Curriculum Vitae

Objective

Post-doc position or assistant professorship, where the profile demands thorough experience with mathematical and computational techniques for the large scale analysis of biological 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

Courses in theoretical computer science, computational modelling, adaptive systems, dynamical systems, machine learning, artificial intelligence and distributed systems
Master thesis From individuals to populations; Computational approaches for the study of emergent biological behaviour in population ecology under supervision of professors B. Manderick, L. Steels and A. Nowe. As a result, I published my first conference proceedings paper with the same title.

Extracurricular credits for (theoretical) Biology courses, 2000

Universiteit Antwerpen, Belgium, Faculty of Sciences, Department of Biology

Course list: Ecology, evolutionary biology, behavioural ecology, genetics, population ecology

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 interested in computation, connectionism and complexity in intracellular biochemical processes. I am especially interested in signalling networks of phosphorylation cycles which serve as a cell's behavioural circuitry to interpret and process real time information. My research interests also include mathematical models of population dynamics, evolutionary game theory, genetic algorithms and other techniques for combinatorial optimisation, bioinformatics; transcriptomics and metabolomics, data mining algorithms, parallel computing.

Computers

Fifteen years of experience with computers, with main focus toward research and development in UNIX environments (currently Mac OS X). Experience with many programming languages (including, but not restricted to C++, Java, C, UNIX shell scripting, PHP, Ruby, Python) and quick learner of new languages. Extensive experience with optimisation techniques, mathematical computing, parallel computing (MPI, Beowulf clusters) and data mining algorithms, mainly in applications inspired by biology. Experienced user of Matlab and familiar with Mathematica. Familiar with SQL databases. LaTeX, gnuplot, xfig are used as daily tools.

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 will finish a four-year course in French cuisine in the summer of 2007.

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

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
M.N. Steijaert, A.M.L. Liekens, H.M.M. ten Eikelder, P.A.J. Hilbers, Multiple Functionalities of Biochemical reaction Networks, Computational Methods in Systems Biology (CMSB 2007), 2007
A.M.L. Liekens, C.T. Fernando, Turing Complete Catalytic Particle Computers, European Conference on Artificial Life (ECAL 2007), 2007
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, 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