Wout Bittremieux
Bioinformatics PhD researcher

Wout Bittremieux

Advanced Database Research and Modelling (ADReM)
biomedical informatics research network Antwerp (biomina)

University of Antwerp
Department of Mathematics and Computer Science
Middelheimlaan 1
2020 Antwerp
Belgium
  • +32 3 265 34 07 (office)
  • first name AT last name DOT be
  • first name DOT last name AT uantwerpen DOT be
  • PGP fingerprint: 083A D4DD D94E BAEB F2EF 31A8 E6EE 659B 9DA2 F90F (show full key)
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About me

I am a PhD researcher at the Advanced Database Research and Modelling (ADReM) group and the biomedical informatics research network Antwerp (biomina) of the University of Antwerp.

My research interests mainly deal with the application of a wide range of data mining and machine learning approaches to data generated from mass spectrometry proteomics experiments. Although I apply these data science techniques to a wide variety of bioinformatics problems, a special focus is devoted to providing novel insights and computational approaches for quality control in mass spectrometry proteomics.

I am looking for a new challenge in data science or bioinformatics starting early 2017. Please contact me if interested.

Curriculum vitae.

Publications

See also Google Scholar.

2016

  • Journal Computational quality control tools for mass spectrometry proteomics. 

    Wout Bittremieux, Dirk Valkenborg, Lennart Martens, Kris Laukens

    PROTEOMICS, Early View (2016)

  • Journal Mining the enriched subgraphs for specific vertices in a biological graph. 

    Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves van de Peer, Bart Goethals, Kris Laukens

    IEEE/ACM Transactions on Computational Biology and Bioinformatics, Early Access (2016)

  • Journal Designing biomedical proteomics experiments: State-of-the-art and future perspectives. 

    Evelyne Maes, Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven de Groeve, Jef Hooyberghs, Inge Mertens, Geert Baggerman, Jan Ramon, Kris Laukens, Lennart Martens, Dirk Valkenborg

    Expert Review of Proteomics 13, 495-511 (2016)

  • Journal Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics. 

    Wout Bittremieux, Pieter Meysman, Lennart Martens, Dirk Valkenborg, Kris Laukens

    Journal of Proteome Research 15, 1300-1307 (2016)

2015

  • Proceeding Discovery of significantly enriched subgraphs associated with selected vertices in a single graph. 

    Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens

    Proceedings of the 14th International Workshop on Data Mining in Bioinformatics - BIOKDD '15 (2015)

  • Journal iMonDB: Mass spectrometry quality control through instrument monitoring. 

    Wout Bittremieux, Hanny Willems, Pieter Kelchtermans, Lennart Martens, Kris Laukens, Dirk Valkenborg

    Journal of Proteome Research 14, 2360–2366 (2015)

  • Journal A primer to frequent itemset mining for bioinformatics. 

    Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens

    Briefings in Bioinformatics 16, 216–231 (2015)

2014

  • Journal Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks. 

    Trung Nghia Vu, Wout Bittremieux, Dirk Valkenborg, Bart Goethals, Filip Lemière, Kris Laukens

    Journal of Proteome Research 13, 4175–4183 (2014)

  • Journal qcML: An exchange format for quality control metrics from mass spectrometry experiments. 

    Mathias Walzer, Lucia Espona Pernas, Sara Nasso, Wout Bittremieux, Sven Nahnsen, Pieter Kelchtermans, Peter Pichler, Henk W. P. van den Toorn, An Staes, Jonathan Vandenbussche, Michael Mazanek, Thomas Taus, Richard A. Scheltema, Christian D. Kelstrup, Laurent Gatto, Bas van Breukelen, Stephan Aiche, Dirk Valkenborg, Kris Laukens, Kathryn S. Lilley, Jesper V. Olsen, Albert J. R. Heck, Karl Mechtler, Ruedi Aebersold, Kris Gevaert, Juan Antonio Vizcaíno, Henning Hermjakob, Oliver Kohlbacher, Lennart Martens

    Molecular & Cellular Proteomics 13, 1905–1913 (2014)

  • Journal jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format. 

    Wout Bittremieux, Pieter Kelchtermans, Dirk Valkenborg, Lennart Martens, Kris Laukens

    Journal of Proteome Research 13, 3484–3487 (2014)

  • Journal Machine learning applications in proteomics research: How the past can boost the future. 

    Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven Degroeve, Jan Ramon, Kris Laukens, Dirk Valkenborg, Harald Barsnes, Lennart Martens

    PROTEOMICS 14, 353-366 (2014)

Presentations

2016

  • Oral Git: How version control can power your research. 

    Biomina Lunch Talks, Antwerp, Belgium (June 24, 2016)

  • Oral Optimized open modification spectral library searching using approximate nearest neighbor techniques. 

    ASMS annual conference, San Antonio, TX, USA (June 9, 2016)

  • Poster Automatic quality assessment of mass spectrometry experiments by multivariate quality control metrics. 

    ASMS annual conference, San Antonio, TX, USA (June 9, 2016)

2015

  • Oral Approaches for mass spectrometry quality control. 

    Biomina Research Day, Antwerp, Belgium (December 9, 2015)

  • Oral Analysis of mass spectrometry quality control metrics. 

    Benelux Bioinformatics Conference, Antwerp, Belgium (December 7, 2015)

    Outstanding oral presentation award

  • Oral Precursor-free and fast spectral library search using approximate nearest neighbor techniques. 

    Benelux Bioinformatics Conference Student Council Symposium, Antwerp, Belgium (December 6, 2015)

  • Poster Mass spectrometry quality control: Instrument monitoring and pattern mining insights. 

    ASMS annual conference, St. Louis, MO, USA (June 2, 2015)

  • Software iMonDB: Mass spectrometry instrument monitoring for quality control.

    Methods and tools for intra- and inter-experiment LC MS performance tracking workshop, ASMS annual conference, St. Louis, MO, USA (June 1, 2015)

2014

  • Poster A comprehensive approach to mass spectrometry quality control. 

    Two-day symposium of the Belgian Proteomics Association, Brussels, Belgium (December 18, 2014)

  • Oral Pattern mining of mass spectrometry quality control data. 

    Benelux Bioinformatics Conference, Luxembourg, Luxembourg (December 9, 2014)

  • Poster Pattern mining of mass spectrometry quality control data. 

    European Conference on Computational Biology, Strasbourg, France (September 7, 2014)

  • Poster Mining mass spectrometry quality control data. 

    ASMS annual conference, Baltimore, MD, USA (June 16, 2014)

  • Oral Collecting and mining mass spectrometry quality control data. 

    Biomina Research Day, Antwerp, Belgium (February 20, 2014)

2013

  • Poster jqcML: An open-source Java API for mass spectrometry quality control data in the qcML format. 

    Benelux Bioinformatics Conference, Brussels, Belgium (December 9, 2013)

Software

ANN SoLo
ANN SoLo
Spectral library searching using approximate nearest neighbor techniques.
iMonDB
iMonDB
Tool suite to automatically extract, store, manage, and visualize mass spectrometer instrument parameters from raw data files.
jqcML
jqcML
Java API for the standard qcML file format for mass spectrometry quality control data.
QC analysis
QC analysis
Workflow to analyze the quality of mass spectrometry proteomics experiments based on multivariate quality control metrics.
QC evaluation
QC evaluation
Classifier to evaluate the performance of various types of quality information in discriminating low-quality from high-quality experiments.