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Showing results 1-50 of 78
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2023
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1. |
Nguyen, Jannie. Evaluation of protein biomarker candidates for multiple sclerosis using mass spectrometry-based proteomics. : Institutt for biomedisin, Universitetet i Bergen 2023 UiB
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Sanchez, Luis Francisco Hernandez; Burger, Bram; Campos, Rodrigo Alexander Castro; Johansson, Stefan; Njølstad, Pål Rasmus; Barsnes, Harald; Vaudel, Marc. Extending protein interaction networks using proteoforms and small molecules. Bioinformatics 2023 ;Volume 39.(10) p. - UiB HAUKELAND FHI
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2022
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Burger, Bram; Vaudel, Marc; Barsnes, Harald. Automated splitting into batches for observational biomedical studies with sequential processing. Biostatistics 2022 ;Volume 24.(4) p. 1031-1044 HAUKELAND UiB
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2021
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Burger, Bram; Vaudel, Marc; Barsnes, Harald. Importance of Block Randomization When Designing Proteomics Experiments. Journal of Proteome Research 2021 ;Volume 20.(1) p. 122-128 UiB
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Farag, Yehia Mokhtar; Horro Marcos, Carlos; Vaudel, Marc; Barsnes, Harald. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. Journal of Proteome Research 2021 ;Volume 20.(12) p. 5419-5423 UiB
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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 ;Volume 11.(1) p. - UiB HAUKELAND
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2020
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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 ;Volume 17:33. p. 1-21 UiB HAUKELAND
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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 ;Volume 15.(5) p. 1067-1079 UiB HAUKELAND
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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 ;Volume 19.(8) p. 3562-3566 UiB
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2019
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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 ;Volume 18.(6) p. 2686-2692 UiB HAUKELAND
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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 UiB
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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. p. 377-391 UiB
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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 ;Volume 8.(8) p. 1-13 HAUKELAND UiB
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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 ;Volume 19.(1) p. 537-542 UiB
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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 ;Volume 38.(4) p. 542-555 UiB HAUKELAND
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2018
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Barsnes, Harald; Vaudel, Marc. SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. Journal of Proteome Research 2018 ;Volume 17.(7) p. 2552-2555 UiB HAUKELAND
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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 ;Volume 17.(11) p. 3801-3809 UiB HAUKELAND
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2017
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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 ;Volume 77.(21) p. e43-e46 UiB HAUKELAND
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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 ;Volume 33.(13) p. 2042-2044 UiB HAUKELAND
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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 ;Volume 16.(1) p. 179-194 UiB HAUKELAND
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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 UiB HAUKELAND
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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 ;Volume 17.(19) UiB
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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 ;Volume 39.(3) p. 292-306 HAUKELAND UiB
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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 ;Volume 16.(7) p. 1275-1285 UiB HAUKELAND
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2016
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25. |
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. p. 261-274 HAUKELAND UiB
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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. p. 275-286 HAUKELAND UiB
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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 p. UiB
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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 ;Volume 16.(2) p. 300-309 UiB HAUKELAND
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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 ;Volume 1394. p. 287-310 HAUKELAND UiB
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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. p. 227-236 HAUKELAND UiB
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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. p. 217-226 HAUKELAND UiB
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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 ;Volume 16.(7) p. 1154-1165 HAUKELAND UiB
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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 ;Volume 17.(1) p. 105-114 UiB
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Vaudel, Marc; Barsnes, Harald; Ræder, Helge; Berven, Frode. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology 2016 ;Volume 926. p. 65-75 UiB
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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 ;Volume 16.(2) p. 214-225 UiB
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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 ;Volume 15.(3) p. 707-712 UiB
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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. p. 147-156 HAUKELAND UiB
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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 ;Volume 15.(6) p. 1963-1970 UiB
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2015
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Barsnes, Harald; Vaudel, Marc; Martens, Lennart. JSparklines: Making tabular proteomics data come alive. Proteomics 2015 ;Volume 15.(8) p. 1428-1431 UiB
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Farag, Yehia Mohamed Mokhtar; Berven, Frode; Jonassen, Inge; Petersen, Kjell; Barsnes, Harald. Distributed and interactive visual analysis of omics data. Journal of Proteomics 2015 ;Volume 129. p. 78-82 UiB HAUKELAND
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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 ;Volume 15.(19) p. 3361-3369 UiB HAUKELAND
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Oveland, Eystein; Muth, Thilo; Rapp, Erdmann; Martens, Lennart; Berven, Frode; Barsnes, Harald. Viewing the proteome: How to visualize proteomics data?. Proteomics 2015 ;Volume 15.(8) p. 1341-1355 UiB HAUKELAND
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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 ;Volume 33.(1) p. 22-24 UiB HAUKELAND
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2014
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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 ;Volume 14.(1) p. 521-530 UiB HAUKELAND
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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 ;Volume 13.(11) p. 3152-3163 UiB HAUKELAND
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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 ;Volume 14.(4-5) p. 353-366 UiB
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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 ;Volume 13.(2) p. 1143-1146 UiB
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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. p. 239-248 UiB
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Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald. Shedding light on black boxes in protein identification. Proteomics 2014 ;Volume 14.(9) p. 1001-1005 HAUKELAND UiB
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50. |
Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics 2014 ;Volume 14.(4-5) p. 367-377 UiB
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