Marc Vaudel - Publications

University of Bergen, Norway, Bergen, Hordaland, Norway 

50 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
2019 Zhang-James Y, Vaudel M, Mjaavatten O, Berven FS, Haavik J, Faraone SV. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism. Attention Deficit and Hyperactivity Disorders. 11: 91-105. PMID 30927234 DOI: 10.1007/s12402-018-0281-x  0.8
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  1
2018 Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come - Current Tools, Recent Use Cases, and Future Avenues for de novo Sequencing in Proteomics. Proteomics. e1700150. PMID 29968278 DOI: 10.1002/pmic.201700150  0.76
2018 Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W. Proceedings of the EuBIC developer's meeting 2018. Journal of Proteomics. PMID 29864591 DOI: 10.1016/j.jprot.2018.05.015  0.52
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  1
2018 Beaumont RN, Warrington NM, Cavadino A, Tyrrell J, Nodzenski M, Horikoshi M, Geller F, Myhre R, Richmond RC, Paternoster L, Bradfield JP, Kreiner-Møller E, Huikari V, Metrustry S, Lunetta KL, ... ... Vaudel M, et al. Genome-wide association study of offspring birth weight in 86,577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics. Human Molecular Genetics. PMID 29309628 DOI: 10.1093/hmg/ddx429  0.52
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  1
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  1
2017 Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Review of Proteomics. 14: 649-663. PMID 28693350 DOI: 10.1080/14789450.2017.1352474  0.6
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2016 Hernandez-Valladares M, Aasebø E, Mjaavatten O, Vaudel M, Bruserud Ø, Berven F, Selheim F. Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients. Biological Procedures Online. 18: 13. PMID 27330413 DOI: 10.1186/s12575-016-0043-0  0.6
2016 Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. Journal of Proteomics. PMID 27107777 DOI: 10.1016/j.jprot.2016.03.049  0.6
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.6
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  1
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  1
2015 Vethe H, Finne K, Skogstrand T, Vaudel M, Vikse BE, Hultström M, Placier S, Scherer A, Tenstad O, Marti HP. Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip rat model. Journal of Hypertension. 33: 126-35. PMID 25304470 DOI: 10.1097/HJH.0000000000000370  0.6
2014 Helgeland E, Breivik LE, Vaudel M, Svendsen ØS, Garberg H, Nordrehaug JE, Berven FS, Jonassen AK. Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution. Plos One. 9: e109279. PMID 25333471 DOI: 10.1371/journal.pone.0109279  0.8
2014 Aasebø E, Vaudel M, Mjaavatten O, Gausdal G, Van der Burgh A, Gjertsen BT, Døskeland SO, Bruserud O, Berven FS, Selheim F. Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines. Proteomics. 14: 1971-6. PMID 25044641 DOI: 10.1002/pmic.201300448  0.8
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  1
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  0.6
2014 Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood. 123: e1-e10. PMID 24324209 DOI: 10.1182/blood-2013-07-512384  0.6
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  1
2014 Vaudel M, Sickmann A, Martens L. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochimica Et Biophysica Acta. 1844: 12-20. PMID 23845992 DOI: 10.1016/j.bbapap.2013.06.019  1
2013 Vaudel M, Breiter D, Beck F, Rahnenführer J, Martens L, Zahedi RP. D-score: a search engine independent MD-score. Proteomics. 13: 1036-41. PMID 23307401 DOI: 10.1002/pmic.201200408  0.6
2012 Vaudel M, Sickmann A, Martens L. Current methods for global proteome identification. Expert Review of Proteomics. 9: 519-32. PMID 23194269 DOI: 10.1586/epr.12.51  1
2012 Vaudel M, Burkhart JM, Radau S, Zahedi RP, Martens L, Sickmann A. Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI). Journal of Proteome Research. 11: 5072-80. PMID 22874012 DOI: 10.1021/pr300247u  0.6
2012 Burkhart JM, Vaudel M, Gambaryan S, Radau S, Walter U, Martens L, Geiger J, Sickmann A, Zahedi RP. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. Blood. 120: e73-82. PMID 22869793 DOI: 10.1182/blood-2012-04-416594  0.6
2012 Vaudel M, Burkhart JM, Zahedi RP, Martens L, Sickmann A. ITRAQ data interpretation Methods in Molecular Biology. 893: 501-509. PMID 22665319 DOI: 10.1007/978-1-61779-885-6_30  0.6
2012 Vaudel M, Burkhart JM, Breiter D, Zahedi RP, Sickmann A, Martens L. A complex standard for protein identification, designed by evolution. Journal of Proteome Research. 11: 5065-71. PMID 22489649 DOI: 10.1021/pr300055q  0.6
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  1
2011 Vaudel M, Burkhart JM, Sickmann A, Martens L, Zahedi RP. Peptide identification quality control Proteomics. 11: 2105-2114. PMID 21500347 DOI: 10.1002/pmic.201000704  0.6
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  1
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  1
2011 Burkhart JM, Vaudel M, Zahedi RP, Martens L, Sickmann A. iTRAQ protein quantification: A quality-controlled workflow Proteomics. 11: 1125-1134. PMID 21328540 DOI: 10.1002/pmic.201000711  0.6
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  1
2010 Vaudel M, Sickmann A, Martens L. Peptide and protein quantification: a map of the minefield. Proteomics. 10: 650-70. PMID 19953549 DOI: 10.1002/pmic.200900481  1
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