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T. Hohm, E. Zitzler, and R. Simon.
A Dynamic Model for Stem Cell Homeostasis and Patterning in
Arabidopsis Meristems.
PLoS ONE, 5(2):e9189, 2010.
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T. Hohm, E. Zitzler, and R. Simon.
A dynamic model for stem cell homeostasis and patterning in
Arabidopsis meristems.
TIK Report 316, Computer Engineering and Networks Laboratory (TIK), ETH
Zurich, 2009.
under review at PLoS ONE.
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T. Hohm and E. Zitzler.
A Multiobjective Evolutionary Algorithm for Numerical Parameter Space
Characterization of Reaction Diffusion Systems.
In V. Kadirkamanathan et al., editors, International Conference on
Pattern Recognition in Bioinformatics (PRIB 2009), volume 5780 of
LNBI, pages 162–174, Heidelberg, Germany, 2009. Springer.
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T. Hohm and E. Zitzler.
Multicellular Pattern Formation: Parameter Estimation for ODE-based
Gene Regulatory Network Models.
IEEE Eng Med Biol, 28(4):52–57, 2009.
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Overall best paper award at PRIB '07
T. Hohm and E. Zitzler.
Multiobjectivization for parameter estimation: a case-study on the
segment polarity network of drosophila.
In F. Rothlauf et al., editors, GECCO '09: Genetic and Evolutionary
Computation Conference (GECCO 2009), pages 209–216, New York, NY,
USA, 2009. ACM.
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W. Gronwald, T. Hohm, and D. Hoffmann.
Evolutionary Pareto-optimization of stably folding peptides.
BMC Bioinformatics, 9(109), 2008.
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S. Bleuler, P. Zimmermann, M. Friberg,
and E. Zitzler.
Discovering Trends in Gene Expression Data Using a Hybrid Evolutionary
Algorithm.
Algorithmic Operations Research, 3(2), 2008.
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M. Terzer, M. Jovanovic, A. Choutko,
O. Nikolayeva, A. Korn, D. Brockhoff, F. Zürcher, M. Friedmann,
R. Schütz, E. Zitzler, J. Stelling, and S. Panke.
Design of a biological half adder.
IET Synthetic Biology, 1(1–2):53–58, 2007.
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S. Bleuler and E. Zitzler.
Discrimination of Metabolic Flux Profiles Using a Hybrid Evolutionary
Algorithm.
In Genetic and Evolutionary Computation Conference (GECCO 2007),
pages 354–360, 2007.
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(suppl. material)
Best paper award at GECCO '07 in 'Biological Applications Track'
T. Hohm and E. Zitzler.
Modeling the Shoot Apical Meristem in A. thaliana: Parameter
Estimation for Spatial Pattern Formation.
In Elena Marchiori, Jason H. Moore, and Jagath C. Rajapakse, editors,
Evolutionary Computation, Machine Learning and Data Mining in
Bioinformatics (evoBIO 2007), volume 4447 of LNCS, pages
102–113. Springer, 2007.
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D. Schöner, S. Barkow, S. Bleuler,
A. Wille, P. Zimmermann, P. Bühlmann, W. Gruissem, and E. Zitzler.
Network Analysis of Systems Elements.
In S. Baginsky and A. R. Fernie, editors, Plant Systems Biology,
pages 331–351. Birkhäuser, Basel, Switzerland, 2007.
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M. Calonder, S. Bleuler, and
E. Zitzler.
Module Identification from Heterogeneous Biological Data Using
Multiobjective Evolutionary Algorithms.
In T. P. Runarsson et al., editors, Conference on Parallel Problem
Solving from Nature (PPSN IX), volume 4193 of LNCS,
pages 573–582. Springer, 2006.
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S. Barkow, S. Bleuler, A. Prelic,
P. Zimmermann, and E. Zitzler.
BicAT: a Biclustering Analysis Toolbox.
Bioinformatics, 22(10):1282–1283, 2006.
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A. Prelic, S. Bleuler,
P. Zimmermann, A. Wille, P. Bühlmann, W. Gruissem, L. Hennig, L. Thiele,
and E. Zitzler.
A Systematic Comparison and Evaluation of Biclustering Methods for
Gene Expression Data.
Bioinformatics, 22(9):1122–1129, 2006.
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A. Prelic, S. Bleuler,
P. Zimmermann, A. Wille, P. Bühlmann, W. Gruissem, L. Hennig, L. Thiele,
and E. Zitzler.
Comparison of Biclustering Methods: A Systematic Comparison and
Evaluation of Biclustering Methods for Gene Expression Data.
TIK Report 227, Computer Engineering and Networks Laboratory (TIK), ETH Zurich,
February 2006.
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S. Bleuler, P. Zimmermann, M. Friberg,
A. Wille, S. Barkow, D. Brockhoff, D. Schöner, L. Hennig, P. Bühlmann,
W. Gruissem, L. Thiele, and E. Zitzler.
Cluster Analysis of Multiple Time Course Data Sets.
TIK Report 241, Computer Engineering and Networks Laboratory (TIK), ETH Zurich,
2006.
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S. Bleuler and E. Zitzler.
Order Preserving Clustering over Multiple Time Course
Experiments.
In EvoWorkshops 2005, volume 3449 of LNCS, pages
33–43. Springer, 2005.
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A. Wille, P. Zimmermann, E. Vranova,
A. Fürholz, O. Laule, S. Bleuler, L. Hennig, A. Prelic, P. von Rohr,
L. Thiele, E. Zitzler, W. Gruissem, and P. Bühlmann.
Sparse Graphical Gaussian Modeling of the Isoprenoid Gene Network in
Arabidopsis thaliana.
Genome Biol, 5(11):R92, 2004.
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S. Bleuler, A. Prelic, and
E. Zitzler.
An EA Framework for Biclustering of Gene Expression Data.
In Congress on Evolutionary Computation (CEC 2004), pages
166–173, Piscataway, NJ, 2004. IEEE.
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R. Hubley, E. Zitzler, and J. Roach.
Evolutionary algorithms for the selection of single nucleotide
polymorphisms.
BMC Bioinformatics, 4(30), 2003.
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R. Hubley, E. Zitzler, A. Siegel, and
J. Roach.
Multiobjective Genetic Marker Selection.
In Advances in Nature-Inspired Computation: The PPSN VII
Workshops, pages 32–33. University of Reading, UK, September 2002.
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