Selected publications

Mathematical and computational biology

     Metabolic networks  

• Wieder F, Henk M, Bockmayr A: On the Geometry of Elementary Flux Modes, Journal of Mathematical Biology, 87:50, Aug 2023
• Thuillier K, Baroukh C, Bockmayr A, Cottret L, Paulevé L, Siegel A: MERRIN: MEtabolic Regulation Rule INference from time series data. Bioinformatics, 38(Supplement_2):ii127-ii133, Sep 2022
• Köbis MA, Bockmayr A, Steuer R: Time-Optimal Adaptation in Metabolic Network Models. Frontiers in Molecular Biosciences, 9:866676, Jul 2022
• Thuillier K, Baroukh C, Bockmayr A, Cottret L, Paulevé L, Siegel A: Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. Computational Methods in Systems Biology, CMSB 2021, Bordeaux. Springer, LNCS 12881, 159-180, Sep 2021 (HAL)
• Liu L, Bockmayr A: Regulatory dynamic enzyme-cost flux balance analysis: A unifying framework for constraint-based modeling. Journal of Theoretical Biology, 501:110317, Sep 2020
• Liu L, Bockmayr A: Formalizing Metabolic-Regulatory Networks by Hybrid Automata. Acta Biotheoretica, 68(1), 73-85, Mar 2020
• Röhl A, Bockmayr A: Finding MEMo: minimum sets of elementary flux modes. Journal of Mathematical Biology, 79(5), 1749-1777, Oct 2019
• Röhl A, Riou T, Bockmayr A: Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection. Bioinformatics, 35(15), 2618-2625, Aug 2019
• Reimers AM, Knoop H, Bockmayr A, Steuer R: Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. Proc Natl Acad Sci USA 114 (31), E6457-E6465, Jul 2017
• Röhl A, Bockmayr A: A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks. BMC Bioinformatics, 18:2, Jan 2017
• 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, Goldstein Y, Bockmayr A: Generic Flux Coupling Analysis. Mathematical Biosciences, 262, 28-35, Apr 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
• 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
• 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, 2013
  
• David L, Bockmayr A: Constrained Flux Coupling Analysis. Workshop on Constraint based Methods for Bioinformatics, WCB'13, Uppsala, 75-83, 2013
• Müller AC, Bockmayr A: Fast Thermodynamically Constrained Flux Variability Analysis. Bioinformatics, 29/7, 903-909, 2013
• Marashi SA, David L, Bockmayr A: Analysis of Metabolic Subnetworks by Flux Cone Projection. Algorithms for Molecular Biology, 7:17, 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, 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
• Marashi SA, David L, Bockmayr A: On flux coupling analysis of metabolic subsystems. Journal of Theoretical Biology, 302, 62-69, 2012
• David L, Marashi SA, Larhlimi A, Mieth B, Bockmayr A: 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, 103/1, 57-66, 2011
• 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
  
• 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
  
• 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
• 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 (Matheon Preprint Nr. 338)
  
• Larhlimi, Abdelhalim and Bockmayr, Alexander: Minimal Metabolic Behaviors and the Reversible Metabolic Space. Matheon Preprint Nr. 299, December 2005
  

     Regulatory networks

• Becker K, Gebser M, Schaub T, Bockmayr A: Answer Set Programming for Logical Analysis of Data. Workshop on Constraint based Methods for Bioinformatics, WCB'16, Toulouse, 15-26, 2016
• Klarner H, Bockmayr A, Siebert H: Computing maximal and minimal trap spaces of Boolean networks. Natural Computing, 14/4, 535-544, 2015
• Klarner H, Bockmayr A, Siebert H: Computing Symbolic Steady States of Boolean Networks. Cellular Automata, ACRI 2014, Krakow, Poland, Springer, LNCS 8751, 561-570, 2014
• Jamshidi, Shahrad and Siebert, Heike and Bockmayr, Alexander: 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, Alexander and Siebert, Heike: Bio-Logics: Logical Analysis of Bioregulatory Networks. Programming Logics. Essays in Memory of Harald Ganzinger. Springer, LNCS 7797, 19-34, 2013
  
• 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
  
• 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
• 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, Perugia, 45-57, 2011
• Siebert, Heike and Bockmayr, Alexander:  Temporal Constraints in the Logical Analysis of Regulatory Networks. Theoretical Computer Science, 391/3, 258-275, 2008 (Matheon Preprint Nr. 385)
• 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 (Matheon Preprint Nr. 373)
• 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 (Matheon Preprint Nr. 333)
  

    Hybrid concurrent constraint programming

• 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.
  
• Eveillard, Damien and Ropers, Delphine and de Jong, Hidde and Branlant, Christiane and Bockmayr, Alexander: A multi-scale constraint programming model of alternative splicing regulation. Theoretical Computer Science, 325/1 (Computational Systems Biology), 3-24, 2004.
• Eveillard, Damien and Ropers, Delphine and de Jong, Hidde and Branlant, Christiane and Bockmayr, Alexander: Multiscale modeling of alternative splicing regulation. Computational Methods in Systems Biology, CMSB'03, Rovereto, Italy, 2003. Springer LNCS 2602, 75-87.
  
• Bockmayr, Alexander and Courtois, Arnaud: Using hybrid concurrent constraint programming to model dynamic biological systems.  18th International Conference on Logic Programming, ICLP'02, Copenhagen, 2002. Springer, LNCS 2401, 85-99.
  
• Bockmayr, Alexander and Courtois, Arnaud: Modeling biological systems in hybrid concurrent constraint programming (Abstract). 2nd International Conference on Systems Biology, ICSB'01, Caltech, November 2001.

    Crystallography

• Lunin, Vladimir Y. and Lunina, Natalia and Podjarny, Alberto and Bockmayr, Alexander and Urzhumtsev, Alexandre: Ab initio phasing starting from low resolution. Z. Kristallogr. 217, 668 - 685, 2002.
• Lunin, Vladimir Y. and Urzhumtsev, Alexandre and Bockmayr, Alexander: Direct phasing by binary integer programming. Acta Crystallographica, A58, 283 - 291, 2002.

Constraint and integer programming

• 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.
• Bockmayr, Alexander and Hooker, John N.: Constraint programming. In Handbooks in Operations Research and Management Science. 12: Discrete Optimization (Eds. K. Aardal, G. Nemhauser, and R. Weismantel), Chapter 10, 559 - 600, Elsevier, 2005.
  
• Balas, Egon and Bockmayr, Alexander and Pisaruk, Nicolai and Wolsey, Laurence: On unions and dominants of polytopes. Mathematical Programming, Ser. A, 99, 223 - 239, 2004.
• Bockmayr, Alexander and Kasper, Thomas: Branch-and-infer: A framework for combining CP and IP. In  Constraint and Integer Programming (Ed. M. Milano), Chapter 3, 59 - 87, Kluwer, 2004.
• Althaus, Ernst and Bockmayr, Alexander and Elf, Matthias and Kasper, Thomas and Jünger, Michael and Mehlhorn, Kurt: SCIL - Symbolic Constraints in Integer Linear Programming. 10th European Symposium on Algorithms, ESA'02, Rome, 2002. Springer, LNCS 2461, 75 - 87.
  
• Bockmayr, Alexander and Pisaruk, Nicolai and Aggoun, Abder: Network flow problems in constraint programming.  Principles and Practice of Constraint Programming, CP'2001, Paphos, Cyprus, 2001. Springer, LNCS 2239, 196 - 210.
  
• Bockmayr, Alexander and Weispfenning, Volker: Solving numerical constraints. In Handbook of Automated Reasoning (Eds. A. Robinson and A. Voronkov). Vol. 1, Chapter 12, 751 - 842, Elsevier, 2001.
• Bockmayr, Alexander and Eisenbrand, Friedrich: Cutting Planes and the Elementary Closure in Fixed Dimension. Mathematics of Operations Research, 26/2, 304 - 312, 2001.
• Bockmayr, Alexander and Eisenbrand, Friedrich: Combining logic and optimization in cutting plane theory. Frontiers of Combining Systems, FROCOS'2000, Nancy, Springer, LNAI 1794, 1- 17, 2000.
• Bockmayr, Alexander and Dimopoulos, Yannis: Integer Programs and Valid Inequalities for Planning Problems. Recent Advances in AI Planning, ECP'99, Durham, United Kingdom. LNAI 1809, 239-251, 2000.
• Bockmayr, Alexander and Eisenbrand, Friedrich and Hartmann, Mark and Schulz, Andreas S.: On the Chvátal Rank of Polytopes in the 0/1 Cube. Discrete Applied Mathematics, 98, 21-27, 1999.
• Bockmayr, Alexander and Kasper, Thomas: Branch-and-Infer: A Unifying Framework for Integer and Finite Domain Constraint Programming. INFORMS J. Computing, 10/3, 287 - 300, 1998.
• Barth , Peter and Bockmayr, Alexander: Modelling Discrete Optimisation Problems in Constraint Logic Programming. Annals of Operations Research, 81, 467 - 495, 1998.
• Barth, Peter and Bockmayr, Alexander: Finite domain and cutting plane techniques in CLP(PB). Logic Programming. 12th International Conference, ICLP'95, Kanagawa, Japan, 133 -147, MIT Press, 1995.
  
• Bockmayr, Alexander: Solving Pseudo-Boolean Constraints. In Constraint Programming: Basics and Trends (Ed. A. Podelski), 22 - 38, Springer, LNCS 910, 1995.
  
• Bockmayr, Alexander: Logic Programming with Pseudo-Boolean Constraints. In Constraint Logic Programming. Selected Research (Eds. F. Benhamou and A. Colmerauer), 327 - 350, MIT Press, 1993.

Computational logic

• Werner, Andreas, and Bockmayr, Alexander and Krischer, Stefan. How to realize LSE narrowing. New Generation Computing, 16(4):397-434, 1998.
• Bockmayr, Alexander and Krischer, Stefan and Werner, Andreas. Narrowing strategies for arbitrary canonical systems. Fundamenta Informaticae, 24(1,2):125 - 155, 1995.
• Bockmayr, Alexander and Werner, Andreas. LSE narrowing for decreasing conditional term rewrite systems. Conditional and Typed Rewriting Systems, CTRS'94, Jerusalem.
  Springer, LNCS 968, 1995.
• Werner, Andreas and Bockmayr, Alexander and Krischer, Stefan. How to realize LSE narrowing. Algebraic and Logic Programming, ALP'94, Madrid, Springer, LNCS 850, 1994.
• Bockmayr, Alexander. Conditional narrowing modulo a set of equations. Applicable Algebra in Engineering, Communication and Computing, 4(3):147 - 168, 1993.
• Bockmayr, Alexander and Krischer, Stefan, and Werner, Andreas. An optimal narrowing strategy for general canonical systems. Conditional Term Rewriting Systems, CTRS'92, Pont-a-Mousson, France. Springer, LNCS 656, 1992.
• Bockmayr, Alexander. Algebraic and logical aspects of unification. Word Equations and Related Topics, IWWERT'90, Tübingen. Springer, LNCS 572, 1992.
• Bockmayr, Alexander. Model-theoretic aspects of unification. Word Equations and Related Topics, IWWERT'90, Tübingen. Springer, LNCS 572, 1992.
• Krischer, Stefan and Bockmayr, Alexander. Detecting redundant narrowing derivations by the LSE-SL reducibility test. Rewriting Techniques and Applications, RTA'91, Como. Springer, LNCS 488, 1991.
• Bockmayr, Alexander and Brzoska, Christoph and Deussen, Peter and Varsek, Igor. KA-Prolog: Erweiterungen einer logischen Programmiersprache und ihre effiziente Implementierung. Informatik Forsch. Entw., 6:128-140, 1991.
• Bockmayr, Alexander. Narrowing with built-in theories. Algebraic and Logic Programming, ALP'88, Gaussig. Springer, LNCS 343, 1988.
• Bockmayr, Alexander. A note on a canonical theory with undecidable unification and matching problem. Journal of Automated Reasoning, 3:379 -381, 1987.

Miscellaneous

• Bockmayr A, Siebert H, Röblitz S, Schütte Ch, Deuflhard P. Advanced mathematical modeling in systems biology. In MATHEON-Mathematics for Key Technologies, 29-44, 2014
• Bockmayr, Alexander and Larhlimi, Abdelhalim. Von Bakterien und Antibiotika. In Besser als Mathe, Part 7, 213-218, 2010

Theses

• Bockmayr, Alexander. Husserl, Dreyfus und die Kognitionswissenschaft, Magisterarbeit  Philosophie, Univ. Karlsruhe, 1993
• Bockmayr, Alexander. Beiträge zur Theorie des logisch-funktionalen Programmierens. Dissertation Informatik, Univ. Karlsruhe, 1990
• Bockmayr, Alexander. Charakterisierung irreduzibler reduzierter komplexer Räume durch ihre meromorphen Funktionenkörper. Diplomarbeit Mathematik, TU München, 1985