1. Lereim RR, Nytrova P, Guldbrandsen A, Havrdova EK, Myhr KM, Barsnes H, Berven FS. Natalizumab promotes anti-inflammatory and repair effects in multiple sclerosis. PLoS One. 2024 Mar 25;19(3):e0300914. doi: 10.1371/journal.pone.0300914.
  2. Hernández Sánchez LF, Burger B, Castro Campos RA, Johansson S, Njølstad PR, Barsnes H, Vaudel M. Extending protein interaction networks using proteoforms and small molecules. Bioinformatics. 2023 Oct 3;39(10):btad598.
  3. Burger B, Vaudel M, Barsnes H. Automated splitting into batches for observational biomedical studies with sequential processing. Biostatistics. 2023 Oct 18;24(4):1031-1044.
  4. Farag YM, Horro C, Vaudel M, Barsnes H: PeptideShaker Online: a web-based framework for interactive visual analysis of proteomics data. J Proteome Res. 2021 Dec 3;20(12):5419-5423.
  5. Oveland E, Ahmad I, Lereim RR, Kroksveen AC, Barsnes H, Guldbrandsen A, Myhr KM, Bø L, Berven FS, Wergeland S: Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Sci Rep. 2021 Mar 30;11(1):7174.
  6. Burger B, Vaudel M, Barsnes H: Importance of block randomization when designing proteomics experiments. J Proteome Res. 2021 Jan 1;20(1):122-128.
  7. Gupta MK, Vethe H, Softic S, Rao TN, Wagh V, Shirakawa J, Barsnes H, Vaudel M, Takatani T, Kahraman S, Sakaguchi M, Martinez R, Hu J, Bjørlykke Y, Raeder H, Kulkarni RN.: Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells. Stem Cell Reports. 2020 Nov 10;15(5):1067-1079
  8. Guldbrandsen A, Lereim RR, Jacobsen M, Garberg H, Kroksveen AC, Barsnes H, Berven FS. Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clin Proteomics. 2020 Sep 18;17:33.
  9. Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, Muth T: Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis. J Proteome Res. 2020 Aug 7;19(8):3562-3566.
  10. 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 Spectrom Rev. 2020 May;39(3):292-306.
  11. Loo LSW, Vethe H, Soetedjo AAP, Paulo JA, Jasmen J, Jackson N, Bjørlykke Y, Valdez IA, Vaudel M, Barsnes H, Gygi SP, Raeder H, Teo AKK, Kulkarni RN: Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells. 2020 Apr;38(4):542-555.
  12. Hulstaert N, Shofstahl J, Sachsenberg T, Walzer Mathias, Barsnes H, Martens L, Perez-Riverol Y: ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion. J Proteome Res. 2020 Jan 3;19(1):537-542.
  13. Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, and Vaudel M: PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping. Gigascience. 2019 Aug 1;8(8).
  14. Guldbrandsen A, Farag Y, Lereim RR, Berven FS, Barsnes H: Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR). Methods Mol Biol. 2019;2044:377-391.
  15. Hernandez M, Wangen R, Berven F, Guldbrandsen A: Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action. Curr Med Chem. 2019;26(28):5317-5337.
  16. Burger B, Lereim RR, Berven FS, Barsnes H: Detecting single amino acids and small peptides by combining isobaric tags and peptidomics. Eur J Mass Spectrom (Chichester). 2019 Dec;25(6):451-456.
  17. Binz PA, Shofstahl J, Vizcaíno J, Barsnes H, Chalkley R, Menschaert G, Alpi E, Clauser K, Eng JK. Lane L, Seymour S, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp E, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW: Proteomics Standards Initiative Extended FASTA Format (PEFF). J Proteome Res. 2019 Jun 7;18(6):2686-2692.
  18. 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. J Proteome Res. 2018 Nov 2;17(11):3801-3809.
  19. Barsnes H, Vaudel M: SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. J Proteome Res. 2018 Jul 6;17(7):2552-2555.
  20. 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. 2017 Oct;17(19).
  21. 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 Res. 2017 Nov 1;77(21):e43-e46.
  22. 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.
  23. 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. 2017 Aug 15;33(16):2580-2582.
  24. Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R: PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping. Bioinformatics. 2017 Jul 1;33(13):2042-2044.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M: Interpretation of Quantitative Shotgun Proteomics Datasets. Methods Mol Biol. 2016;1394:261-73.
  38. 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.