Leen Stougie
 Full Name
 Prof.dr. L. Stougie
 Function(s)
 Scientific Staff Member
 Leen.Stougie@cwi.nl
 Telephone
 +31 20 592 4381
 Room
 M243
 Department(s)
 Networks and Optimization
Biography
Leen Stougie obtained his PhD in Operations Research at the Erasmus University Rotterdam in 1985. His PhDresearch and a Post Doc year he did at CWI in the Operations Research and Systems Theory group in the period 19801985. In 1986 he joined the department of Econometrics and Operations Research of the University of Amsterdam as assistant professor. From 1997 till 2008 he worked in the Combinatorial Optimisation group of the Department of Mathematics and Computing Science of the Technical University Eindhoven, where he became associate professor. Since end of 2008 he is full professor of Operations Research in the Department of Econometrics and Operations Research at the Vrije Universiteit (VU) Amsterdam. Since Spring 2017 his main occupation became senior researcher and group leader of the Life Sciences and Health group at CWI, keeping a parttime full professorship at the VU. He held several visiting professorships, among others at UC Berkeley, La Sapienza University of Rome, and Technical University of Berlin. Since 2015 he is member of the INRIA European Research Team ERABLE https://team.inria.fr/erable/en/ From 2011 till 2016 he was chairman of the National Network for Mathematics of Operations Research (LNMB) http://www.lnmb.nlResearch
His research interests are mathematics on the interface of operations research, combinatorial optimization and probability theory with applications in life sciences and logistics. Specifically his interest in these fields is on algorithm design and analysis related to complexity theory. A common theme in his research is optimization under uncertainty: stochastic programming, online optimization and more recently optimization under scenarios.
In (stochastic) combinatorial optimization his work is lately concentrating on scheduling.
Since 2004 he is involved in projects on computational biology. From 2005 till 2009 he was Project leader of BSIK/BRICKSproject AFM2 on Computational Life Sciences. Since then computational biology remained an important part of his research and will be a dominant part from now on. In this area his work is concentrated on metabolic network analysis and algorithms for phylogenetic trees and networks. For his bioinformatics research he is teammember of ERABLE (see biography).
He was supervisor of 10 PhDstudents and is currently (co)supervising 4 PhDstudents. He (co)authored over 100 papers in journals, reviewed conference proceedings and books.
Publications

Bernardini, G, van Iersel, L.J.J, Julien, E, & Stougie, L. (2022). Reconstructing phylogenetic networks via cherry picking and machine learning. In Leibniz International Proceedings in Informatics. doi:10.4230/LIPIcs.WABI.2022.16

Bernardini, G, Chen, H, Loukides, G, Pissis, S, Stougie, L, & Sweering, M.J.M. (2022). Making de Bruijn graphs Eulerian. In Leibniz International Proceedings in Informatics, LIPIcs. doi:10.4230/LIPIcs.CPM.2022.12

Olver, N.K, Schalekamp, F, van der Ster, S.L, Stougie, L, & van Zuylen, A. (2022). A duality based 2approximation algorithm for maximum agreement forest. Mathematical Programming. doi:10.1007/s1010702201790y

Bernardini, G, Conte, A., Gourdel, G., Grossi, R, Loukides, G, Pisanti, N, … Sweering, M.J.M. (2022). Hide and mine in strings: Hardness, algorithms, and experiments. IEEE Transactions on Knowledge and Data Engineering. doi:10.1109/TKDE.2022.3158063

Chen, H, Dong, C, Fan, L, Loukides, G, Pissis, S, & Stougie, L. (2021). Differentially Private string sanitization for frequencybased mining tasks. In Proceedings of the 21st IEEE International Conference on Data Mining, ICDM 2021 (pp. 41–50). doi:10.1109/ICDM51629.2021.00014

Wallin, R.A, van Iersel, L.J.J, Kelk, S.M, & Stougie, L. (2021). Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARSCoV2. BMC Ecology and Evolution, 21, 220‐1–220‐14. doi:10.1186/s1286202101946y

Dyer, M, Greenhill, C, Kleer, P.S, Ross, J, & Stougie, L. (2021). Sampling hypergraphs with given degrees. Discrete Mathematics, 344(11). doi:10.1016/j.disc.2021.112566

Mieno, T, Pissis, S, Stougie, L, & Sweering, M.J.M. (2021). String Sanitization Under Edit Distance: Improved and Generalized. In Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching CPM 2021 (pp. 19:1–19:18).

Bernardini, G, Marchetti Spaccamela, A, Pissis, S, Stougie, L, & Sweering, M.J.M. (2021). Constructing strings avoiding forbidden substrings. In Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching CPM 2021 (pp. 9.1–9.18). doi:10.4230/LIPIcs.CPM.2021.9

Jones, M.E.L, Kelk, S.M, & Stougie, L. (2021). Maximum parsimony distance on phylogenetic trees: A linear kernel and constant factor approximation algorithm. Journal of Computer and System Sciences, 117, 165–181. doi:10.1016/j.jcss.2020.10.003
Current projects with external funding

Algorithms for PAngenome Computational Analysis (ALPACA)

Networks

Optimization for and with Machine Learning (OPTIMAL)

Pangenome Graph Algorithms and Data Integration (PANGAIA)
Professional activities
 Member: Management Team of Gravity project Networks
 Organizer: MAPSP 2019, June 2019, Hotel Zeeuwse Stromen, Renesse
 Organizer: The Networks Workshop on Random graphs, counting and sampling, 11 September 2019, CWI, Amsterdam
 Board Member: General Board of the Dutch Network on the Mathematics of Operations Research (Landelijk Netwerk Mathematische Besliskunde (LNMB))
 Editor: AIMS Journal of Industrial and Management Optimization
 Member: Management Team of Gravity project Networks
 Committee member: PhDcommittee Thomas Bosman (VU 2019)
 Committee member: PhDcommittee Annelieke Baller (VU 2019)
 Committee member: PhDcommittee Pieter Kleer (VU 2019)
 Committee member: PhDcommittee Maaike Hoogeboom (VU 2019)
 Committee member: PhDcommittee Teun Janssen (TU Delft 2019)
 Committee member: PhDcommittee Peter van der Gulik (UvA 2019)
Awards
 Harold W. Kuhn Award (2006)