| Year |
Citation |
Score |
| 2023 |
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 (Oxford, England). 39. PMID 37756698 DOI: 10.1093/bioinformatics/btad598 |
0.719 |
|
| 2022 |
Burger B, Vaudel M, Barsnes H. Automated splitting into batches for observational biomedical studies with sequential processing. Biostatistics (Oxford, England). PMID 35536588 DOI: 10.1093/biostatistics/kxac014 |
0.714 |
|
| 2021 |
Farag YM, Horro C, Vaudel M, Barsnes H. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. Journal of Proteome Research. 20: 5419-5423. PMID 34709836 DOI: 10.1021/acs.jproteome.1c00678 |
0.696 |
|
| 2021 |
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications. 12: 5854. PMID 34615866 DOI: 10.1038/s41467-021-26111-3 |
0.751 |
|
| 2020 |
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, et al. Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells. Stem Cell Reports. PMID 33125875 DOI: 10.1016/j.stemcr.2020.10.001 |
0.583 |
|
| 2020 |
Burger B, Vaudel M, Barsnes H. On the importance of block randomisation when designing proteomics experiments. Journal of Proteome Research. PMID 32969222 DOI: 10.1021/acs.jproteome.0c00536 |
0.706 |
|
| 2020 |
Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers. 12. PMID 32192169 DOI: 10.3390/Cancers12030709 |
0.305 |
|
| 2019 |
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 (Dayton, Ohio). PMID 31828876 DOI: 10.1002/Stem.3135 |
0.633 |
|
| 2019 |
Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. Gigascience. 8. PMID 31363752 DOI: 10.1093/Gigascience/Giz088 |
0.74 |
|
| 2019 |
Grüning BA, Lampa S, Vaudel M, Blankenberg D. Software engineering for scientific big data analysis. Gigascience. 8. PMID 31121028 DOI: 10.1093/Gigascience/Giz054 |
0.405 |
|
| 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 |
0.329 |
|
| 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 |
0.756 |
|
| 2018 |
Li K, Vaudel M, Zhang B, Ren Y, Wen B. PDV: an integrative proteomics data viewer. Bioinformatics (Oxford, England). PMID 30169737 DOI: 10.1093/Bioinformatics/Bty770 |
0.463 |
|
| 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 |
0.736 |
|
| 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 |
0.738 |
|
| 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 |
0.753 |
|
| 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 |
0.802 |
|
| 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 |
0.486 |
|
| 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 |
0.709 |
|
| 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 |
0.666 |
|
| 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 |
0.668 |
|
| 2017 |
Schwämmle V, Vaudel M. Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis. Methods in Molecular Biology (Clifton, N.J.). 1558: 437-458. PMID 28150251 DOI: 10.1007/978-1-4939-6783-4_21 |
0.464 |
|
| 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 |
0.671 |
|
| 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 |
0.718 |
|
| 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 |
0.814 |
|
| 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 |
0.804 |
|
| 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 |
0.686 |
|
| 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 |
0.372 |
|
| 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 |
0.387 |
|
| 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 |
0.659 |
|
| 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 |
0.643 |
|
| 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 |
0.702 |
|
| 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 |
0.705 |
|
| 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 |
0.75 |
|
| 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 |
0.791 |
|
| 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 DOI: 10.2174/1389201016666150817095348 |
0.665 |
|
| 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 |
0.723 |
|
| 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 |
0.726 |
|
| 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 |
0.633 |
|
| 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 |
0.352 |
|
| 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 |
0.315 |
|
| 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 |
0.723 |
|
| 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 |
0.775 |
|
| 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 |
0.497 |
|
| 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 |
0.804 |
|
| 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 |
0.653 |
|
| 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 |
0.577 |
|
| 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 |
0.644 |
|
| 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 |
0.527 |
|
| 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 |
0.522 |
|
| 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 |
0.589 |
|
| 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 |
0.609 |
|
| 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 |
0.781 |
|
| 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 |
0.559 |
|
| 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 |
0.799 |
|
| 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 |
0.752 |
|
| 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 |
0.566 |
|
| 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 |
0.797 |
|
| 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 |
0.601 |
|
| 2010 |
Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A. Erratum: XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results Proteomics. 10: 2560-2560. DOI: 10.1002/pmic.201090058 |
0.688 |
|
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