Harald Barsnes - Publications

Affiliations: 
University of Bergen, Norway, Bergen, Hordaland, Norway 

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Burger B, Hernández Sánchez LF, Lereim RR, Barsnes H, Vaudel M. Analysing the structure of pathways and its influence on the interpretation of biomedical proteomics datasets. Journal of Proteome Research. PMID 30251541 DOI: 10.1021/acs.jproteome.8b00464  0.88
2018 Barsnes H, Vaudel M. SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. Journal of Proteome Research. PMID 29774740 DOI: 10.1021/acs.jproteome.8b00175  0.88
2017 Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ. An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Cancer Research. 77: e43-e46. PMID 29092937 DOI: 10.1158/0008-5472.CAN-17-0331  0.88
2017 Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrometry Reviews. PMID 28902424 DOI: 10.1002/mas.21543  0.88
2017 Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA. OLS Client and OLS Dialog: Open source tools to annotate public omics datasets. Proteomics. PMID 28792687 DOI: 10.1002/pmic.201700244  0.52
2017 Vizcaíno JA, Mayer G, Perkins SR, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, et al. The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics : McP. PMID 28515314 DOI: 10.1074/mcp.M117.068429  0.88
2017 Leprevost FD, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, et al. BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England). PMID 28379341 DOI: 10.1093/bioinformatics/btx192  0.88
2017 Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R. PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping. Bioinformatics (Oxford, England). PMID 28334306 DOI: 10.1093/bioinformatics/btx122  0.88
2017 Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS. 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. 16: 179-194. PMID 27728768 DOI: 10.1021/acs.jproteome.6b00659  0.88
2016 Lereim RR, Oveland E, Berven FS, Vaudel M, Barsnes H. Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. Advances in Experimental Medicine and Biology. 919: 227-235. PMID 27975220 DOI: 10.1007/978-3-319-41448-5_11  0.88
2016 Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics. Advances in Experimental Medicine and Biology. 919: 217-226. PMID 27975219 DOI: 10.1007/978-3-319-41448-5_10  0.88
2016 Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M. Database Search Engines: Paradigms, Challenges and Solutions. Advances in Experimental Medicine and Biology. 919: 147-156. PMID 27975215 DOI: 10.1007/978-3-319-41448-5_6  0.88
2016 Guldbrandsen A, Farag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H. CSF-PR 2.0: an interactive literature guide to quantitative cerebrospinal fluid mass spectrometry data from neurodegenerative disorders. Molecular & Cellular Proteomics : McP. PMID 27890865 DOI: 10.1074/mcp.O116.064477  0.88
2016 Vaudel M, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology. 926: 65-75. PMID 27686806 DOI: 10.1007/978-3-319-42316-6_5  0.88
2016 Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L. A pipeline for differential proteomics in unsequenced species. Journal of Proteome Research. PMID 27089233 DOI: 10.1021/acs.jproteome.6b00140  0.88
2016 Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics. 16: 1154-65. PMID 26841090 DOI: 10.1002/pmic.201500284  0.88
2016 Hernández Sánchez LF, Aasebø E, Selheim F, Berven FS, Ræder H, Barsnes H, Vaudel M. Systemic Analysis of Regulated Functional Networks. Methods in Molecular Biology (Clifton, N.J.). 1394: 287-310. PMID 26700057 DOI: 10.1007/978-1-4939-3341-9_21  0.88
2016 Guldbrandsen A, Barsnes H, Kroksveen AC, Berven FS, Vaudel M. A Simple Workflow for Large Scale Shotgun Glycoproteomics. Methods in Molecular Biology (Clifton, N.J.). 1394: 275-286. PMID 26700056 DOI: 10.1007/978-1-4939-3341-9_20  0.88
2016 Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M. Interpretation of Quantitative Shotgun Proteomic Data. Methods in Molecular Biology (Clifton, N.J.). 1394: 261-273. PMID 26700055 DOI: 10.1007/978-1-4939-3341-9_19  0.88
2016 Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics. Journal of Proteome Research. 15: 707-12. PMID 26510693 DOI: 10.1021/acs.jproteome.5b00850  0.88
2016 Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Exploring the potential of public proteomics data. Proteomics. 16: 214-25. PMID 26449181 DOI: 10.1002/pmic.201500295  0.88
2016 Vaudel M, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T. Practical Considerations for Omics Experiments in Biomedical Sciences. Current Pharmaceutical Biotechnology. 17: 105-14. PMID 26278526  0.88
2015 Kroksveen AC, Jaffe JD, Aasebø E, Barsnes H, Bjørlykke Y, Franciotta D, Keshishian H, Myhr KM, Opsahl JA, van Pesch V, Teunissen CE, Torkildsen Ø, Ulvik RJ, Vethe H, Carr SA, et al. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics. 15: 3361-9. PMID 26152395 DOI: 10.1002/pmic.201400142  0.88
2015 Farag Y, Berven FS, Jonassen I, Petersen K, Barsnes H. Distributed and interactive visual analysis of omics data. Journal of Proteomics. 129: 78-82. PMID 26047716 DOI: 10.1016/j.jprot.2015.05.029  0.88
2015 Vizcaíno JA, Barsnes H, Hermjakob H. Proteomics data visualisation. Proteomics. 15: 1339-40. PMID 25854789 DOI: 10.1002/pmic.201570063  0.52
2015 Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nature Biotechnology. 33: 22-4. PMID 25574629 DOI: 10.1038/nbt.3109  0.76
2015 Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H. Viewing the proteome: how to visualize proteomics data? Proteomics. 15: 1341-55. PMID 25504833 DOI: 10.1002/pmic.201400412  0.88
2015 Barsnes H, Vaudel M, Martens L. JSparklines: making tabular proteomics data come alive. Proteomics. 15: 1428-31. PMID 25422159 DOI: 10.1002/pmic.201400356  0.88
2015 Bjorlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H. Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice. Journal of Proteome Research. 14: 521-30. PMID 25369532 DOI: 10.1021/pr500750z  0.88
2014 Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Molecular & Cellular Proteomics : McP. 13: 3152-63. PMID 25038066 DOI: 10.1074/mcp.M114.038554  0.88
2014 Vaudel M, Barsnes H, Martens L, Berven FS. Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community. Methods in Molecular Biology (Clifton, N.J.). 1156: 239-48. PMID 24791993 DOI: 10.1007/978-1-4939-0685-7_16  0.88
2014 Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H. Shedding light on black boxes in protein identification. Proteomics. 14: 1001-5. PMID 24678044 DOI: 10.1002/pmic.201300488  0.76
2014 Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L. Machine learning applications in proteomics research: how the past can boost the future. Proteomics. 14: 353-66. PMID 24323524 DOI: 10.1002/pmic.201300289  0.88
2014 Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. Journal of Proteome Research. 13: 1143-6. PMID 24295440 DOI: 10.1021/pr4008078  0.88
2014 Verheggen K, Barsnes H, Martens L. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. 14: 367-77. PMID 24285552 DOI: 10.1002/pmic.201300288  0.88
2013 Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L. Pride-asap: automatic fragment ion annotation of identified PRIDE spectra. Journal of Proteomics. 95: 89-92. PMID 23603108 DOI: 10.1016/j.jprot.2013.04.011  0.88
2013 Barsnes H, Martens L. Crowdsourcing in proteomics: Public resources lead to better experiments Amino Acids. 44: 1129-1137. PMID 23377569 DOI: 10.1007/s00726-012-1455-z  0.76
2013 Kroksveen AC, Aasebø E, Vethe H, Van Pesch V, Franciotta D, Teunissen CE, Ulvik RJ, Vedeler C, Myhr KM, Barsnes H, Berven FS. Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. Journal of Proteomics. 78: 312-25. PMID 23059536 DOI: 10.1016/j.jprot.2012.09.037  0.88
2012 Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, et al. 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 : McP. 11: 1682-9. PMID 22949509 DOI: 10.1074/mcp.O112.021543  0.76
2012 Aye TT, Low TY, Bjørlykke Y, Barsnes H, Heck AJ, Berven FS. 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. PMID 22548487 DOI: 10.1021/ac300596r  0.88
2011 Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. Journal of Proteome Research. 10: 3840-3. PMID 21714566 DOI: 10.1021/pr2005154  0.88
2011 Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L. compomics-utilities: an open-source Java library for computational proteomics. Bmc Bioinformatics. 12: 70. PMID 21385435 DOI: 10.1186/1471-2105-12-70  0.88
2011 Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 11: 996-9. PMID 21337703 DOI: 10.1002/pmic.201000595  0.88
2011 Barsnes H, Eidhammer I, Martens L. A global analysis of peptide fragmentation variability. Proteomics. 11: 1181-8. PMID 21328539 DOI: 10.1002/pmic.201000640  0.88
2011 Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L. Submitting proteomics data to PRIDE using PRIDE Converter. Methods in Molecular Biology (Clifton, N.J.). 694: 237-53. PMID 21082439 DOI: 10.1007/978-1-60761-977-2_16  0.88
2011 Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B. IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT. Journal of Proteome Research. 10: 913-20. PMID 21067241 DOI: 10.1021/pr1009977  0.88
2010 Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H. The Ontology Lookup Service: bigger and better. Nucleic Acids Research. 38: W155-60. PMID 20460452 DOI: 10.1093/nar/gkq331  0.76
2010 Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 10: 1522-4. PMID 20140905 DOI: 10.1002/pmic.200900759  0.88
2010 Barsnes H, Côté RG, Eidhammer I, Martens L. OLS dialog: an open-source front end to the ontology lookup service. Bmc Bioinformatics. 11: 34. PMID 20078892 DOI: 10.1186/1471-2105-11-34  0.88
2010 Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L. ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics. 10: 1261-4. PMID 20058248 DOI: 10.1002/pmic.200900409  0.88
2010 Barsnes H, Eidhammer I, Martens L. FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics. 10: 1087-90. PMID 20049869 DOI: 10.1002/pmic.200900681  0.88
2010 Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L. The Proteomics Identifications database: 2010 update. Nucleic Acids Research. 38: D736-42. PMID 19906717 DOI: 10.1093/nar/gkp964  0.76
2009 Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics. 9: 3772-4. PMID 19639591 DOI: 10.1002/pmic.200900037  0.88
2009 Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics. 9: 3626-9. PMID 19639582 DOI: 10.1002/pmic.200900205  0.76
2009 Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, et al. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-33. PMID 19637238 DOI: 10.1002/pmic.200900247  0.76
2009 Barsnes H, Vizcaíno JA, Eidhammer I, Martens L. PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology. 27: 598-9. PMID 19587657 DOI: 10.1038/nbt0709-598  0.88
2009 Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics. 9: 218-22. PMID 19105180 DOI: 10.1002/pmic.200800732  0.76
2008 Barsnes H, Mikalsen SO, Eidhammer I. Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases. Bmc Research Notes. 1: 130. PMID 19099572 DOI: 10.1186/1756-0500-1-130  0.52
2008 Barsnes H, Eidhammer I, Cruciani V, Mikalsen SO. Protease-dependent fractional mass and peptide properties. European Journal of Mass Spectrometry (Chichester, England). 14: 311-7. PMID 19023148 DOI: 10.1255/ejms.934  0.52
2008 Eidhammer I, Barsnes H, Mikalsen SO. MassSorter: peptide mass fingerprinting data analysis. Methods in Molecular Biology (Clifton, N.J.). 484: 345-59. PMID 18592191 DOI: 10.1007/978-1-59745-398-1_23  0.52
2006 Barsnes H, Mikalsen SO, Eidhammer I. MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. Bmc Bioinformatics. 7: 42. PMID 16438723 DOI: 10.1186/1471-2105-7-42  0.52
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