Projects per year
Personal profile
Expertise
Structural Bioinformatics and computational biology
- Prediction of biophysical characteristics of proteins from their sequence
- Effect of amino acid variants on proteins and organisms
Computational aspects of Nuclear Magnetic Resonance (NMR)
- Statistical analysis of NMR data in relation to protein structure
- Structure determination of proteins from experimental NMR data
Education/Academic qualification
Chemistry, Ph.D., Ghent University
1 Dec 1992 → 19 Dec 1996
Award Date: 19 Dec 1996
External positions
VUB director, Interuniversity Institute of Bioinformatics in Brussels
Apr 2014 → …
Maitre d'enseignement, Université libre de Bruxelles
2011 → …
Scientific officer (NMR), European Bioinformatics Institute
1 Oct 2001 → 30 Sep 2010
Research Fellow, Biotechnology Research Institute, National Research Council, Montreal
1 Jan 2000 → 31 Aug 2001
Postdoctoral researcher, Université libre de Bruxelles
1 Jan 1999 → 31 Dec 1999
Postdoctoral researcher, Biotechnology Research Institute, National Research Council, Montreal
1 Jan 1997 → 31 Dec 1998
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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IRP27: TumorScope: Digital health research on data, AI and legal challenges at the VUB and UZB
Vranken, W., Vandemeulebroucke, J., Cornu, P., Quinn, P., Van Dooren, S., Duerinck, J., Olsen, C. & Forsyth, R.
1/11/24 → 30/04/27
Project: Fundamental
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EU670: Prokaryote proteomics at high temperature for single cells
1/01/24 → 31/12/27
Project: Fundamental
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OZR4184: OZR Ad hoc financiering: ELIXIR Infrastructure for Data and Services to strengthen Life-Sciences Research in Flanders.
1/01/23 → 31/12/26
Project: Fundamental
Research output
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Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics
Gavalda-Garcia, J., Dixit, B., Díaz, A., Ghysels, A. & Vranken, W., 15 Jan 2025, In: Journal of Molecular Biology. 437, 2, p. 168900 168900.Research output: Contribution to journal › Article › peer-review
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Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models
Roca-Martínez, J., Kang, H-S., Sattler, M. & Vranken, W., 1 Mar 2024, In: NAR genomics and bioinformatics. 6, 1, 16 p., lqae002.Research output: Contribution to journal › Article › peer-review
Open AccessFile1 Citation (Scopus)2 Downloads (Pure) -
bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties
Gavalda-Garcia, J., Díaz, A. & Vranken, W., 1 Sep 2024, In: Bioinformatics. 40, 9, btae543.Research output: Contribution to journal › Article › peer-review
Open Access -
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep
Tzavella, K., Diaz, A., Olsen, C. & Vranken, W., 22 Nov 2024, In: Briefings in Bioinformatics. 26, 1, 13 p., bbae664.Research output: Contribution to journal › Article › peer-review
Open Access -
Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP
Dixit, B., Vranken, W. & Ghysels, A., Feb 2024, In: Proteins. 92, 2, p. 246-264 19 p.Research output: Contribution to journal › Article › peer-review
1 Citation (Scopus)
Datasets
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Prediction of Conformational Variability for RRM proteins in inter3m data base
Gavalda Garcia, J. (Creator) & Vranken, W. (Supervisor), Zenodo, 14 Feb 2023
DOI: 10.5281/zenodo.7640833, https://doi.org/10.5281/zenodo.7640833
Dataset
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Protein ambiguity
Lazar, T. (Creator), Roca Martinez, J. (Researcher), Pancsa, R. (Creator) & Vranken, W. (Supervisor), Frontiers in Molecular Biosciences, 3 Aug 2022
DOI: 10.3389/fmolb.2022.959956, https://bitbucket.org/bio2byte/protein_ambiguity/src/master/
Dataset
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RRMScorer datasets
Roca Martinez, J. (Creator), Vranken, W. (Supervisor) & Dhondge, H. B. (Data Collector), PLOS Computational Biology, 28 Jun 2022
DOI: 10.1371/journal.pcbi.1010859, https://bitbucket.org/bio2byte/rrmscorer/src/master/Supplementary_information/
Dataset
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Bio2Byte SARS-CoV-2
Kagami, L. P. (Creator), Roca Martinez, J. (Creator), Gavalda Garcia, J. (Creator), Ramasamy, P. (Creator), Feenstra, K. A. (Creator) & Vranken, W. (Supervisor), BMC Molecular and Cell Biology, 7 Dec 2020
DOI: 10.1186/s12860-021-00362-w, https://bio2byte.be/sars2/
Dataset
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ConforMine Molecular Dynamics Data: Conformational Variability, Secondary Structure Propensities and Molecular Dynamics Simulations
Gavalda Garcia, J. (Creator), Roca Martinez, J. (Creator) & Vranken, W. (Supervisor), Zenodo, 2023
DOI: 10.5281/zenodo.7575777, https://doi.org/10.5281/zenodo.7575777
Dataset
Activities
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A.I. in Structural Biology
Carl Mensch (Organiser), Wim Vranken (Chair), Tamas Lazar (Chair), Savvas Savvides (Chair), Wouter Van Putte (Chair), Marc F Lensink (Chair) & Arne Elofsson (Chair)
19 Jan 2024Activity: Participating in or organising an event › Participation in conference
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Department of Bio-engineering Sciences (Organisational unit)
Wim Vranken (Chair), Eveline Peeters (Jury), Jean-Pierre Hernalsteens (Jury), Jos Ruytinx (Jury), Geert Angenon (Supervisor), Sofie Goormachtig (Jury) & Elizabeth Kairuz Hernández-Díaz (Jury)
15 Jun 2023Activity: Membership › Member of PhD committee
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Model-guided engineering of transcription-factor-based biosensor modules and their implementation for dynamic pathway control to improve bioproduction
Vincent Crabbe (Recipient), Eveline Peeters (Supervisor), Wim Vranken (Supervisor), Sophie de Buyl (Participant) & Indra Bervoets (Supervisor)
1 Mar 2023Activity: Other › Written proposal
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Department of Bio-engineering Sciences (Organisational unit)
Eveline Peeters (Supervisor), Wim Vranken (Supervisor), Dominique Maes (Chair), Charles Van der Henst (Jury), Geert Angenon (Jury), Kiavash Movahedi (Jury), Sébastien Ferreira-Cerca (Jury) & Louis Droogmans (Jury)
9 Mar 2023Activity: Membership › Member of PhD committee
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Université libre de Bruxelles (External organisation)
Wim Versées (Jury), François Ancien (Presenter), Wim Vranken (Supervisor), Marianne Rooman (Supervisor) & Ann Nowe (Chair)
14 Jan 2022Activity: Membership › Member of PhD committee
Thesis
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Identification and characterization of putative transcriptional regulators in archaea
Author: Donvil, L., Peeters, E. & Vranken, W., 10 Sep 2018Supervisor: Orlando, G. (Advisor), de Buyl, S. (Jury) & De Greve, H. (Jury)
Student thesis: Master's Thesis
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Surface Interactions and Sperm Motility in Microfluidic Chips
Author: Ndayra, O., Messens, J., Vranken, W., Misko, V. R. & De Malsche, W., 25 Jun 2024Supervisor: Benko, L. M. (Advisor)
Student thesis: Master's Thesis
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Unravelling the microbial ecosystems of food-related brines through a metagenomics approach
Author: Vermote, L., Weckx, S., Peeters, E. & Vranken, W., Jul 2016Student thesis: Master's Thesis