er nå forsker ved Klinisk institutt 2 tilknyttet Helge Ræder sin forskningsgruppe.

Hovedfokuset i forskningen er utvikling av brukervennlige og fritt tilgjengelige bioinformatikkløsninger som lar forskere selv analysere sine egne proteomikkdata. Dette har resultert i en rekke publikasjoner og en lang liste med fritt tilgjengelig programvare, for eksempel PRIDE Converter, SearchGUIog PeptideShaker.

Barsnes har også vært gjesteredaktør i tidsskriftet PROTEOMICS og har vært medforfatter på en lærebok: Computational and Statistical Methods for Protein Quantification by Mass Spectrometry.

I 2015 mottok han Meltzerprisen for unge forskere ved Universitet i Bergen.

 

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
  • Barsnes, Harald; Vaudel, Marc; Martens, Lennart. 2015. JSparklines: Making tabular proteomics data come alive. Proteomics. 15: 1428-1431. doi: 10.1002/pmic.201400356
  • Oveland, Eystein; Muth, Thilo; Rapp, Erdmann; Martens, Lennart; Berven, Frode; Barsnes, Harald. 2015. Viewing the proteome: How to visualize proteomics data? Proteomics. 15: 1341-1355. doi: 10.1002/pmic.201400412
  • Vaudel, Marc; Burkhart, Julia M.; Zahedi, René P.; Oveland, Eystein; Berven, Frode; Sickmann, Albert; Martens, Lennart; Barsnes, Harald. 2015. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nature Biotechnology. 33: 22-24. doi: 10.1038/nbt.3109
  • Bjørlykke, Yngvild; Vethne, Heidrun; Vaudel, Marc; Barsnes, Harald; Berven, Frode; Tjora, Erling; Ræder, Helge. 2014. Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice. Journal of Proteome Research. 14: 521-530. doi: 10.1021/pr500750z
  • Guldbrandsen, Astrid; Vethne, Heidrun; Farag, Yehia Mohamed Mokhtar; Oveland, Eystein; Garberg, Hilde Kristin; Berle, Magnus Foldal; Myhr, Kjell-Morten; Opsahl, Jill Anette; Barsnes, Harald; Berven, Frode. 2014. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Molecular & Cellular Proteomics. 13: 3152-3163. doi: 10.1074/mcp.M114.038554
  • 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
  • Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart. 2014. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. 14: 367-377. doi: 10.1002/pmic.201300288
  • 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
  • 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
  • Vaudel, Marc; Barsnes, Harald; Martens, Lennart; Berven, Frode. 2014. Bioinformatics for Proteomics: Opportunities at the interface between the scientists, their experiments and the community. Part VI, sider 239-248. I:
    • Martins-de-Souza, Daniel. 2014. Shotgun Proteomics. Springer. 492 sider. ISBN: 978-1-4939-0684-0.
  • 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.

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