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Publications

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Preprints

Reimers AC, Reimers AM, Goldstein Y: Minimal equivalent subgraphs containing a given set of arcs. Matheon Preprint #1053, Mar 2014.


Articles, Book Chapters

2016

Reimers A-M, Reimers AC: The steady-state assumption in oscillating and growing systems. Journal of Theoretical Biology, 406, 176-186, Oct 2016.

2015

Klarner H, Bockmayr A, Siebert H: Computing maximal and minimal trap spaces of Boolean networks. Natural Computing, 14(4): 535-544, Dec 2015.

Streck A, Lorenz T, Siebert H: Minimization and equivalence in multi-valued logical models of regulatory networks. Natural Computing, 14(4): 555-566, Dec 2015.

Rügen M, Bockmayr A, Steuer R: Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA. Scientific Reports, 5:15247, Oct 2015.

Reimers AC, Bruggeman FJ, Olivier BG, Stougie L: Fast Flux Module Detection Using Matroid Theory. Journal of Computational Biology, 22(5): 414-424, May 2015.

Reimers AC, Goldstein Y, Bockmayr A: Generic Flux Coupling Analysis. Mathematical Biosciences, 262, 28-35, Apr 2015.

Röhl A, Goldstein Y, Bockmayr A: EFM-Recorder - Faster Elementary Mode Enumeration via Reaction Coupling Order. Strasbourg Spring School on Advances in Systems and Synthetic Biology, Strasbourg, 91-100, Mar 2015.

Palinkas A, Bulik S, Bockmayr A, Holzhütter HG: Sequential Metabolic Phases as a Means to Optimize Cellular Output in a Constant Environment. PLoS ONE, 10(3): e0118347, Mar 2015.

Waldherr S, Oyarzún DA, Bockmayr A: Dynamic optimization of metabolic networks coupled with gene expression. Journal of Theoretical Biology, 365, 469-485, Jan 2015 (arXiv).

Goldstein Y, Bockmayr A: Double and Multiple Knockout Simulations for Genome-Scale Metabolic Network Reconstructions. Algorithms for Molecular Biology, 10:1, Jan 2015.

2014

David L, Bockmayr A: Computing elementary flux modes involving a set of target reactions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11/6, 1099-1107, Nov/Dec 2014.

Müller AC, Bockmayr A: Flux Modules in Metabolic Networks. Journal of Mathematical Biology, 69/5, 1151-1179, Nov 2014.

Klarner H, Bockmayr A, Siebert H: Computing Symbolic Steady States of Boolean Networks. Cellular Automata, ACRI 2014, Krakow, Poland, Springer, LNCS 8751, 561-570, Sep 2014.

Müller AC, Bruggeman FJ, Olivier BG, Stougie L: Fast Flux Module Detection Using Matroid Theory Research in Computational Molecular Biology, RECOMB 2014, Springer, LNCS 8394, 192-206, 2014.

Bockmayr A, Siebert H, Röblitz S, Schütte Ch, Deuflhard P: Advanced mathematical modeling in systems biology. MATHEON-Mathematics for Key Technologies, 29-44, European Mathematical Society, 2014.

2013

Goldstein Y, Bockmayr A: A Lattice-Theoretic Framework for Metabolic Pathway Analysis. Computational Methods in Systems Biology, CMSB 2013, Klosterneuburg. Springer, LNBI 8130, 178-191, Sep 2013.

David L, Bockmayr A: Constrained Flux Coupling Analysis. Workshop on Constraint Based Methods for Bioinformatics, WCB'13, Uppsala, 75-83, Sep 2013.

Jamshidi S, Siebert H, Bockmayr A: Preservation of Dynamic Properties in Qualitative Modeling Frameworks for Gene Regulatory Networks. Biosystems, 112/2, 171-179, 2013.

Lorenz, Therese and Siebert, Heike and Bockmayr, Alexander: Analysis and characterization of asynchronous state transition graphs using extremal states. Bulletin of Mathematical Biology, 75/6, 920-938, 2013

Bockmayr A, Siebert H: Bio-Logics: Logical Analysis of Bioregulatory Networks. Programming Logics. Essays in Memory of Harald Ganzinger. Springer, LNCS 7797, 19-34, 2013.

Müller AC, Bockmayr A: Fast Thermodynamically Constrained Flux Variability Analysis. Bioinformatics, 29/7, 903-909, 2013.

2012

Hannes Klarner, Adam Streck, David Safránek, Juraj Kolcák, Heike Siebert: Parameter Identification and Model Ranking of Thomas Networks. CMSB 2012, 207-226, 2012.

Jamshidi, Shahrad and Siebert, Heike and Bockmayr, Alexander: Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks. Information Processing in Cells and Tissues, IPCAT 2012, Cambridge, UK. Springer, LNCS 7223, 17-24, 2012.

Marashi SA, David L, Bockmayr A: Analysis of Metabolic Subnetworks by Flux Cone Projection. Algorithms for Molecular Biology, 7:17, 29 May 2012.

Klarner, Hannes and Siebert, Heike and Bockmayr, Alexander: Time Series Dependent Analysis of Unparametrized Thomas Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9/5, 1338-1351, 2012

Larhlimi A, David L, Selbig J, Bockmayr A: F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. BMC Bioinformatics 13:57, 23 April 2012.

Marashi SA, David L and Bockmayr A: On flux coupling analysis of metabolic subsystems. J. Theoretical Biology, 302, 62-69, 2012.

Rügen M, Bockmayr A, Legrand J, and Cogne G: Network reduction in metabolic pathway analysis: Elucidation of the key pathways involved in the photoautotrophic growth of the green alga Chlamydomonas reinhardtii. Metabolic Engineering, 14, 458-467, 2012.

2011

Siebert, Heike: Analysis of discrete bioregulatory networks using symbolic steady states. Bull. Math. Biol., 73 (4): 873-898, 2011.

David, Laszlo and Marashi, Sayed-Amir and Larhlimi, Abdelhalim and Mieth, Bettina and Bockmayr Alexander:  FFCA: a feasibility-based method for flux coupling analysis of metabolic networks. BMC Bioinformatics 12:236, 2011.

Cogne G, Rügen M, Bockmayr A, Titica M, Dussap CG, Cornet JF and Legrand J: A model- based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: Application to the green algae Chlamydomonas reinhardtii. Biotechnology Progress, 27/3, 631-40, 2011.

Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A, and Planes FJ: Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics, 27/4, 534-540, 2011.

Marashi, Sayed-Amir and Bockmayr, Alexander: Flux coupling analysis of metabolic networks is sensitive to missing reactions. BioSystems,103, 57-66, 2011.

Klarner, Hannes and Siebert, Heike and Bockmayr, Alexander: Parameter Inference for Ansynchronous Logical Networks Using Discrete Times Series. Computational Methods in Systems Biology, CMSB 2011, Paris. ACM Digital Library, 2011.

Palinkas, Aljoscha and Bockmayr, Alexander: Petri Nets for Integrated Models of Metabolic and Gene Regulatory Networks. Workshop on Constraint based Methods for Bioinformatics, WCB'11, WCB'11, Perugia, 45-57, 2011.

2010

Twardziok, Sven and Siebert, Heike and Heyl, Alexander: Stochasticity in reactions: A probabilistic Boolean modeling approach. Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB'10, Trento, Italy, ACM, NY, USA, pages 76-85, 2010.

Cogne G, Rügen M, Bockmayr A, Titica M, Dussap CG and Legrand J: Constraint-Based Modelling of Chlamydomonas Reinhardtii Photoautotrophic Metabolism. Computer Applications in Biotechnology, CAB'10, Leuven 2010

Heldt, Corinna and Bockmayr, Alexander: Geometric Constraints for the Phase Problem in X-Ray Crystallography. WCB'10 - Workshop on Constraint Based Methods for Bioinformatics associated to FLOC 2010, Edinburgh, 2010.

2009

Larhlimi, Abdelhalim and Bockmayr, Alexander:  A new constraint-based description of the steady-state flux cone of metabolic networks. Discrete Applied Mathematics, 157, 2257-2266, 2009.

Siebert, Heike: Dynamical and structural modularity of discrete regulatory networks. Computational Models for Cell Processes, CompMod 2009, Eindhoven, Netherlands, volume 6 of EPTCS, pages 109-124, 2009.

Siebert, Heike:  Deriving behavior of Boolean bioregulatory networks from subnetwork dynamics. Math. Comput. Sci., 2(3):421-442, 2009.

2008

Larhlimi, Abdelhalim and Bockmayr, Alexander: On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network.. Computational Methods in Systems Biology, CMSB 2008, Rostock. Springer, LNBI 5307, 308-327, 2008.

Siebert, Heike and Bockmayr, Alexander: Temporal Constraints in the Logical Analysis of Regulatory Networks.  Theoretical Computer Science, 391/3, 258-275, 2008.

Siebert, Heike: Local Structure and Behavior of Boolean Bioregulatory Networks. Algebraic Biology, AB 2008, Castle of Hagenberg, Austria, volume 5147 of LNCS, pages 185-199, Springer, 2008.

Brinkmann, Corinna and Bockmayr, Alexander: A Constraint-based Approach to the Phase Problem in X-ray Crystallography. WCB'08 - Workshop on Constraint Based Methods for Bioinformatics associated to CPAIOR 2008 in Paris, 2008.

2007

Larhlimi, Abdelhalim and Bockmayr, Alexander: Minimal Direction Cuts in Metabolic Networks.Computational Life Sciences III, CompLife'07, Utrecht, October 2007. AIP Conference Proceedings, Vol. 940, 73-86, 2007.

Larhlimi, Abdelhalim and Bockmayr, Alexander: Constraint-based Analysis of Gene Deletion in a Metabolic Network. Workshop on Constraint based Methods for Bioinformatics, WCB'07, Porto, 48-55, 2007.

Siebert, Heike and Bockmayr, Alexander: Context Sensitivity in Logical Modelling with Time Delays. Computational Methods in Systems Biology, CMSB 2007, Edinburgh. Springer, LNBI 4695, 64-79, 2007.

Siebert, Heike and Bockmayr, Alexander: Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks. Algebraic Biology, AB 2007, Hagenberg Austria. Springer, LNCS 4545, 36-50, 2007.

2006

Larhlimi, Abdelhalim and Bockmayr, Alexander: A New Approach to Flux Coupling Analysis of Metabolic Networks.Computational Life Sciences II, CompLife'06, Cambridge, UK. Springer LNBI 4216, 205-215, 2006.

Siebert, Heike and Bockmayr, Alexander: Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks. Computational Methods in Systems Biology, CMSB 2006, Trento, Italy. Springer, LNBI 4210, 169-183, 2006.

Bockmayr, Alexander and Pisaruk, Nicolai: Detecting infeasibility and generating cuts for mixed integer programming using constraint programming. Computers & Operations Research, 33/10, 2777-2786, 2006.

Siebert, Heike: Fixed points and normal families of quasiregular mappings. J. Analyse Math. 98, 145-168, 2006.

2005

Larhlimi, Abdelhalim and Bockmayr, Alexander: Minimal Metabolic Behaviors and the Reversible Metabolic Space. Matheon Preprint Nr. 299, December 2005.

Bockmayr, Alexander and Courtois, Arnaud and Eveillard, Damien and Vezain, Myriam: Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing. Computational Methods in Systems Biology, CMSB'04, Paris. Springer LNBI 3082, 43-57, 2005.

Bockmayr, Alexander and Hooker, John N.: Constraint programming. In Handbooks in Operations Research and Management Science. 12: Discrete Optimization (Eds. Aardal K, Nemhauser G, and Weismantel R), Chapter 10, 559 - 600, Elsevier, 2005.

Popular

Mit Mathe durch das Netz der Algen und Bakterien Interview mit Alexander Bockmayr und Heike Siebert im Wissenschaftsmagazin fundiert, 2012

Bockmayr, Alexander and Larhlimi, Abdelhalim. Von Bakterien und Antibiotika. In Besser als Mathe, Part 7, 213-218, 2010.

Bockmayr, Alexander. Sprechen Sie biologisch? Interview in WIR (Alumni magazin), 2007.