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,
- 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.
- 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