Jaap Heringa
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Jaap Heringa is full professor of Bioinformatics at Vrije Universiteit Amsterdam, The Netherlands since 2002, and head of the Department of Computer Science at VU Amsterdam since 2018. He earned his PhD in bioinformatics in 1993 (Cum Laude), has been programmer at the International Network Development Centre of IBM Netherlands (1984-1988), staff researcher at the European Molecular Biology Laboratory (EMBL) in Heidelberg (1988-1996) and senior group leader at the National Institute for Medical Research (NIMR) in London (1996-2002). He has been scientific co-director of the Netherlands Bioinformatics Centre (NBIC) from 2009- 2013, has served as deputy Head of Node of ELIXIR-NL (i.e. the Dutch node of the ESFRI Landmark ELIXIR)) from 2013-2016, and is ELIXIR-NL's Head of Node since April 2016. Since 2014 he is director of the Netherlands Bioinformatics and Systems Biology Research School (BioSB) and as of January 2016 he is scientific lead of the Dutch Techcentre for Life Sciences (DTL). Heringa has been executive editor of Computational Chemistry and Biology (Elsevier) from 2014-2018 and founding executive editor of Molecular Data Science (Elsevier) from 2018-2020.
Heringa's areas of research are Bioinformatics and Systems Biology, while current research interests revolve around formal modelling strategies, sequence analysis, protein structure and interaction prediction, cancer- related data integration, molecular data science, data stewardship (FAIR principles) and data-tools interoperability
Heringa founded the MSc Bioinformatics programme in 2003. In 2009 the programme was extended with a systems biology track to become the MSc Bioinformatics & Systems Biology. In 2011 the programme became a joint-degree masters programme together with the University of Amsterdam.
Notredame, C., Higgins D., and Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217
Simossis V.A., and Heringa J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, Nucl. Acids Res., Vol. 33, W1-W6.
Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens (2013). Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model, Bioinformatics, 29 (13), i80–i88, https://doi.org/10.1093/bioinformatics/btt243
Wilkinson, M.D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao & Barend Mons (2016) The FAIR Guiding Principles for scientific data management and stewardship, Sci. Data 3: 160018 doi:10.1038/sdata.2016.18 (Nature group).
Van Gool, A.J., Bietrix, F., Caldenhoven, E., Zatloukal, K., Scherer, A., Litton, J.-E., Meijer, G.A., Blomberg, N., Smith, A., Mons, B., Heringa, J., Koot, W.-J., Smit, M.J., Hadjuch, M., Rijnders, T., Ussi, A. (2017). Crossing the translational innovation gap through Good Biomarker Practice? Nature Review Drug Discovery, 28 April 2017, doi:10.1038/nrd.2017.72
Gary Saunders, Michael Baudis, Regina Becker, Sergi Beltran, Christophe Béroud, Ewan Birney, Cath Brooksbank, Søren Brunak, Marc Van den Bulcke, Rachel Drysdale, Salvador Capella-Gutierrez, Paul Flicek, Francesco Florindi, Peter Goodhand, Ivo Gut, Jaap Heringa, Petr Holub, Jef Hooyberghs, Nick Juty, Thomas M. Keane, Jan O. Korbel, Ilkka Lappalainen, Brane Leskosek, Gert Matthijs, Michaela Th. Mayrhofer, Andres Metspalu, Arcadi Navarro, Steven Newhouse, Tommi Nyrönen, Angela Page, Bengt Persson, Aarno Palotie, Helen Parkinson, Jordi Rambla, David Salgado, Erik Steinfelder, Morris A. Swertz, Alfonso Valencia, Susheel Varma, Niklas Blomberg and Serena Scollen (2019). Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews Genetics, SN-1471-0064, https://doi.org/10.1038/s41576-019-0156-9.
Proceedings Chair, European Conference on Computational Biology (ECCB) 2009, Ghent, Belgium
General Chair, European Conference on Computational Biology (ECCB) 2016, The Hague, Netherlands
Heringa is considered an authority on multiple sequence alignment and other sequence analysis techniques. Since 2014, he has been one of the driving forces of the FAIR data principles, which are now being endorsed and implemented worldwide.