Jonathan K. Vis

Gorlaeus Building
Einsteinweg 55
2333 CC Leiden
Office: BE.2.01
e-mail: j (dot) k (dot) vis (at) liacs (dot) leidenuniv (dot) nl
phone: +31 (0) 71 527 7062

Curriculum Vitae

LIACS, Leiden University

Assistant professor — September 2025–now

Dept. of Human Genetics, LUMC

(Senior) Researcher — October 2018–September 2025

Dept. of Human Genetics, LUMC

Post-doc — December 2016–October 2018

Dept. of Human Genetics, LUMC

Scientific programmer — October 2015–December 2016

LUMC & LIACS, Leiden University

PhD candidate — September 2011–December 2016
Dissertation: Algorithms for the description of molecular sequences

LIACS, Leiden University

Master Computer Science — September 2009–June 2011
Thesis: Discrete Tomography A Neural Network Approach

LIACS, Leiden University

Bachelor Informatica — September 2006–June 2009
Thesis: Particle Swarm Optimizer for Finding Robust Optima

Hogeschool Rotterdam & Omstreken

Werktuigbouwkunde — September 2002–June 2006

Nederlandsch Genootschap voor Edelsteenkunde

Vakopleiding Edelsteenkunde — June 2000–December 2000

Teaching

Programmeertechnieken

2^nd semester Bachelor Informatica — February 2020–now

Programmeermethoden

1^st semester Bachelor Informatica — September 2020–now

Datastructuren

3^rd semester Bachelor Informatica — September 2018–Februray 2019

Publications

Mark A Santcroos, Walter A Kosters, Mihai Lefter, Jeroen FJ Laros, Jonathan K Vis. A Graph-based Approach to Variant Extraction from Sequences. NAR Genomics and Bioinformatics, 7.4, 2025.

Jonathan K Vis, Mark A Santcroos, Walter A Kosters, and Jeroen FJ Laros. A Boolean algebra for genetic variants. Bioinformatics, 39(1), 2023.

Mihai Lefter, Jonathan K Vis, Martijn Vermaat, Johan T den Dunnen, Peter EM Taschner, and Jeroen FJ Laros. Mutalyzer 2: Next generation HGVS nomenclature checker. Bioinformatics, 37(18):2811–2817, 2021

Jan N van Rijn, Frank W Takes, and Jonathan K Vis. Computing and predicting winning hands in the trick-taking game of Klaverjas. In Proceedings of the 30th Benelux Conference on Artificial Intelligence, pages 106–120, 2018.

Jonathan K Vis, Martijn Vermaat, Peter EM Taschner, Joost N Kok, and Jeroen FJ Laros. An efficient algorithm for the extraction of HGVS variant descriptions from sequences. Bioinformatics, 31(23):3751–3757, 2015.

Jan N van Rijn, Frank W Takes, and Jonathan K Vis. The complexity of Rummikub problems. In Proceedings of the 27th Benelux Conference on Artificial Intelligence, 2015.

Jonathan K Vis and Joost N Kok. Meta-analysis of disjoint sets of attributes in large cohort studies. In Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications: 6th International Symposium, pages 407–419, 2014.

Hendrik Jan Hoogeboom, Walter A Kosters, Jan N van Rijn, and Jonathan K Vis. Acyclic constraint logic and games. ICGA Journal, 37(1):3–16, 2014.

Jan N van Rijn and Jonathan K Vis. Endgame analysis of Dou Shou Qi. ICGA Journal, 37(2):120–124, 2014.

Jan N van Rijn and Jonathan K Vis. Complexity and retrograde analysis of the game Dou Shou Qi. In Proceedings of the 25nd Benelux Conference on Artificial Intelligence, 2013.

Jonathan K Vis, Walter A Kosters, and K Joost Batenburg. Discrete tomography: A neural network approach. In Proceedings of the 23rd Benelux Conference on Artificial Intelligence, pages 328–335, 2011.

Jonathan K Vis, Walter A Kosters, and Antonio Terroba. Tennis patterns: Player, match and beyond. In Proceedings of the 22nd Benelux Conference on Artificial Intelligence, 2010.

Antonio Terroba, Walter A Kosters, and Jonathan K Vis. Tactical analysis modeling through data mining. In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval, pages 176– 181, 2010.