Barsnes Group | Publications

2017 (8)
  1. 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. (in press)
  2. Verheggen K, Berven FS, Martens L, Barsnes H, Vaudel M: Anatomy and evolution of database search engines, a central cog in mass spectrometry based proteomic workflows. Mass Spectrometry Reviews. (in press)
  3. 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. (in press)
  4. Vizcaíno JA, Mayer G, Perkins S, 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, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR: The mzIdentML data standard v1.2 – supporting advances in proteome informatics. Mol Cell Proteomics. 2017 Jul;16(7):1275-1285.
  5. Leprevost FdV, Aflitos SA, Grüning BA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeufferz J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y: BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics. (in press)
  6. Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R: PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping. Bioinformatics. (in press)
  7. 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. Mol Cell Proteomics. 2017 Feb;16(2):300-309.
  8. 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. J Proteome Res. 2017 Jan 6;16(1):179-194.
2016 (12)
  1. Verheggen K, Martens L, Berven FS, Barsnes H and Vaudel M: Database Search Engines: Paradigms, Challenges and Solutions. Adv Exp Med Biol. 2016;919:147-156.
  2. Lereim RR, Oveland E, Berven FS, Vaudel M and Barsnes H: Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. Adv Exp Med Biol. 2016;919:227-235.
  3. Muth T, Rapp E, Berven FS, Barsnes H and Vaudel M: Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics. Adv Exp Med Biol. 2016;919:217-226.
  4. Vaudel M, Barsnes H, Ræder H, Berven FS: Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Adv Exp Med Biol. 2016;926:65-75.
  5. 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. J Proteome Res. 2016 Jun 3;15(6):1963-70.
  6. 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. 2016 Apr;16(7):1154-65.
  7. Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M: Pladipus enables universal distributed computing in proteomics bioinformatics. J Proteome Res. 2016 Mar 4;15(3):707-12.
  8. Vaudel M, Verheggen K, Csordas A, Ræder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H: Exploring the potential of public proteomics data. Proteomics. 2016 Jan;16(2):214-25.
  9. Sánchez LFH, Aasebø E, Selheim F, Berven F, Ræder H, Barsnes H, Vaudel M:Systemic Analysis of Regulated Functional Networks. Methods Mol Biol. 2016;1394:287-310.
  10. Guldbrandsen A, Barsnes H, Kroksveen AC, Berven F, Vaudel M: A Simple Workflow for Large Scale Shotgun Glycoproteomics. Methods Mol Biol. 2016;1394:275-86.
  11. Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M: Interpretation of Quantitative Shotgun Proteomics  Datasets. Methods Mol Biol. 2016;1394:261-73.
  12. Vaudel M, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T: Practical Considerations for Omics Experiments in Biomedical Sciences. Curr Pharm Biotechnol. 2016;17(1):105-14.