Publications
- Chemogenomics: Looking at biology through the lens of chemistry - Statistical Analysis and Data Mining, 2010
link - Predicting the functions of proteins in PPI networks from global information, Journal of Machine Learning Research, 2010
(in press) - Mining protein dynamics from Sets of crystal structures using Consensus Structures, Protein Science 2010
link - Adaptive Niche-Radii and Niche-Shapes Approaches for Niching with the CMA-ES - Evolutionary Computation, 2010
link - J. Kruisselbrink, A. Aleman, M. Emmerich, A. IJzerman, A. Bender, Th. Baeck, E.v.d. Horst. Enhancing search space diversity in multiobjective evolutionary drug molecule design using niching. Int. ACM Conf. GECCO 2009: 217-224
- J. Kruisselbrink, M. Emmerich, Th. Baeck, A. Bender, A. IJzerman, E. v.d. Horst. Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design, In: M. Ehrgott et al.: Evolutionary Multicriterion Optimization, LNCS 5467, Springer 2009, 453-467
- Michael T. M. Emmerich, Johannes W. Kruisselbrink, Eelke van der Horst, Ad P. IJzerman, Andreas Bender and Thomas Baeck. Combined Interactive and Automated Adaptive Search for Molecular Design. Proceedings of Adaptive Computing in Design and Manufacture 2008 (ACDM08) - extended abstract PDF poster PDF
- Johannes W. Kruisselbrink, Thomas Baeck, Ad P. IJzerman and Eelke van der Horst. Evolutionary Algorithms for automated drug design towards target molecule properties. GECCO 2008, Atlanta, GA (in print).
- Thomas J. Crisman et al. "Virtual Fragment Linking": An Approach To Identify Potent Binders from Low Affinity Fragment Hits.J. Med. Chem. 2008 (in press) DOI: 10.1021/jm701314u
- D. W. Young et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chem. Biol. 2008 (4)59 – 68. DOI: 10.1038/nchembio.2007.53
- Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints. A. Bender et al. Comb. Chem. High-Throughput Screen. 2007 (10) 719 - 731. DOI: 10.2174/138620707782507313
- G. Sand, S. Engell, M. Emmerich, M. Urselmann, and J. Till: Engineered vs. Standard Evolutionary Algorithms: A Case Study in Batch Scheduling with Recourse, Computers & Chemical Engineering, Enterprise-Wide Optimization special issue (2007), preprint. DOI: 10.1016/j.compchemeng.2007.09.006
- Ron Breukelaer, Michael Emmerich, and Thomas Back. On interactive evolution strategies. In Applications of Evolutionary Computing EvoWorkshops 2006: EvoINTERACTION, volume 3907 of Lecture Notes in Computer Science, pages 530-541, Budapest, Hungary, April 2006. Springer Berlin / Heidelberg. DOI: 10.1007/11732242_51
- Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, and Adriaan P. IJzerman. The molecule evoluator. an interactive evolutionary algorithm for the design of drug-like molecules. Journal of Chemical Information and Modeling, 46(2):545-552, 2006. DOI: 10.1021/ci050369d.
- Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, and Adriaan P. IJzerman. Mining a chemical database for fragment co-occurrence: Discovery of chemical clichés. Journal of Chemical Information and Modeling, 46(2):553-562, 2006.DOI: 10.1021/ci050370c