Description
Leader of the group Life Sciences and Health: Leen Stougie.
The CWI Life Sciences and Health (LSH) group is a group of computer scientists and mathematicians whose research focus is on the analysis and design of models and algorithms as well as their direct application to important challenges in the LSH domain.
On the application side, our present team of researchers has expertise in, e.g., computational genomics, medical informatics, computational phylogenetics, and biological network analysis. On the methodological side, we come from different backgrounds, e.g., computational intelligence, computational data science, and operations research. Methodologically, we develop new theories, models, algorithms and decision support tools, for problems that arise mostly in collaboration with experimental biologists and medical experts. We actively collaborate in projects with academic hospitals, biological and biochemical research institutes, and industry. Click here for more information about our group structure.
The LSH group participates in the INRIA International team ERABLE.
Seminars: The LSH group organizes a biweekly seminar.
Watch our group video to get a glimpse of our activities.
Vacancies
PhD students on innovating model-based evolutionary algorithms from algorithmic foundations to medical applications
Centrum Wiskunde & Informatica (CWI, the Dutch national research institute for mathematics and computer science) located in Amsterdam, and the Leiden University Medical Centre (LUMC) together have 10 vacancies for fully funded PhD students, on innovating model-based evolutionary algorithms from algorithmic foundations to medical applications.
News
Alexander Schoenhuth appointed Professor Genome Data Science
Starting 1 October 2017, Alexander Schoenhuth of Centrum Wiskunde & Informatica (CWI) in Amsterdam is appointed Professor ‘Genome Data Science’ at the Faculty of Science of Utrecht University. It concerns a part-time appointment for one day a week.
CWI PhD student Jasmijn Baaijens wins Best Talk Award at the ISMB-HitSeq conference
Jasmijn Baaijens, PhD student from CWI’s Life Sciences and Health group, has won the Best Talk Award at ISMB-HitSeq, the world's leading conference on high-throughput genomics.
Instable blood supply may help healthy cells compete with tumor cells
Researchers of CWI’s Scientific Computing group have found that instabilities in the blood supply in cancerous tissue can, surprisingly, lead to a less favorable environment for tumor cells. Their findings shed light on the potential negative side effects of current treatments that aim to actually normalize the blood supply in cancerous tissues.
Comparing medical images better
Together with the radiation oncology department of AMC, Peter Bosman of CWI’s Life Sciences and Health group has been awarded 1.4 million euros for a project in NWO’s Open Technology Programme for the research and development of a new medical image registration method. This project is co-funded by companies Elekta and Xomnia.
Members
Associated Members
Publications
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van den Broek d'Obrenan, A, Ridder, A, Roubos, D, & Stougie, L. (2020). Minimizing bed occupancy variance by scheduling patients under uncertainty. European Journal of Operational Research, 286(1).
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Lähnemann, D, Köster, J, Szczurek, E, McCarthy, D.J, Hicks, S.C, Robinson, M.D, … Schönhuth, A. (2020). Eleven grand challenges in single-cell data science. Genome Biology, 21. doi:10.1186/s13059-020-1926-6
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Pusa, T, Galvão Ferrarini, M, Andrade, R, Mary, A, Marchetti Spaccamela, A, Stougie, L, & Sagot, M.-F. (2020). MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network. Bioinformatics, 36(2), 514–523. doi:10.1093/bioinformatics/btz584
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Bernardini, G, Chen, H, Fici, G, Loukides, G, & Pissis, S. (2020). Reverse-safe data structures for text indexing. In Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 199–213).
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Maree, S.C, Bosman, P.A.N, van Wieringen, N, Niatsetski, Y, Pieters, B.R, Bel, A, & Alderliesten, T. (2020). Automatic bi-objective parameter tuning for inverse planning of high-dose-rate prostate brachytherapy. Physics in Medicine and Biology, 65(7). doi:10.1088/1361-6560/ab7362
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Baaijens, J.A, Stougie, L, & Schönhuth, A. (2020). Strain-aware assembly of genomes from mixed samples using flow variation graphs. In Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence. doi:10.1007/978-3-030-45257-5_14
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Nersisyan, L, Nikoghosyan, M, Arakelyan, A, Francioli, L.C, Menelaou, A. (Androniki), Pulit, S.L. (Sara L.), … The Genome of the Netherlands Consortium, . (2019). WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene. Nature Scientific Reports, 9(1). doi:10.1038/s41598-019-55109-7
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Bosman, T. (2019, November 26). Relax, Round, Reformulate: Near-Optimal Algorithms for Planning Problems in Network Design and Scheduling.
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Luong, N.H, Alderliesten, T, Pieters, B.R, Bel, A, Niatsetski, Y, & Bosman, P.A.N. (2019). Fast and insightful bi-objective optimization for prostate cancer treatment planning with high-dose-rate brachytherapy. Applied Soft Computing, 84. doi:10.1016/j.asoc.2019.105681
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Baller, A.C, van Ee, M, Hoogeboom, M, & Stougie, L. (2019). Complexity of inventory routing problems when routing is easy. Networks. doi:10.1002/net.21908
Software
VirtualLeaf: a modeling framework for plant tissue morphogenesis
VirtualLeaf is a computer modeling framework for the simulation of plant tissue morphogenesis, i.e., the biological development of an organism's shape
Current projects with external funding
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Improving Childhood Cancer Care when Parents Cannot be There - Reducing Medical Traumatic Stress in Childhood Cancer Patients by Bonding with a Robot Companion ()
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Enhancing protein-drug binding prediction
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ICT based Innovations in the Battle against Cancer – Next - Generation Patient -Tailored Brachytherapy Cancer Treatment Planning
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Statistical Models for Structural Genetic Variants in the Genome of the Netherlands
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Algorithms for PAngenome Computational Analysis (ALPACA)
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Fast, accurate, and insightful brachytherapy treatment planning for cervical cancer through artificial intelligence (Brachytherapy treatment)
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Evolutionary eXplainable Artificial Medical INtelligence Engine (EXAMINE)
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Fusible Evolutionary Deep Neural Network Mixture Learning from Distributed Data for Robust Medical Image Analysis (FEDMix)
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Multi-Objective Deformable Image Registration (MODIR) – An Innovative Synergy of Multi-Objective Optimization, Machine Learning, and Biomechanical Modeling for the Registration of Medical Images with (MODIR)
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Networks
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Optimization for and with Machine Learning (OPTIMAL)
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Pan-genome Graph Algorithms and Data Integration (PANGAIA)
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Transparent, Reliable and Unbiased Smart Tool for AI (TRUST-AI)
Related partners
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AMC Medical Research
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CNRS
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Elekta Limited
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European Molecular Biology Laboratory
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INRIA
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Nucletron Operations BV
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Universita di Pisa
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Xomnia
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Academisch Medisch Centrum
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Biomedical Imaging Group Rotterdam
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Erasmus Universiteit Rotterdam
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Geneton S.R.O.
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Heinrich-Heine-Universitaet Dusseldorf
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Illumina Cambridge
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Institut Pasteur
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Leids Universitair Mediach Centrum
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Technische Universiteit Delft
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Univerzita Komenskeho V Bratislave
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Universiteit Leiden
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Universitaet Bielefeld
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Universita' Degli Studi di Milano-Bicocca
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Universiteit van Tilburg