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Besancon, M., Kratochvil, M., Kuate, C. A. F., Trefois, C., Gu, W., & Ebenhöh, O. (2022). Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models. bioRxiv. https://doi.org/10.1101/2022.07.11.499575

Saadat, N. P., van Aalst, M., & Ebenhöh, O. (2022). Network Reconstruction and Modelling Made Reproducible with moped. Metabolites, 12(4), 275. https://doi.org/10.3390/metabo12040275


Kratochvíl, M., Heirendt, L., Wilken, S. E., Pusa, T., Arreckx, S., Noronha, A., ... & Gu, W. (2022). COBREXA. jl: constraint-based reconstruction and exascale analysis. Bioinformatics, 38(4), 1171-1172. https://doi.org/10.1093/bioinformatics/btab782

Saadat, N. P., Nies, T., Van Aalst, M., Hank, B., Demirtas, B., Ebenhöh, O., & Matuszyńska, A. (2021). Computational analysis of alternative photosynthetic electron flows linked with oxidative stress. Frontiers in plant science, 12, 750580. https://doi.org/10.3389/fpls.2021.750580

Wilken, S. E., Frazão, V. V., Saadat, N. P., & Ebenhöh, O. (2021). The view of microbes as energy converters illustrates the trade-off between growth rate and yield. Biochemical Society transactions, 49(4), 1663–1674. https://doi.org/10.1042/BST20200977

Nies, T., Niu, Y., Ebenhöh, O., Matsubara, S., & Matuszyńska, A. (2021). Chlorophyll fluorescence: How the quality of information about PAM instrument parameters may affect our research. bioRxiv. https://doi.org/10.1101/2021.05.12.443801

van Aalst, M., Ebenhöh, O., & Matuszyńska, A. (2021). Constructing and analysing dynamic models with modelbase v1. 2.3: a software update. BMC bioinformatics, 22(1), 1-15. https://doi.org/10.1186/s12859-021-04122-7


Popa, O., Oldenburg, E., & Ebenhöh, O. (2020). From sequence to information. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1814), 20190448. https://doi.org/10.1098/rstb.2019.0448

Saadat, N. P., Nies, T., Rousset, Y., & Ebenhöh, O. (2020). Thermodynamic limits and optimality of microbial growth. Entropy, 22(3), 277. https://doi.org/10.3390/e22030277

Saker, H., Machné, R., Fallmann, J., Murray, D. B., Shahin, A. M., & Stadler, P. F. (2021). Weighted Consensus Segmentations. Computation, 9(2), 17. https://doi.org/10.3390/computation9020017

McFarland, M. R., Keller, C. D., Childers, B. M., Adeniyi, S. A., Corrigall, H., Raguin, A., ... & Stansfield, I. (2020). The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic acids research, 48(6), 3071-3088. https://doi.org/10.1093/nar/gkaa055

Raguin, A., Kern, N., Parmeggiani, A., (2020) Stochastic modelling of collective motor protein transport through a crossing of microtubules. Journal of Theoretical Biology 110370. https://doi.org/10.1016/j.jtbi.2020.110370 . (Also available via arxiv.org/abs/2006.10416)

Saadat, N.P., Nies, T., Rousset, Y., Ebenhöh, O., (2020) Thermodynamic Limits and Optimality of Microbial Growth. Entropy 22, 277. https://doi.org/10.3390/e22030277

Pfister, B., Zeeman, S.C., Rugen, M.D., Field, R.A., Ebenhöh, O., Raguin, A., (2020) Theoretical and experimental approaches to understand the biosynthesis of starch granules in a physiological context. Photosynthesis Research. https://doi.org/10.1007/s11120-019-00704-y


Sharma, S., Popa, O., Ebenhoeh, O., Kopriva, S., (2019) An integrative approach to investigate natural variation in the accumulation of aliphatic glucosinolates in Arabidopsis thaliana. bioRxiv. https://doi.org/10.1101/838227

Tacchino, F., Succurro, A., Ebenhöh, O., Gerace, D., (2019) Optimal efficiency of the Q-cycle mechanism around physiological temperatures from an open quantum systems approach. Scientific Reports 9. https://doi.org/10.1038/s41598-019-52842-x

Zhao, J., Pokhilko, A., Ebenhöh, O., Rosser, S.J., Colloms, S.D., (2019) A single-input binary counting module based on serine integrase site-specific recombination. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz245

Matuszyńska, A., Saadat, N.P., Ebenhöh, O., (2019) Balancing energy supply during photosynthesis – a theoretical perspective. Physiologia Plantarum. https://doi.org/10.1111/ppl.12962

Succurro, A., Segrè, D., Ebenhöh, O., (2019) Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth. mSystems 4. https://doi.org/10.1128/mSystems.00230-18


Ebenhöh, O., van Aalst, M., Saadat, N.P., Nies, T., Matuszyńska, A., (2018) Building Mathematical Models of Biological Systems with modelbase. Journal of Open Research Software 6. https://doi.org/10.5334/jors.236

Magni, S., Succurro, A., Skupin, A., Ebenhöh, O., (2018) Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation. Journal of The Royal Society Interface 15, 20170965. https://doi.org/10.1098/rsif.2017.0965

Pfau, T., Christian, N., Masakapalli, S.K., Sweetlove, L.J., Poolman, M.G., Ebenhöh, O., (2018) The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Scientific Reports 8. https://doi.org/10.1038/s41598-018-30884-x

Pokhilko, A., Ebenhöh, O., Stark, W.M., Colloms, S.D., (2018) Mathematical model of a serine integrase-controlled toggle switch with a single input. Journal of The Royal Society Interface 15, 20180160. https://doi.org/10.1098/rsif.2018.0160

Singh, D., Nedbal, L., Ebenhöh, O., (2018) Modelling phosphorus uptake in microalgae. Biochemical Society Transactions 46, 483–490. https://doi.org/10.1042/BST20170262

Succurro, A., Ebenhöh, O., (2018) Review and perspective on mathematical modeling of microbial ecosystems. Biochemical Society Transactions 46, 403–412. https://doi.org/10.1042/BST20170265

Oliver Ebenhöh and Stephanie Spelberg. (2018) The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham cycle Biochem. Soc. Trans. doi:10.1042/bst20170245

Christina Schreiber, Henning Schiedung, Lucy Harrison, Christoph Briese, Bärbel Ackermann, Josefine Kant, Silvia D Schrey, Diana Hofmann, Dipali Singh, Oliver Ebenhöh, Wulf Amelung, Ulrich Schurr, Tabea Mettler-Altmann, Gregor Huber, Nicolai David Jablonowski, and Ladislav Nedbal. (2018) Evaluating potential of green alga Chlorella vulgaris to accumulate phosphorus and to fertilize nutrient-poor soil substrates for crop plants J. Appl. Phycol. doi:10.1007/s10811-018-1390-9


F.W. Moejes, A. Matuszynska, K. Adhikari, R. Bassi, F. Cariti, G. Cogne, I. Dikaios, A. Falciatore, G. Finazzi, S. Flori, M. Goldschmidt-Clermont, S. Magni, J. Maguire, A. Le Monnier, K. Müller, M. Poolman, D. Singh, S. Spelberg, G.R. Stella, A. Succurro, L. Taddei, B. Urbain, V. Villanova, C. Zabke, and O. Ebenhöh. (2017) A systems-wide understanding of photosynthetic acclimation in algae and higher plants J. Exp. Bot. doi:10.1093/jxb/erx137

Fiona Moejes, Antonella Succurro, Ovidiu Popa, Julie Maguire, and Oliver Ebenhöh. (2017) Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures Processes doi:10.3390/pr5040077

A Pokhilko and O Ebenhöh. (2017) A Mathematical Model Of Bacteria Capable Of Complete Oxidation Of Ammonium Predicts Improved Nitrogen Removal And Reduced Production Of Nitrous Oxide J. Multidiscip. Eng. Sci. Technol.

Alexandra Pokhilko, Jia Zhao, W Marshall Stark, Sean D Colloms, and Oliver Ebenhöh. (2017) A simplified mathematical model of directional DNA site-specific recombination by serine integrases J. R. Soc. Interface doi:10.1098/rsif.2016.0618

A Raguin and O Ebenhöh. (2017) Design Starch: Stochastic modeling of starch granule biogenesis Biochem. Soc. Trans.

Antonella Succurro, Fiona Wanjiku Moejes, and Oliver Ebenhöh. (2017) A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia J. Bacteriol.


Andrea Christopher, Heike Hameister, Holly Corrigall, Oliver Ebenhöh, Berndt Müller, and Ekkehard Ullner. (2016) Modelling Robust Feedback Control Mechanisms That Ensure Reliable Coordination of Histone Gene Expression with DNA Replication PLoS One doi:10.1371/journal.pone.0165848

Anna B Matuszyńska, Somayyeh Heidari, Peter Jahns, and Oliver Ebenhöh. (2016) A mathematical model of non-photochemical quenching to study short-term light memory in plants Biochim. Biophys. Acta - Bioenerg. doi:10.1016/j.bbabio.2016.09.003

Thomas Pfau, Nils Christian, Shyam K Masakapalli, Lee J Sweetlove, Mark G Poolman, and Oliver Ebenhoeh. (2016) The intertwined metabolism of Medicago truncatula and its nitrogen fixing symbiont Sinorhizobium meliloti elucidated by genome-scale metabolic models. bioRxiv doi:10.1101/067348

Alexandra Pokhilko, Jia Zhao, Oliver Ebenhöh, Margaret C M Smith, W Marshall Stark, and Sean D Colloms. (2016) The mechanism of phi C31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Res doi:10.1093/nar/gkw616

S L Samodelov, H M Beyer, X Guo, M Augustin, K.-P. Jia, L Baz, O Ebenhöh, P Beyer, W Weber, S Al-Babili, and M D Zurbriggen. (2016) StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity Sci. Adv. doi:10.1126/sciadv.1601266


Nidhi Adlakha, Thomas Pfau, Oliver Ebenhöh, and Syed Yazdani. (2015) Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008 Biotechnol. Biofuels doi:10.1186/s13068-015-0338-4

Anna Matuszyńska, Oliver Ebenhöh, Anna Matuszyńska, Oliver Ebenhöh, Anna Matuszynska, and Oliver Ebenhoeh. (2015) A reductionist approach to model photosynthetic self-regulation in eukaryotes in response to light Biochem. Soc. Trans. doi:10.1042/BST20150136

Alexandra Pokhilko, Jordi Bou-Torrent, Pablo Pulido, Manuel Rodr\'\iguez-Concepción, and Oliver Ebenhöh. (2015) Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis New Phytol doi:10.1111/nph.13258

Alexandra Pokhilko and Oliver Ebenhöh. (2015) Mathematical modelling of diurnal regulation of carbohydrate allocation by osmo-related processes in plants J. R. Soc. Interface doi:10.1098/rsif.2014.1357


Nils Christian, Alexander Skupin, Silvia Morante, Karl Jansen, Giancarlo Rossi, and Oliver Ebenhöh. (2014) Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels J. Theor. Biol. doi:http://dx.doi.org/10.1016/j.jtbi.2013.11.010

Oliver Ebenhöh, Geoffrey Fucile, Giovanni Finazzi, Jean-David Rochaix, and Michel Goldschmidt-Clermont. (2014) Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model Philos. Trans. R. Soc. Lond. B. Biol. Sci. doi:10.1098/rstb.2013.0223

Önder Kartal and Oliver Ebenhöh. (2014) Modelling reactions catalysed by carbohydrate-active enzymes bioRxiv doi:10.1101/008615

Alexandra Pokhilko, Anna Flis, Ronan Sulpice, Mark Stitt, and Oliver Ebenhöh. (2014) Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model Mol. BioSyst. doi:10.1039/C3MB70459A

Daniel D Seaton, Oliver Ebenhöh, Andrew J Millar, and Alexandra Pokhilko. (2014) Regulatory principles and experimental approaches to the circadian control of starch turnover. J R Soc Interface doi:10.1098/rsif.2013.0979

Sizhong Yang, Susanne Liebner, Mashal Alawi, Oliver Ebenhöh, and Dirk Wagner. (2014) Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR J. Microbiol. Methods doi:http://dx.doi.org/10.1016/j.mimet.2014.05.006

before 2014

Guangyou Duan, Nils Christian, Jens Schwachtje, Dirk Walther, and Oliver Ebenhöh. (2013) The Metabolic Interplay between Plants and Phytopathogens Metabolites doi:10.3390/metabo3010001

Oliver Ebenhöh and David Hazlerigg. (2013) Modelling a molecular calendar: The seasonal photoperiodic response in mammals Chaos, Solitons \&\ Fractals doi:10.1016/j.chaos.2012.11.007

Oliver Ebenhöh, Alexander Skupin, Önder Kartal, Sebastian Mahlow, and Martin Steup. Thermodynamic Characterisation of Carbohydrate-active Enzymes. In Proc. "5th Int. ESCEC Symp. Exp. Stand. Cond. Enzym. Charact. 2013.

Onder Kartal and Oliver Ebenhöh. (2013) A generic rate law for surface-active enzymes FEBS Lett doi:10.1016/j.febslet.2013.07.026

Adam H Price, Gareth J Norton, David E Salt, Oliver Ebenhöh, Andrew A Meharg, Caroline Meharg, M Rafiqul Islam, Ramen N Sarma, Tapash Dasgupta, Abdelbagi M Ismail, Kenneth L McNally, Hao Zhang, Ian C Dodd, and William J Davies. (2013) Alternate wetting and drying irrigation for rice in Bangladesh: Is it sustainable and has plant breeding something to offer? Food Energy Secur. doi:10.1002/fes3.29

Christian Ruzanski, Julia Smirnova, Martin Rejzek, Darrell Cockburn, Henriette L Pedersen, Marilyn Pike, William G T Willats, Birte Svensson, Martin Steup, Oliver Ebenhöh, Alison M Smith, and Robert A Field. (2013) A bacterial glucanotransferase can replace the complex maltose metabolism required for starch-to-sucrose conversion in leaves at night J Biol Chem doi:10.1074/jbc.M113.497867

Georg Basler, Sergio Grimbs, Oliver Ebenhöh, Joachim Selbig, and Zoran Nikoloski. (2012) Evolutionary significance of metabolic network properties J. R. Soc. Interface

Ines Heiland, Christian Bodenstein, Thomas Hinze, Olga Weisheit, Oliver Ebenhöh, Maria Mittag, and Stefan Schuster. (2012) Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii J. Biol. Phys.

Georg Basler, Oliver Ebenhöh, Joachim Selbig, and Zoran Nikoloski. (2011) Mass-balanced randomization of metabolic networks Bioinformatics doi:10.1093/bioinformatics/btr145

Oliver Ebenhöh, Torsten Houwaart, Heiko Lokstein, Stephanie Schlede, and Katrin Tirok. (2011) A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence Biosystems. doi:10.1016/j.biosystems.2010.10.011

O Kartal, S Mahlow, A Skupin, and O Ebenhöh. (2011) Carbohydrate-active enzymes exemplify entropic principles in metabolism Mol Syst Biol doi:10.1038/msb.2011.76

Patrick May, Nils Christian, Oliver Ebenhöh, Wolfram Weckwerth, and Dirk Walther. (2011) Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks Methods Mol Biol doi:10.1007/978-1-60761-977-2_21

Thomas Pfau, Nils Christian, and Oliver Ebenhöh. (2011) Systems approaches to modelling pathways and networks Brief. Funct. Genomics doi:10.1093/bfgp/elr022

Chris A Brackley, Oliver Ebenhöh, Celso Grebogi, Jürgen Kurths, Alessandro de Moura, M Carmen Romano, and Marco Thiel. (2010) Introduction to Focus Issue: Dynamics in Systems Biology Chaos doi:10.1063/1.3530126

Marek Mutwil, Björn Usadel, Moritz Schütte, Ann Loraine, Oliver Ebenhöh, and Staffan Persson. (2010) Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm Plant Physiol doi:10.1104/pp.109.145318

M Schütte, M Mutwil, S Persson, and O Ebenhöh. (2010) Analyzing Gene Coexpression Data by an Evolutionary Model Genome Informatics

Moritz Schütte, Alexander Skupin, Daniel Segrè, and Oliver Ebenhöh. (2010) Modeling the complex dynamics of enzyme-pathway coevolution. Chaos doi:10.1063/1.3530440

Takeyuki Tamura, Nils Christian, Kazuhiro Takemoto, Oliver Ebenhöh, and Tatsuya Akutsu. (2010) Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines. Genome Inf.

Franziska Witzel, Jan Götze, and Oliver Ebenhöh. (2010) Slow deactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase elucidated by mathematical models. FEBS J doi:10.1111/j.1742-4658.2009.07541.x

Nils Christian, Patrick May, Stefan Kempa, Thomas Handorf, and Oliver Ebenhöh. (2009) An integrative approach towards completing genome-scale metabolic networks. Mol Biosyst doi:10.1039/B915913b

Oliver Ebenhöh and Thomas Handorf. (2009) Functional Classification Of Genome-Scale Metabolic Networks EURASIP J. Bioinforma. Syst. Biol. doi:10.1155/2009/570456

Önder Kartal and Oliver Ebenhöh. (2009) Ground State Robustness as an Evolutionary Design Principle in Signaling Networks PLoS One doi:10.1371/journal.pone.0008001

S Kempa, O Ebenhöh, D Walther, and W Weckwerth. Molecular Biology and Biotechnology, chapter 7: Metabolic Engineering, pages 194–217. Royal Society of Chemistry, 2009.

M Schütte, N Klitgord, D Segrè, and O Ebenhöh. (2009) Co-evolution of metabolism and protein sequences Genome Informatics

G Basler, Z Nikoloski, O Ebenhöh, and T Handorf. (2008) Biosynthetic potentials from species-specific metabolic networks Genome Inf.

Thomas Handorf, Nils Christian, Oliver Ebenhöh, and Daniel Kahn. (2008) An environmental perspective on metabolism. J Theor Biol doi:10.1016/j.jtbi.2007.10.036

Ö Kartal and O Ebenhöh. The Glucan, Water Dikinase - A Kinetic Model to Understand the Initial Step in Starch Mobilization in Plant Leaves. In Ulrich H E Hansmann, Jan H Meinke, Sandipan Mohanty, Walter Nadler, and Olav Zimmermann, editors, From Comput. Biophys. to Syst. Biol., volume 40 of NIC Series, 245–248. John von Neumann Institute for Computing, Jülich, 2008.

K Kruse and O Ebenhöh. (2008) Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds Genome Inf.

Franziska Matthäus, Carlos Salazar, and Oliver Ebenhöh. (2008) Biosynthetic potentials of metabolites and their hierarchical organization. PLoS Comput Biol doi:10.1371/journal.pcbi.1000049

Patrick May, Stefanie Wienkoop, Stefan Kempa, Björn Usadel, Nils Christian, Jens Rupprecht, Julia Weiss, Luis Recuenco-Munoz, Oliver Ebenhöh, Wolfram Weckwerth, and Dirk Walther. (2008) Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii. Genetics doi:10.1534/genetics.108.088336

Z Nikoloski, S Grimbs, J Selbig, and O Ebenhöh. (2008) Hardness and Approximability of the Inverse Scope Problem Lect. Notes Comput. Sci. doi:10.1007/978-3-540-87361-7

J Numata, O Ebenhöh, and E W Knapp. (2008) Measuring correlations in metabolomic networks with mutual information Genome Inf.

Nils Christian, Thomas Handorf, and Oliver Ebenhöh. (2007) Metabolic synergy: increasing biosynthetic capabilities by network cooperation. Genome Inf.

Thomas Handorf and Oliver Ebenhöh. (2007) MetaPath Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res doi:10.1093/nar/gkm287

B Binder, O Ebenhöh, K Hashimoto, and R Heinrich. (2006) Expansion of signal transduction networks. Syst Biol

József Bruck, Oliver Ebenhöh, and Reinhart Heinrich. (2006) Patterns of interactions of reaction pairs in metabolic networks. Genome Inf.

O Ebenhöh, T Handorf, and D Kahn. (2006) Evolutionary changes of metabolic networks and their biosynthetic capacities. Syst Biol

Oliver Ebenhöh and Wolfram Liebermeister. (2006) Structural analysis of expressed metabolic subnetworks. Genome Inf.

T Handorf, O Ebenhöh, D Kahn, and R Heinrich. (2006) Hierarchy of metabolic compounds based on their synthesising capacity. Syst Biol

F Matthäus, C Salazar, and O Ebenhöh. (2006) Large-scale analysis of metabolic networks: clustering metabolites by their synthesizing capacities InterJournal Compex Syst.

C Ringemann, O Ebenhöh, R Heinrich, and H Ginsburg. (2006) Can biochemical properties serve as selective pressure for gene selection during inter-species and endosymbiotic lateral gene transfer? Syst Biol

Carlos Salazar, Jana Schütze, and Oliver Ebenhöh. (2006) Bioinformatics meets systems biology. Genome Biol doi:10.1186/gb-2006-7-1-303

Oliver Ebenhöh, Thomas Handorf, and Reinhart Heinrich. (2005) A cross species comparison of metabolic network functions. Genome Inf.

Thomas Handorf, Oliver Ebenhöh, and Reinhart Heinrich. (2005) Expanding metabolic networks: scopes of compounds, robustness, and evolution. J Mol Evol doi:10.1007/s00239-005-0027-1

Oliver Ebenhöh, Thomas Handorf, and Reinhart Heinrich. (2004) Structural analysis of expanding metabolic networks. Genome Inf.

Oliver Ebenhöh and Reinhart Heinrich. (2003) Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness. Bull Math Biol doi:10.1016/S0092-8240(03)00002-8

Oliver Ebenhöh and Reinhart Heinrich. (2001) Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADPH producing systems. Bull Math Biol doi:10.1006/bulm.2000.0197