Hjem
  • E-postHarald.Barsnes@uib.no
  • Telefon+47 55 58 66 65
  • Besøksadresse
    Jonas Lies vei 91
  • Postadresse
    Postboks 7804
    5020 Bergen

Harald Barsnes er gruppeleder ved både proteomikkenheten i Bergen (PROBE)Institutt for biomedisin og ved Computational Biology Unit (CBU)Institutt for informatikk.

Hovedfokuset for gruppens forskning er utvikling av brukervennlige og fritt tilgjengelige bioinformatikkløsninger som lar forskere selv analysere og dele sine egne forskningsdata. For mer informasjon om gruppen se www.cbu.uib.no/barsnes.

Barsnes har sin PhD fra Institutt for informatikk ved Universitetet i Bergen i 2010, med et fokus på bioinformatikk og proteomikk. Etter PhD'en jobbet han ved PROBE ved Institutt for biomedisin, først som senioringeniør og deretter som postdoc finansiert via NFR. Etterfulgt av en periode som forsker ved Klinisk institutt 2 tilknyttet Helge Ræder sin gruppe, før han i 2016 startet sin egen forskningsgruppe finansiert av Bergen forskningsstiftelse og Norges forskningsråd.

Forskningen har resultert i en rekke publikasjoner og en lang liste med fritt tilgjengelig programvare, for eksempel PeptideShakerSearchGUI og PRIDE Converter.

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

I 2015 mottok han Meltzerprisen for unge forskere ved Universitet i Bergen, og i 2016 ble han tildelt rekrutteringsstipend fra Bergen forskningsstiftelse.

Vitenskapelig artikkel
  • Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset. 2019. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of Proteome Research.
  • Binz, Pierre-Alain; Shofstahl, Jim; Vizcaino, Juan Antonio; Barsnes, Harald; Chalkley, Robert J.; Menschaert, Gerben; Alpi, Emanuele; Clauser, Karl; Eng, Jimmy K.; Lane, Lydie; Seymour, Sean L.; Hernández Sánchez, Luis Francisco; Mayer, Gerhard; Eisenacher, Martin; Perez-Riverol, Yasset; Kapp, Eugene A.; Mendoza, Luis; Baker, Peter R.; Collins, Andrew; Van Den Bossche, Tim; Deutsch, Eric W. 2019. Proteomics Standards Initiative Extended FASTA Format. Journal of Proteome Research. 2686-2692.
  • Hernández Sánchez, Luis Francisco; Burger, Bram; Horro Marcos, Carlos; Fabregat, Antonio; Johansson, Stefan; Njølstad, Pål Rasmus; Barsnes, Harald; Hermjakob, Henning; Vaudel, Marc. 2019. PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping. GigaScience. 1-13.
  • Loo, Larry Sai Weng; Vethe, Heidrun; Soetedjo, Andreas Alvin Purnomo; Paulo, Joao A.; Jasmen, Joanita; Jackson, Nicholas; Bjørlykke, Yngvild; Valdez, Ivan A.; Vaudel, Marc; Barsnes, Harald; Gygi, Steven P.; Ræder, Helge; Teo, Adrian Kee Keong; Kulkarni, Rohit N. 2019. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells.
  • Burger, Bram; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald. 2019. Detecting single amino acids and small peptides by combining isobaric tags and peptidomics. European Journal of Mass Spectrometry.
  • Barsnes, Harald; Vaudel, Marc. 2018. SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. Journal of Proteome Research. 2552-2555.
  • Burger, Bram; Hernández Sánchez, Luis Francisco; Lereim, Ragnhild Reehorst; Barsnes, Harald; Vaudel, Marc. 2018. Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets. Journal of Proteome Research. 3801-3809.
  • Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; Rappsilber, Juri; Netza, Eugen; Walzer, Mathias; Kohlbacher, Oliver; Leitner, Alexander; Chalkley, Robert J.; Ghali, Fawaz; Martínez-Bartolomé, Salvador; Deutsch, Eric W.; Jones, Andrew R. 2017. The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 1275-1285.
  • Kopczynski, Dominik; Barsnes, Harald; Njølstad, Pål Rasmus; Sickmann, Albert; Vaudel, Marc; Ahrends, Robert. 2017. PeptideMapper: Efficient and versatile amino acid sequence and tag mapping. Bioinformatics. 2042-2044.
  • Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio. 2017. OLS Client and OLS Dialog: Open source tools to annotate public omics datasets. Proteomics.
  • Kroksveen, Ann Cathrine; Guldbrandsen, Astrid; Vaudel, Marc; Lereim, Ragnhild Reehorst; Barsnes, Harald; Myhr, Kjell-Morten; Torkildsen, Øivind; Berven, Frode. 2017. In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: presenting a comprehensive picture of pathways and processes affected by multiple sclerosis. Journal of Proteome Research. 179-194.
  • Leprevost, Felipe da Veiga; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset. 2017. BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics.
  • Vaudel, Marc; Barsnes, Harald; Ræder, Helge; Berven, Frode. 2016. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology. 65-75.
  • Hernandez Sanchez, Luis Francisco; Aasebø, Elise; Selheim, Frode; Berven, Frode; Ræder, Helge; Barsnes, Harald; Vaudel, Marc. 2016. Systemic Analysis of Regulated Functional Networks. Methods in molecular biology. 287-310.
  • Vaudel, Marc; Barsnes, Harald; Bjerkvig, Rolf; Bikfalvi, Andreas; Selheim, Frode; Berven, Frode; Daubon, Thomas. 2016. Practical considerations for omics experiments in biomedical sciences. Current Pharmaceutical Biotechnology. 105-114.
  • Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc. 2016. Pladipus enables universal distributed computing in proteomics bioinformatics. Journal of Proteome Research. 707-712.
  • Opsahl, Jill Anette; Vaudel, Marc; Guldbrandsen, Astrid; Aasebø, Elise; Van Pesch, Vincent; Franciotta, Diego; Myhr, Kjell-Morten; Barsnes, Harald; Berle, Magnus Foldal; Torkildsen, Øivind; Kroksveen, Ann Cathrine; Berven, Frode. 2016. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics. 1154-1165.
  • Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Kroksveen, Ann Cathrine; Oveland, Eystein; Lereim, Ragnhild Reehorst; Opsahl, Jill Anette; Myhr, Kjell-Morten; Berven, Frode; Barsnes, Harald. 2016. CSF-PR 2.0: an interactive literature guide to quantitative cerebrospinal fluid mass spectrometry data from neurodegenerative disorders. Molecular & Cellular Proteomics. 300-309.
  • Yllmaz, Sule; Victor, Björn; Hulstaert, Niels; Vandermarliere, Elien; Barsnes, Harald; Degroeve, Sven; Gupta, Surya; Sticker, Adriaan; Gabriel, Sarah; Dorny, Pierre; Palmblad, Magnus; Martens, Lennart. 2016. A pipeline for differential proteomics in unsequenced species. Journal of Proteome Research. 1963-1970.
  • Kroksveen, Ann Cathrine; Jaffe, Jacob D.; Aasebø, Elise; Barsnes, Harald; Bjørlykke, Yngvild; Franciotta, Diego; Keshishian, Hasmik; Myhr, Kjell-Morten; Opsahl, Jill Anette; van Pesch, Vincent; Teunissen, Charlotte E.; Torkildsen, Øivind; Ulvik, Rune Johan; Vethne, Heidrun; Carr, Steven A.; Berven, Frode. 2015. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics. 3361-3369.
  • Barsnes, Harald; Vaudel, Marc; Martens, Lennart. 2015. JSparklines: Making tabular proteomics data come alive. Proteomics. 1428-1431.
  • Farag, Yehia Mohamed Mokhtar; Berven, Frode; Jonassen, Inge; Petersen, Kjell; Barsnes, Harald. 2015. Distributed and interactive visual analysis of omics data. Journal of Proteomics. 78-82.
  • Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald. 2014. Shedding light on black boxes in protein identification. Proteomics. 1001-1005.
  • 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. 3152-3163.
  • Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart. 2014. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. 367-377.
  • 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. 1143-1146.
  • 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. 521-530.
  • 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. 312-325.
  • 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. 4999-5006.
  • 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. 1682-1689.
  • 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. 3840-3843.
  • 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. 5 sider.
  • Barsnes, Harald; Vizcaíno, Juan Antonio; Reisinger, Florian; Eidhammer, Ingvar; Martens, Lennart. 2011. Submitting proteomics data to PRIDE using PRIDE Converter. Methods in molecular biology. 237-253.
  • 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. 996-999.
  • 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. 913-920.
  • Barsnes, Harald; Eidhammer, Ingvar; Martens, Lennart. 2011. A global analysis of peptide fragmentation variability. Proteomics. 1181-1188.
  • 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. 1261-1264.
  • 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. 1522-1524.
  • 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. D736-D742.
  • 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. W155-W160.
  • Barsnes, Harald; Côté, Richard G.; Eidhammer, Ingvar; Martens, Lennart. 2010. OLS Dialog: An open-source front end to the Ontology Lookup Service. BMC Bioinformatics.
  • Barsnes, Harald; Eidhammer, Ingvar; Martens, Lennart. 2010. Fragmentation Analyzer: An open-source tool to analyze MS/MS fragmentation data. Proteomics. 1087-1090.
  • 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. 218-222.
  • 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. 3626-3629.
  • 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. 3772-3774.
  • 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. 3928-3933.
  • Barsnes, Harald; Eidhammer, Ingvar; Cruciani, Véronique; Mikalsen, Svein-Ole. 2008. Protease-dependent fractional mass and peptide properties. European Journal of Mass Spectrometry. 311-317.
  • 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.
  • 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. 9 sider.
Leserinnlegg
  • Barsnes, Harald; Vizcaíno, Juan Antonio; Eidhammer, Ingvar; Martens, Lennart. 2009. PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology. 598-599.
Short communication
  • Chambers, Matthew C.; Jagtap, Pratik D.; Johnson, James E.; McGowan, Thomas; Kumar, Praveen; Onsongo, Getiria; Guerrero, Candace R.; Barsnes, Harald; Vaudel, Marc; Martens, Lennart; Grüning, Björn; Cooke, Ira R.; Heydarian, Mohammad; Reddy, Karen L.; Griffin, Timothy J. 2017. An accessible proteogenomics informatics resource for cancer researchers. Cancer Research. e43-e46.
  • 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. 89-92.
Vitenskapelig monografi
  • Eidhammer, Ingvar; Barsnes, Harald; Eide, Geir Egil; Martens, Lennart. 2013. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry.
Brev til redaktøren
  • 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. 22-24.
Doktorgradsavhandling
  • Guldbrandsen, Astrid. 2016. Proteome and deglycopeptide analyses of neurologically healthy and multiple sclerosis affected cerebrospinal fluid: Mass spectrometry experiments, literature mining and data sharing .
Vitenskapelig Kapittel/Artikkel/Konferanseartikkel
  • Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald. 2019. Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR). 15 sider.
  • Lereim, Ragnhild Reehorst; Oveland, Eystein; Berven, Frode; Vaudel, Marc; Barsnes, Harald. 2016. Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. 10 sider.
  • Muth, Thilo; Rapp, Erdmann; Berven, Frode; Barsnes, Harald; Vaudel, Marc. 2016. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics. 10 sider.
  • Aasebø, Elise; Berven, Frode; Selheim, Frode; Barsnes, Harald; Vaudel, Marc. 2016. Interpretation of Quantitative Shotgun Proteomic Data. 14 sider.
  • Verheggen, Kenneth; Martens, Lennart; Berven, Frode; Barsnes, Harald; Vaudel, Marc. 2016. Database Search Engines: Paradigms, Challenges and Solutions. 10 sider.
  • Guldbrandsen, Astrid; Barsnes, Harald; Kroksveen, Ann Cathrine; Berven, Frode; Vaudel, Marc. 2016. A Simple Workflow for Large Scale Shotgun Glycoproteomics. 12 sider.
  • Vaudel, Marc; Barsnes, Harald; Martens, Lennart; Berven, Frode. 2014. Bioinformatics for Proteomics: Opportunities at the interface between the scientists, their experiments and the community. 10 sider.
  • Eidhammer, Ingvar; Barsnes, Harald; Mikalsen, Svein-Ole. 2008. MassSorter: Peptide Mass Fingerprinting Data Analysis. 15 sider.
Poster
  • Arntzen, Magnus; Koehler, Christian; Barsnes, Harald; Berven, Frode; Treumann, Achim; Thiede, Bernd. 2011. IsobariQ: Software for isobaric quantitative proteomics using IPTL, iTRAQ and TMT.
Vitenskapelig oversiktsartikkel/review
  • Verheggen, Kenneth; Ræder, Helge; Berven, Frode; Martens, Lennart Martens; Barsnes, Harald; Vaudel, Marc. 2017. Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows. 292-306.
  • Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode; Martens, Lennart; Vizcaíno, Juan Antonio; Barsnes, Harald. 2016. Exploring the potential of public proteomics data. 214-225.
  • Oveland, Eystein; Muth, Thilo; Rapp, Erdmann; Martens, Lennart; Berven, Frode; Barsnes, Harald. 2015. Viewing the proteome: How to visualize proteomics data? 1341-1355.
  • 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. 353-366.
  • Barsnes, Harald; Martens, Lennart. 2013. Crowdsourcing in proteomics: public resources lead to better experiments. 1129-1137.

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