Curriculum Vitae

Objective

Research 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.

Personalia

dr. Anthony (Mariette Louis) Liekens

Manebruggestraat 366
B-2150 Borsbeek
Belgium
+32 32 95 50 53

anthony@liekens.net
http://anthony.liekens.net

Born December 12, 1975 in Sint-Niklaas, Belgium. Married to Els de Ketelaere, father of Staf and Louis.

Education and Professional Experience

Postdoctoral researcher, March 2008 - current

Universiteit Antwerpen, Belgium, Applied Molecular Genomics, Molecular Genetics Department of the Flanders Institute for Biotechnology. Funded by the BioGraph GOA project on Biomedical Text and Data Mining.

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

Technische Universiteit Eindhoven, the Netherlands, Faculty of Biomedical Technology under supervision of professor P.A.J. Hilbers.

Defended my thesis Evolution of Finite Populations in Dynamic Environments on July, 5 2005.

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)

Universiteit Antwerpen, Belgium, Faculty of Sciences, Department of Mathematics and Computer Science

Interests

Subjects of interest

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;.

Computers

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.

Miscellaneous

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.

Teaching activities

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.

Publications

1. 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, accepted (to appear), 2010
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. A.M.L. Liekens, C.T. Fernando, Turing Complete Catalytic Particle Computers, European Conference on Artificial Life (ECAL 2007), 2007
11. A.M.L. Liekens, Evolution of Finite Populations in Dynamic Environments, Ph D thesis, Technische Universiteit Eindhoven, 2005
12. 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
13. 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
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. A.M.L. Liekens, Open Source Business Models, in Xootic Magazine, volume 10, number 1, pages 11-14, magazine article, 2002
21. H.M.M. ten Eikelder, A.M.L. Liekens, First Order Parallel Shop Scheduling Problems, internal report for the Metaheuristics Network, 2001
22. 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
23. 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