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2021
1 Burger, Bram; Vaudel, Marc; Barsnes, Harald.
Importance of Block Randomization When Designing Proteomics Experiments. Journal of Proteome Research 2021 ;Volum 20.(1) s. 122-128
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2 Oveland, Eystein; Ahmad, Intakhar; Lereim, Ragnhild Reehorst; Kroksveen, Ann Cathrine; Barsnes, Harald; Guldbrandsen, Astrid; Myhr, Kjell-Morten; Bø, Lars; Berven, Frode Steingrimsen; Wergeland, Stig.
Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Scientific Reports 2021 ;Volum 11.(1) s. -
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2020
3 Guldbrandsen, Astrid; Lereim, Ragnhild Reehorst; Jacobsen, Mari; Garberg, Hilde Kristin; Kroksveen, Ann Cathrine; Barsnes, Harald; Berven, Frode.
Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clinical Proteomics 2020 ;Volum 17:33. s. 1-21
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4 Gupta, Manoj K.; Vethe, Heidrun; Softic, Samir; Rao, Tata Nageswara; Wagh, Vilas; Shirakawa, Jun; Barsnes, Harald; Vaudel, Marc; Takatani, Tomozumi; Kahraman, Sevim; Sakaguchi, Masaji; Martinez, Rachael; Hu, Jiang; Bjørlykke, Yngvild; Ræder, Helge; Kulkarni, Rohit N..
Leptin receptor signaling regulates protein synthesis pathways and neuronal differentiation in pluripotent stem cells. Stem Cell Reports 2020 ;Volum 15.(5) s. 1067-1079
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5 Van Den Bossche, Tim; Verschaffelt, Pieter; Schallert, Kay; Barsnes, Harald; Dawyndt, Peter; Benndorf, Dirk; Renard, Bernhard Y; Mesuere, Bart; Martens, Lennart; Muth, Thilo.
Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis. Journal of Proteome Research 2020 ;Volum 19.(8) s. 3562-3566
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2019
6 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..
Proteomics Standards Initiative Extended FASTA Format. Journal of Proteome Research 2019 ;Volum 18.(6) s. 2686-2692
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7 Burger, Bram; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald.
Detecting single amino acids and small peptides by combining isobaric tags and peptidomics. European Journal of Mass Spectrometry 2019
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8 Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald.
Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR). I: Cerebrospinal Fluid (CSF) Proteomics. Humana Press 2019 ISBN 978-1-4939-9706-0. s. 377-391
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9 Hernández Sánchez, Luis Francisco; Burger, Bram; Horro Marcos, Carlos; Fabregat, Antonio; Johansson, Stefan; Njølstad, Pål Rasmus; Barsnes, Harald; Hermjakob, Henning; Vaudel, Marc.
PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping. GigaScience 2019 ;Volum 8.(8) s. 1-13
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10 Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset.
ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of Proteome Research 2019 ;Volum 19.(1) s. 537-542
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11 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..
Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells 2019 ;Volum 38.(4) s. 542-555
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2018
12 Barsnes, Harald; Vaudel, Marc.
SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. Journal of Proteome Research 2018 ;Volum 17.(7) s. 2552-2555
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13 Burger, Bram; Hernández Sánchez, Luis Francisco; Lereim, Ragnhild Reehorst; Barsnes, Harald; Vaudel, Marc.
Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets. Journal of Proteome Research 2018 ;Volum 17.(11) s. 3801-3809
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2017
14 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..
An accessible proteogenomics informatics resource for cancer researchers. Cancer Research 2017 ;Volum 77.(21) s. e43-e46
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15 Kopczynski, Dominik; Barsnes, Harald; Njølstad, Pål Rasmus; Sickmann, Albert; Vaudel, Marc; Ahrends, Robert.
PeptideMapper: Efficient and versatile amino acid sequence and tag mapping. Bioinformatics 2017 ;Volum 33.(13) s. 2042-2044
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16 Kroksveen, Ann Cathrine; Guldbrandsen, Astrid; Vaudel, Marc; Lereim, Ragnhild Reehorst; Barsnes, Harald; Myhr, Kjell-Morten; Torkildsen, Øivind; Berven, Frode.
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 2017 ;Volum 16.(1) s. 179-194
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17 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.
BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics 2017
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18 Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio.
OLS Client and OLS Dialog: Open source tools to annotate public omics datasets. Proteomics 2017 ;Volum 17.(19)
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19 Verheggen, Kenneth; Ræder, Helge; Berven, Frode; Martens, Lennart Martens; Barsnes, Harald; Vaudel, Marc.
Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows. Mass spectrometry reviews (Print) 2017 ;Volum 39.(3) s. 292-306
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20 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..
The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics 2017 ;Volum 16.(7) s. 1275-1285
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2016
21 Aasebø, Elise; Berven, Frode; Selheim, Frode; Barsnes, Harald; Vaudel, Marc.
Interpretation of Quantitative Shotgun Proteomic Data. I: Proteomics in Systems Biology. Springer 2016 ISBN 978-1-4939-3339-6. s. 261-274
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22 Guldbrandsen, Astrid; Barsnes, Harald; Kroksveen, Ann Cathrine; Berven, Frode; Vaudel, Marc.
A Simple Workflow for Large Scale Shotgun Glycoproteomics. I: Proteomics in Systems Biology. Springer 2016 ISBN 978-1-4939-3339-6. s. 275-286
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23 Guldbrandsen, Astrid.
Proteome and deglycopeptide analyses of neurologically healthy and multiple sclerosis affected cerebrospinal fluid: Mass spectrometry experiments, literature mining and data sharing. Bergen: Universitetet i Bergen 2016 (ISBN 978-82-308-3171-7) 187 s.
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24 Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Kroksveen, Ann Cathrine; Oveland, Eystein; Lereim, Ragnhild Reehorst; Opsahl, Jill Anette; Myhr, Kjell-Morten; Berven, Frode; Barsnes, Harald.
CSF-PR 2.0: an interactive literature guide to quantitative cerebrospinal fluid mass spectrometry data from neurodegenerative disorders. Molecular & Cellular Proteomics 2016 ;Volum 16.(2) s. 300-309
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25 Hernandez Sanchez, Luis Francisco; Aasebø, Elise; Selheim, Frode; Berven, Frode; Ræder, Helge; Barsnes, Harald; Vaudel, Marc.
Systemic Analysis of Regulated Functional Networks. Methods in molecular biology 2016 ;Volum 1394. s. 287-310
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26 Lereim, Ragnhild Reehorst; Oveland, Eystein; Berven, Frode; Vaudel, Marc; Barsnes, Harald.
Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. I: Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Springer 2016 ISBN 978-3-319-41446-1. s. 227-236
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27 Muth, Thilo; Rapp, Erdmann; Berven, Frode; Barsnes, Harald; Vaudel, Marc.
Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics. I: Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Springer 2016 ISBN 978-3-319-41446-1. s. 217-226
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28 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.
Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 2016 ;Volum 16.(7) s. 1154-1165
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29 Vaudel, Marc; Barsnes, Harald; Bjerkvig, Rolf; Bikfalvi, Andreas; Selheim, Frode; Berven, Frode; Daubon, Thomas.
Practical considerations for omics experiments in biomedical sciences. Current Pharmaceutical Biotechnology 2016 ;Volum 17.(1) s. 105-114
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30 Vaudel, Marc; Barsnes, Harald; Ræder, Helge; Berven, Frode.
Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology 2016 ;Volum 926. s. 65-75
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31 Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode; Martens, Lennart; Vizcaíno, Juan Antonio; Barsnes, Harald.
Exploring the potential of public proteomics data. Proteomics 2016 ;Volum 16.(2) s. 214-225
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32 Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc.
Pladipus enables universal distributed computing in proteomics bioinformatics. Journal of Proteome Research 2016 ;Volum 15.(3) s. 707-712
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33 Verheggen, Kenneth; Martens, Lennart; Berven, Frode; Barsnes, Harald; Vaudel, Marc.
Database Search Engines: Paradigms, Challenges and Solutions.. I: Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Springer 2016 ISBN 978-3-319-41446-1. s. 147-156
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34 Yllmaz, Sule; Victor, Björn; Hulstaert, Niels; Vandermarliere, Elien; Barsnes, Harald; Degroeve, Sven; Gupta, Surya; Sticker, Adriaan; Gabriel, Sarah; Dorny, Pierre; Palmblad, Magnus; Martens, Lennart.
A pipeline for differential proteomics in unsequenced species. Journal of Proteome Research 2016 ;Volum 15.(6) s. 1963-1970
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2015
35 Barsnes, Harald; Vaudel, Marc; Martens, Lennart.
JSparklines: Making tabular proteomics data come alive. Proteomics 2015 ;Volum 15.(8) s. 1428-1431
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36 Farag, Yehia Mohamed Mokhtar; Berven, Frode; Jonassen, Inge; Petersen, Kjell; Barsnes, Harald.
Distributed and interactive visual analysis of omics data. Journal of Proteomics 2015 ;Volum 129. s. 78-82
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37 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.
Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics 2015 ;Volum 15.(19) s. 3361-3369
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38 Oveland, Eystein; Muth, Thilo; Rapp, Erdmann; Martens, Lennart; Berven, Frode; Barsnes, Harald.
Viewing the proteome: How to visualize proteomics data?. Proteomics 2015 ;Volum 15.(8) s. 1341-1355
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39 Vaudel, Marc; Burkhart, Julia M.; Zahedi, René P.; Oveland, Eystein; Berven, Frode; Sickmann, Albert; Martens, Lennart; Barsnes, Harald.
PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nature Biotechnology 2015 ;Volum 33.(1) s. 22-24
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2014
40 Bjørlykke, Yngvild; Vethne, Heidrun; Vaudel, Marc; Barsnes, Harald; Berven, Frode; Tjora, Erling; Ræder, Helge.
Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice. Journal of Proteome Research 2014 ;Volum 14.(1) s. 521-530
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41 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.
In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Molecular & Cellular Proteomics 2014 ;Volum 13.(11) s. 3152-3163
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42 Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, S; Ramon, Jan; Laukens, Kris; Valkenborg, Dirk; Barsnes, Harald; Martens, Lennart.
Machine learning applications in proteomics research: How the past can boost the future. Proteomics 2014 ;Volum 14.(4-5) s. 353-366
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43 Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald.
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. Journal of Proteome Research 2014 ;Volum 13.(2) s. 1143-1146
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44 Vaudel, Marc; Barsnes, Harald; Martens, Lennart; Berven, Frode.
Bioinformatics for Proteomics: Opportunities at the interface between the scientists, their experiments and the community. I: Shotgun Proteomics. Springer 2014 ISBN 978-1-4939-0684-0. s. 239-248
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45 Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald.
Shedding light on black boxes in protein identification. Proteomics 2014 ;Volum 14.(9) s. 1001-1005
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46 Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart.
Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics 2014 ;Volum 14.(4-5) s. 367-377
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2013
47 Barsnes, Harald; Martens, Lennart.
Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013 ;Volum 44.(4) s. 1129-1137
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48 Eidhammer, Ingvar; Barsnes, Harald; Eide, Geir Egil; Martens, Lennart.
Computational and Statistical Methods for Protein Quantification by Mass Spectrometry. John Wiley & Sons 2013 (ISBN 978-1-119-96400-1) 334 s.
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49 Hulstaert, Niels; Reisinger, Florian; Rameseder, Jonathan; Barsnes, Harald; Vizcaíno, Juan Antonio; Martens, Lennart.
Pride-asap: automatic fragment ion annotation of identified PRIDE spectra. Journal of Proteomics 2013 ;Volum 95. s. 89-92
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50 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.
Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. Journal of Proteomics 2013 ;Volum 78. s. 312-325
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