Wout Bittremieux

Title(s)Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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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. to make corrections and additions.
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    1. A learned embedding for efficient joint analysis of millions of mass spectra. Nat Methods. 2022 Jun; 19(6):675-678. Bittremieux W, May DH, Bilmes J, Noble WS. PMID: 35637305.
      View in: PubMed   Mentions:
    2. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. J Proteome Res. 2022 May 13. Luo X, Bittremieux W, Griss J, Deutsch EW, Sachsenberg T, Levitsky LI, Ivanov MV, Bubis JA, Gabriels R, Webel H, Sanchez A, Bai M, Käll L, Perez-Riverol Y. PMID: 35549218.
      View in: PubMed   Mentions:
    3. Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. J Proteome Res. 2022 04 01; 21(4):1189-1195. LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA. PMID: 35290070; PMCID: PMC7612572.
      View in: PubMed   Mentions:
    4. Physicochemical properties determining drug detection in skin. Clin Transl Sci. 2022 03; 15(3):761-770. Bittremieux W, Advani RS, Jarmusch AK, Aguirre S, Lu A, Dorrestein PC, Tsunoda SM. PMID: 34793633; PMCID: PMC8932847.
      View in: PubMed   Mentions:
    5. ppx: Programmatic Access to Proteomics Data Repositories. J Proteome Res. 2021 09 03; 20(9):4621-4624. Fondrie WE, Bittremieux W, Noble WS. PMID: 34342226; PMCID: PMC8457024.
      View in: PubMed   Mentions:    Fields:    
    6. Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. Brief Bioinform. 2021 07 20; 22(4). Moris P, De Pauw J, Postovskaya A, Gielis S, De Neuter N, Bittremieux W, Ogunjimi B, Laukens K, Meysman P. PMID: 33346826; PMCID: PMC8294552.
      View in: PubMed   Mentions: 5     Fields:    
    7. Universal Spectrum Identifier for mass spectra. Nat Methods. 2021 07; 18(7):768-770. Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N. PMID: 34183830; PMCID: PMC8405201.
      View in: PubMed   Mentions: 1     Fields:    
    8. Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. Rapid Commun Mass Spectrom. 2021 Jun 25; e9153. Bittremieux W, Laukens K, Noble WS, Dorrestein PC. PMID: 34169593; PMCID: PMC8709870.
      View in: PubMed   Mentions:    Fields:    
    9. Current and future deep learning algorithms for tandem mass spectrometry (MS/MS)-based small molecule structure elucidation. Rapid Commun Mass Spectrom. 2021 May 06; e9120. Liu Y, De Vijlder T, Bittremieux W, Laukens K, Heyndrickx W. PMID: 33955607.
      View in: PubMed   Mentions: 1     Fields:    
    10. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): an open community for bioinformatics training and research. Rapid Commun Mass Spectrom. 2021 Apr 16; e9087. Bittremieux W, Bouyssié D, Dorfer V, Locard-Paulet M, Perez-Riverol Y, Schwämmle V, Uszkoreit J, Van Den Bossche T. PMID: 33861485.
      View in: PubMed   Mentions:    Fields:    
    11. Sharing biological data: why, when, and how. FEBS Lett. 2021 04; 595(7):847-863. Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. PMID: 33843054.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    12. Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. J Proteome Res. 2021 03 05; 20(3):1464-1475. Bittremieux W, Adams C, Laukens K, Dorrestein PC, Bandeira N. PMID: 33605735.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    13. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol. 2021 02; 39(2):169-173. Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. PMID: 33169034; PMCID: PMC7971188.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    14. MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra. PLoS One. 2020; 15(1):e0226770. Liu Y, Mrzic A, Meysman P, De Vijlder T, Romijn EP, Valkenborg D, Bittremieux W, Laukens K. PMID: 31945070; PMCID: PMC6964822.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    15. Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires. Methods Mol Biol. 2020; 2120:183-195. Gielis S, Moris P, Bittremieux W, De Neuter N, Ogunjimi B, Laukens K, Meysman P. PMID: 32124320.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    16. spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization. Anal Chem. 2020 01 07; 92(1):659-661. Bittremieux W. PMID: 31809021.
      View in: PubMed   Mentions: 1     Fields:    
    17. Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires. Front Immunol. 2019; 10:2820. Gielis S, Moris P, Bittremieux W, De Neuter N, Ogunjimi B, Laukens K, Meysman P. PMID: 31849987; PMCID: PMC6896208.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    18. 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample. J Proteome Res. 2019 11 01; 18(11):3936-3943. Pino L, Lin A, Bittremieux W. PMID: 31556620; PMCID: PMC6824964.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    19. 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. Bittremieux W, Laukens K, Noble WS. PMID: 31448616; PMCID: PMC6886738.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    20. Proceedings of the EuBIC Winter School 2019. EuPA Open Proteom. 2019 Mar; 22-23:4-7. Kopczynski D, Bittremieux W, Bouyssié D, Dorfer V, Locard-Paulet M, Van Puyvelde B, Schwämmle V, Soggiu A, Willems S, Uszkoreit J. PMID: 31890545; PMCID: PMC6924290.
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    21. Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis. Metabolites. 2019 Mar 20; 9(3). Beirnaert C, Peeters L, Meysman P, Bittremieux W, Foubert K, Custers D, Van der Auwera A, Cuykx M, Pieters L, Covaci A, Laukens K. PMID: 30897797; PMCID: PMC6468718.
      View in: PubMed   Mentions: 2  
    22. Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. J Proteome Res. 2018 10 05; 17(10):3463-3474. Bittremieux W, Meysman P, Noble WS, Laukens K. PMID: 30184435; PMCID: PMC6173621.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    23. Grasping frequent subgraph mining for bioinformatics applications. BioData Min. 2018; 11:20. Mrzic A, Meysman P, Bittremieux W, Moris P, Cule B, Goethals B, Laukens K. PMID: 30202444; PMCID: PMC6122726.
      View in: PubMed   Mentions: 1  
    24. Proceedings of the EuBIC developer's meeting 2018. J Proteomics. 2018 09 15; 187:25-27. 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. PMID: 29864591.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    25. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res. 2017 12 01; 16(12):4288-4298. 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. PMID: 28849660; PMCID: PMC5715286.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    26. Quality control in mass spectrometry-based proteomics. Mass Spectrom Rev. 2018 09; 37(5):697-711. Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. PMID: 28802010.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    27. On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition. Immunogenetics. 2018 03; 70(3):159-168. De Neuter N, Bittremieux W, Beirnaert C, Cuypers B, Mrzic A, Moris P, Suls A, Van Tendeloo V, Ogunjimi B, Laukens K, Meysman P. PMID: 28779185.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    28. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017; 6. 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. PMID: 28713550; PMCID: PMC5499783.
      View in: PubMed   Mentions: 4     Fields:    
    29. 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. Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL. PMID: 28318237.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    30. Computational quality control tools for mass spectrometry proteomics. Proteomics. 2017 02; 17(3-4). Bittremieux W, Valkenborg D, Martens L, Laukens K. PMID: 27549080.
      View in: PubMed   Mentions: 8     Fields:    
    31. Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct; 16(5):1496-1507. Meysman P, Saeys Y, Sabaghian E, Bittremieux W, Van de Peer Y, Goethals B, Laukens K. PMID: 27295680.
      View in: PubMed   Mentions:    Fields:    
    32. Designing biomedical proteomics experiments: state-of-the-art and future perspectives. Expert Rev Proteomics. 2016 05; 13(5):495-511. 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. PMID: 27031651.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    33. Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics. J Proteome Res. 2016 Apr 01; 15(4):1300-7. Bittremieux W, Meysman P, Martens L, Valkenborg D, Laukens K. PMID: 26974716.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    34. iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring. J Proteome Res. 2015 May 01; 14(5):2360-6. Bittremieux W, Willems H, Kelchtermans P, Martens L, Laukens K, Valkenborg D. PMID: 25798920.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    35. 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. Vu TN, Bittremieux W, Valkenborg D, Goethals B, Lemière F, Laukens K. PMID: 25004400.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    36. 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. Bittremieux W, Kelchtermans P, Valkenborg D, Martens L, Laukens K. PMID: 24906114.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    37. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Aug; 13(8):1905-13. 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. PMID: 24760958; PMCID: PMC4125725.
      View in: PubMed   Mentions: 10     Fields:    
    38. Machine learning applications in proteomics research: how the past can boost the future. Proteomics. 2014 Mar; 14(4-5):353-66. Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L. PMID: 24323524.
      View in: PubMed   Mentions: 12     Fields:    
    39. A primer to frequent itemset mining for bioinformatics. Brief Bioinform. 2015 Mar; 16(2):216-31. Naulaerts S, Meysman P, Bittremieux W, Vu TN, Vanden Berghe W, Goethals B, Laukens K. PMID: 24162173; PMCID: PMC4364064.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
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