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Wout Bittremieux

Title(s)Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
SchoolHealth Sciences
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Liu Y, Mrzic A, Meysman P, De Vijlder T, Romijn EP, Valkenborg D, Bittremieux W, Laukens K. MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra. PLoS One. 2020; 15(1):e0226770. PMID: 31945070.
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    2. Gielis S, Moris P, Bittremieux W, De Neuter N, Ogunjimi B, Laukens K, Meysman P. Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires. Methods Mol Biol. 2020; 2120:183-195. PMID: 32124320.
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    3. Bittremieux W. spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization. Anal Chem. 2020 01 07; 92(1):659-661. PMID: 31809021.
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    4. Gielis S, Moris P, Bittremieux W, De Neuter N, Ogunjimi B, Laukens K, Meysman P. Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires. Front Immunol. 2019; 10:2820. PMID: 31849987.
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    5. Pino L, Lin A, Bittremieux W. 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample. J Proteome Res. 2019 11 01; 18(11):3936-3943. PMID: 31556620.
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    6. Bittremieux W, Laukens K, Noble WS. Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. J Proteome Res. 2019 10 04; 18(10):3792-3799. PMID: 31448616.
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    7. Kopczynski D, Bittremieux W, Bouyssié D, Dorfer V, Locard-Paulet M, Van Puyvelde B, Schwämmle V, Soggiu A, Willems S, Uszkoreit J. Proceedings of the EuBIC Winter School 2019. EuPA Open Proteom. 2019 Mar; 22-23:4-7. PMID: 31890545.
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    8. Beirnaert C, Peeters L, Meysman P, Bittremieux W, Foubert K, Custers D, Van der Auwera A, Cuykx M, Pieters L, Covaci A, Laukens K. Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis. Metabolites. 2019 Mar 20; 9(3). PMID: 30897797.
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    9. Bittremieux W, Meysman P, Noble WS, Laukens K. Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. J Proteome Res. 2018 10 05; 17(10):3463-3474. PMID: 30184435.
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    10. Mrzic A, Meysman P, Bittremieux W, Moris P, Cule B, Goethals B, Laukens K. Grasping frequent subgraph mining for bioinformatics applications. BioData Min. 2018; 11:20. PMID: 30202444.
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    11. 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. J Proteomics. 2018 09 15; 187:25-27. PMID: 29864591.
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    12. Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res. 2017 12 01; 16(12):4288-4298. PMID: 28849660.
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    13. Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. Mass Spectrom Rev. 2018 09; 37(5):697-711. PMID: 28802010.
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    14. De Neuter N, Bittremieux W, Beirnaert C, Cuypers B, Mrzic A, Moris P, Suls A, Van Tendeloo V, Ogunjimi B, Laukens K, Meysman P. On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition. Immunogenetics. 2018 03; 70(3):159-168. PMID: 28779185.
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    15. Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017; 6. PMID: 28713550.
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    16. Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL. The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry. Anal Chem. 2017 04 18; 89(8):4474-4479. PMID: 28318237.
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    17. Bittremieux W, Valkenborg D, Martens L, Laukens K. Computational quality control tools for mass spectrometry proteomics. Proteomics. 2017 02; 17(3-4). PMID: 27549080.
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    18. Meysman P, Saeys Y, Sabaghian E, Bittremieux W, Van de Peer Y, Goethals B, Laukens K. Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct; 16(5):1496-1507. PMID: 27295680.
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    19. Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, Mertens I, Baggerman G, Ramon J, Laukens K, Martens L, Valkenborg D. Designing biomedical proteomics experiments: state-of-the-art and future perspectives. Expert Rev Proteomics. 2016 05; 13(5):495-511. PMID: 27031651.
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    20. Bittremieux W, Meysman P, Martens L, Valkenborg D, Laukens K. Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics. J Proteome Res. 2016 Apr 01; 15(4):1300-7. PMID: 26974716.
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    21. Bittremieux W, Willems H, Kelchtermans P, Martens L, Laukens K, Valkenborg D. iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring. J Proteome Res. 2015 May 01; 14(5):2360-6. PMID: 25798920.
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    22. Vu TN, Bittremieux W, Valkenborg D, Goethals B, Lemière F, Laukens K. Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks. J Proteome Res. 2014 Sep 05; 13(9):4175-83. PMID: 25004400.
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    23. Bittremieux W, Kelchtermans P, Valkenborg D, Martens L, Laukens K. jqcML: an open-source java API for mass spectrometry quality control data in the qcML format. J Proteome Res. 2014 Jul 03; 13(7):3484-7. PMID: 24906114.
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    24. Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Aug; 13(8):1905-13. PMID: 24760958.
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    25. 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. 2014 Mar; 14(4-5):353-66. PMID: 24323524.
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    26. Naulaerts S, Meysman P, Bittremieux W, Vu TN, Vanden Berghe W, Goethals B, Laukens K. A primer to frequent itemset mining for bioinformatics. Brief Bioinform. 2015 Mar; 16(2):216-31. PMID: 24162173.
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