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Systems Optimization (SOP)

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ETH Zürich - D-ITET - TIK - Publications
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Publications - Biological Networks

[1 — hzs2010a]
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. (PDF) (doi) (bibtex)
[2 — hzs2009b]
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. (PDF) (bibtex)
[3 — hz2009b]
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. (PDF) (doi) (bibtex) (online access)
[4 — hz2009c]
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. (PDF) (bibtex) (suppl. material) Overall best paper award at PRIB '07
[5 — hz2009a]
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. (PDF) (doi) (bibtex)
[6 — ghh2008a]
W. Gronwald, T. Hohm, and D. Hoffmann. Evolutionary Pareto-optimization of stably folding peptides. BMC Bioinformatics, 9(109), 2008. (PDF) (doi) (bibtex)
[7 — bzfz2008a]
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. (bibtex)
[8 — bleu2007a]
S. Bleuler. Search Heuristics for Module Identification from Biological High-Throughput Data. PhD thesis, ETH Zurich, Switzerland, 2007. (PDF) (bibtex) (online access)
[9 — tjcn2007a]
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. (PDF) (bibtex) (online access)
[10 — bz2007b]
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. (PDF) (bibtex) (suppl. material) Best paper award at GECCO '07 in 'Biological Applications Track'
[11 — hz2007a]
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. (PDF) (doi) (bibtex)
[12 — sbbw2007a]
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. (bibtex) (online access)
[13 — cbz2006a]
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. (PDF) (bibtex) (online access) (suppl. material)
[14 — bbpz2006a]
S. Barkow, S. Bleuler, A. Prelic, P. Zimmermann, and E. Zitzler. BicAT: a Biclustering Analysis Toolbox. Bioinformatics, 22(10):1282–1283, 2006. (bibtex) (online access) (suppl. material)
[15 — pbzw2006a]
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. (bibtex) (online access) (suppl. material)
[16 — pbzw2006b]
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. (PDF) (bibtex)
[17 — bzfw2006a]
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. (bibtex)
[18 — bz2005a]
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. (PDF) (bibtex) (online access)
[19 — wzvf2004a]
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. (PDF) (bibtex) (online access)
[20 — bpz2004a]
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. (PDF) (bibtex)
[21 — hzr2003a]
R. Hubley, E. Zitzler, and J. Roach. Evolutionary algorithms for the selection of single nucleotide polymorphisms. BMC Bioinformatics, 4(30), 2003. (bibtex) (online access)
[22 — hzsr2002a]
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. (PDF) (bibtex)
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