Scientific or entrepreneurial offerings that demand thorough experience with both biological and computational techniques and their applications in the large scale analysis of biomedical databases, processes and networks.
Postdoctoral researcher, July 2005 - February 2008
Technische Universiteit Eindhoven, the Netherlands, Faculty of Biomedical Technology. Funded by the Evolving Cell Signaling Networks project (ESIGNET) of the Sixth Framework, the European Community Framework Programme for Research, Technological Development and Demonstration.
PhD student, October 2000 - July 2005 (Doctor in Biomedical Technology)
Licentiaat Informatica, 2000 (Master in Computer Science)
Vrije Universiteit Brussel, Belgium, Faculty of Sciences, Department of Mathematics and Computer Science. With extracurricular credits for (theoretical) Biology courses, Universiteit Antwerpen, Belgium, Faculty of Sciences, Department of Biology.
Kandidaat Informatica, 1998 (Bachelor in Computer Science)
Currently I am working on the integration of biomedical databases, text and data mining in the biomedical domain, with specific applications toward psychiatric genetics and the discovery of disease-causing genes in relation to next generation full genome sequencing.
My research interests also include bioinformatics; transcriptomics and metabolomics, data mining algorithms, parallel computing; computation, connectionism and complexity in intracellular biochemical processes; mathematical models of population dynamics; evolutionary game theory; genetic algorithms and other techniques for combinatorial optimisation.
A recent interest is the study of entrepreneurship, for which I have followed the VIB course on Entrepreneurship in Life Sciences (2011), the Interreg IV A Master Class High-Tech Entrepreneurship (2012) and am member of the VOKA (Flemish chamber of commerce) Bryo project (2011-2013).
Exhaustive computing experience, with a main focus toward research and development of biomedical applications in UNIX environments (currently Mac OS X). Experience with many programming languages (including, but not restricted to C++, Ruby, Java, C, UNIX shell scripting, PHP, Python) and quick learner of new languages. Extensive experience with data mining algorithms, optimisation techniques, mathematical computing and parallel computing (MPI, Beowulf clusters) mainly in applications inspired by biology.
During my off-time, I work on various computer related and scientifically inspired projects. I am an enthusiast of astronomy; the pictures of Titan on my web site have been widely reported on in highly respected media (Nature, New Scientist, Discovery Channel, Der Spiegel, The London Times, ...). I finished a four-year course in French cuisine in the summer of 2007. I have built my own electric vehicle and want to build my own garage laboratory for DIY biochemical research.
Besides my research, I am given the opportunity to work together with students on courses, internships and master theses. I helped out with various computer related courses (introductory Java, genetic algorithms, combinatorial optimisation, neural networks) for biology students and mentored group projects on the processing and analysis through clustering techniques of mRNA micro-array data (transcriptomics). I have (directly and indirectly) advised internships and master theses in neural networks, Markov chain analyses, genetic algorithms, evolutionary game theory, parallel implementations, bioinformatics, -omics, and others.
M.J. Van Den Bossche, M. Strazisar, S. Cammaerts, A.M. Liekens, G. Vandeweyer, V. Depreeuw, M. Mattheijssens, A.-S. Lenaerts, S. De Zutter, P. De Rijk, B. Sabbe, J. Del-Favero, Identiﬁcation of Rare Copy Number Variants in High Burden Schizophrenia Families, American Journal of Medical Genetics Part B, 162B, 273-282, 2013 10.1002/ajmg.b.32146
J. Reumers, P. De Rijk, H. Zhao, A. Liekens, D. Smeets, J. Cleary, P. Van Loo, M. Van Den Bossche, K. Catthoor, B. Sabbe, E. Despierre, I. Vergote, B. Hilbush, D. Lambrechts, J. Del-Favero, Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing, Nature Biotechnology, 30, 61–68, 2012 DOI: 10.1038/nbt.2053
J. De Knijf, A.M.L. Liekens, W. Daelemans, B. Goethals, P. De Rijk, J. Del-Favero, BioGraph: Knowledge Discovery and Exploration in the Biomedical domain, Demo at the 2011 IEEE International Conference on Data Mining (ICDM 2011), 2011
A.M.L. Liekens, J. De Knijf, W. Daelemans, B. Goethals, P. De Rijk, J. Del-Favero, BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation, Proceedings of the 6th BeNeLux Bioinformatics Conference (BBC11), 2011
J. De Knijf, A.M.L. Liekens, and B. Goethals, GaMuSo: Graph based Music recommendation in a Social bookmarking service., Proceedings of the 10th International Symposium on Intelligent Data Analysis (IDA 2011), 2011.
J. De Knijf, A.M.L. Liekens, and B. Goethals, "Tell me more": Finding Related Items from User Provided Feedback., Proceedings of the Fourteenth International Conference on Discovery Science (DS 2011), 2011.
A.M.L. Liekens, J. De Knijf J, W. Daelemans, B. Goethals, P. De Rijk, J. Del-Favero J, BioGraph: Unsupervised Biomedical Knowledge Discovery via Automated Hypothesis Generation, Genome Biology 12:R57, 2011 DOI: 10.1186/gb-2011-12-6-r57
S. Ceulemans, K. van der Ven, S. De Zutter, A.-S. Lenaerts, K.-F.Norrback, A. Nordin, P. De Rijk, R. Adolfsson, A.M.L. Liekens, J. Del-Favero, Genetic analysis of PRL in an isolated northern Swedish schizophrenia sample, XVIIIth World Congress on Psychiatric Genetics, abstract in refereed conference proceedings, 2010
A.M.L. Liekens, J. De Knijf J, W. Daelemans, B. Goethals, P. De Rijk, J. Del-Favero J, BioGraph: discovering biomedical relations by unsupervised hypothesis generation, European Conference on Computational Biology (ECCB10), abstract in refereed conference proceedings, 2010
M.N. Steijaert, A.M.L. Liekens, D. Bosnacki, P.A.J. Hilbers, H.M.M. ten Eikelder, Single-variable Reaction Systems: Deterministic and Stochastic Models, Mathematical Biosciences, 2010 DOI:10.1016/j.mbs.2010.06.006
M.N. Steijaert, J.H.K. Van Dan Brink, A.M.L. Liekens, P.A.J. Hilbers, and H.M.M. Ten Eikelder, Computing the Stochastic Dynamics of Phosphorylation Networks, Journal of Computational Biology, Vol 17 Issue 2, 2010 DOI:10.1089/cmb.2009.0059
C.T. Fernando, A.M.L. Liekens, L.E.H. Bingle, C. Beck, T. Lenser, D.J. Stekel, J.E. Rowe, Molecular Circuits for Associative Learning in Single-Celled Organisms, Journal of the Royal Society Interface, Vol 6 Issue 34:463-9, 2009 DOI:10.1098/rsif.2008.0344
H.J. Buisman, H.M.M. ten Eikelder, P.A.J. Hilbers, A.M.L. Liekens, Computing Algebraic Functions with Biochemical reaction Networks, Artificial Life Journal (Special Issue on Artificial Chemistries), Vol 15 Issue 1, 2009 DOI:10.1162/artl.2009.15.1.15101
R. Morante, A.M.L. Liekens, W. Daelemans, Learning the Scope of Negation in Biomedical Texts, in Proceedings of the Conference on Empirical Methods in Natural Language Processing, Hawaii, USA, refereed conference proceedings, 2008
A.M.L. Liekens, H.M.M. Ten Eikelder, M.N. Steijaert, P.A.J. Hilbers, Artiﬁcial Evolution of Mass Conserving Reaction Networks, in Artificial Life XI, Southampton, United Kingdom, refereed conference proceedings, 2008
M.N. Steijaert, A.M.L. Liekens, H.M.M. Ten Eikelder, P.A.J. Hilbers, Multiple Functionalities of Biochemical Reaction Networks, in Artificial Life XI, Southampton, United Kingdom, refereed conference proceedings, 2008
M.N. Steijaert, H.M.M. ten Eikelder, A.M.L. Liekens, D. Bosnacki, P.A.J. Hilbers, Stochastic Switching Behavior of a Bistable Auto-phosphorylation Network, 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), 2008
H.M.M. ten Eikelder, S.P.M. Crijns, M.N. Steijaert, A.M.L. Liekens, P.A.J. Hilbers, Computing with Feedforward Networks of Artificial Biochemical Neurons, 2nd International Workshop on Natural Computation (IWNC 2007), 2007
A.M.L. Liekens, C.T. Fernando, Turing Complete Catalytic Particle Computers, European Conference on Artificial Life (ECAL 2007), 2007
A.M.L. Liekens, Evolution of Finite Populations in Dynamic Environments, Ph D thesis, Technische Universiteit Eindhoven, 2005
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Genetic Drift in 2x2 Games, in 2004 Genetic and Evolutionary Computation COnference (GECCO 2004); Seattle, WA, United States, refereed conference proceedings, 2004
A.M.L. Liekens, Artificial Life, in Encyclopaedia of Computer Science, Concise Edition; Editors: Anthony Ralston, Edwin D. Reilly and David Hemmendinger; John Wiley and Sons, reprint of book chapter, 2004
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Finite Population Models of Dynamic Optimisation with Stochastically Alternating Fitness Functions, in 2003 Congress of Evolutionary Computation (CEC 2003); Editors: B. McKay, H. Abbass; Canberra, Australia, refereed conference proceedings, 2003
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, A Finite Population Model Analysis of Co-Evolution with Matching Pennies, in Fifth International Workshop on Frontiers in Evolutionary Algorithms (FEA 2003); P.P. Wang; Cary, North Carolina, United States, pages 199-203, refereed conference proceedings, 2003
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Finite Population Models of Co-Evolution and their Application to Haploidy versus Diploidy (nominated for best paper at GECCO award), in 2003 Genetic and Evolutionary Computation COnference (GECCO 2003); E. Cantu-Paz; Chicago, IL, United States, pages 344-355, refereed conference proceedings, 2003
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Finite Population Models of Dynamic Optimisation with Alternating Fitness Functions, in Workshop on Evolutionary Algorithms for Dynamic Optimisation Problems, 2003 Genetic and Evolutionary Computation COnference (GECCO 2003); E. Cantu-Paz; Chicago, IL, United States, pages 113-117, refereed conference proceedings, 2003
A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Modeling and Simulating Diploid Simple Genetic Algorithms, in FOundations of Genetic Algorithms VII (FOGA VII); Editors: K.A. Dejong, R. Poli, J.E. Rowe; Malaga, Spain, pages 151-167, refereed conference proceedings, 2003
A.M.L. Liekens, Artificial Life, in Computer Graphics Companion; Editors: Jeffrey J. McConnell, Anthony Ralston, Edwin D. Reilly, David Hemmendinger; Nature publishing group, ISBN 0 333 997859, reprint of book chapter, 2002
A.M.L. Liekens, Open Source Business Models, in Xootic Magazine, volume 10, number 1, pages 11-14, magazine article, 2002
H.M.M. ten Eikelder, A.M.L. Liekens, First Order Parallel Shop Scheduling Problems, internal report for the Metaheuristics Network, 2001
A.M.L. Liekens, From Individuals to Populations, Approaches to the Study of Biological Emergent Phenomena, in Artificial Life VII; Editors: Mark A. Bedau, John S. McCaskill, Norman H. Packard, Steen Rasmussen; Portland, OR, United States, refereed conference proceedings, 2000
A.M.L. Liekens, Artificial Life, in Encyclopaedia of Computer Science, Fourth Edition; Editors: Anthony Ralston, Edwin D. Reilly and David Hemmendinger; Nature publishing group, ISBN 0 333 77879 0, book chapter, 2000