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Scopus Author ID: 8980340100
Loop profile: 33308
ResearcherID: C-8974-2011

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COBREXA 2: tidy and scalable construction of complex metabolic models

Bioinformatics
2025-02-04 | Journal article
DOI: 10.1093/bioinformatics/btaf056
Contributors: Miroslav Kratochvíl; St Elmo Wilken; Oliver Ebenhöh; Reinhard Schneider; Venkata P Satagopam; Pier Luigi Martelli
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Crossref

Rule-Based Deconstruction and Reconstruction of Diterpene Libraries: Categorizing Patterns & Unravelling the Structural Landscape

2024-12-24 | Preprint
DOI: 10.1101/2024.12.20.629783
Contributors: Davis T. Mathieu; Nicholas Schlecht; Marvin van Aalst; Kevin M. Shebek; Lucas Busta; Nicole Babineau; Oliver Ebenhöh; Björn Hamberger
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Crossref

Beyond blooms: the winter ecosystem reset determines microeukaryotic community dynamics in the Fram Strait

Communications Earth & Environment
2024-10-29 | Journal article
DOI: 10.1038/s43247-024-01782-0
Contributors: Ellen Oldenburg; Raphael M. Kronberg; Katja Metfies; Matthias Wietz; Wilken-Jon von Appen; Christina Bienhold; Ovidiu Popa; Oliver Ebenhöh
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Crossref

Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity

2024-10-17 | Preprint
DOI: 10.1101/2024.10.16.618214
Contributors: Edward N. Smith; Marvin van Aalst; Andreas P.M. Weber; Oliver Ebenhöh; Matthias Heinemann
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Crossref

Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803

PLOS Computational Biology
2024-09-12 | Journal article
DOI: 10.1371/journal.pcbi.1012445
Contributors: Tobias Pfennig; David Lea-Smith; Elena Kullmann; Tomáš Zavřel; Andreas Nakielski; Oliver Ebenhöh; Jan Červený; Gábor Bernát; Anna Barbara Matuszyńska
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Crossref

A new era of synthetic biology—microbial community design

Synthetic Biology
2024-07-31 | Journal article
DOI: 10.1093/synbio/ysae011
Contributors: Anna Matuszyńska; Oliver Ebenhöh; Matias D Zurbriggen; Daniel C Ducat; Ilka M Axmann
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Crossref

Beyond blooms: A novel time series analysis framework predicts seasonal keystone species and sheds light on Arctic pelagic ecosystem stability

2024-03-13 | Preprint
DOI: 10.1101/2024.03.11.583746
Contributors: Ellen Oldenburg; Raphael M. Kronberg; Katja Metfies; Matthias Wietz; Wilken-Jon von Appen; Christina Bienhold; Ovidiu Popa; Oliver Ebenhöh
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Crossref

Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies

2024-02-23 | Other
DOI: 10.1093/ismeco/ycae027
Contributors: Ellen Oldenburg; Ovidiu Popa; Matthias Wietz; Wilken-Jon von Appen; Sinhue Torres-Valdes; Christina Bienhold; Oliver Ebenhöh
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Crossref

Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes

Life
2024-02-09 | Journal article
DOI: 10.3390/life14020247
Contributors: Oliver Ebenhöh; Josha Ebeling; Ronja Meyer; Fabian Pohlkotte; Tim Nies
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A mathematical model of photoinhibition: exploring the impact of quenching processes

in silico Plants
2024-01-01 | Journal article
DOI: 10.1093/insilicoplants/diae001
Contributors: Tim Nies; Shizue Matsubara; Oliver Ebenhöh; Xin-Guang Zhu
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Crossref

Microbial pathway thermodynamics: structural models unveil anabolic and catabolic processes

2023-12-04 | Preprint
DOI: 10.1101/2023.12.01.569601
Contributors: Oliver Ebenhöh; Josha Ebeling; Ronja Meyer; Fabian Pohlkotte; Tim Nies
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Crossref

dismo: building and analysing discrete spatial ODE models

2023-10-23 | Preprint
DOI: 10.1101/2023.10.17.562679
Contributors: Marvin van Aalst; Oliver Ebenhöh
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Crossref

Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes

The Plant Journal
2023-09 | Journal article
DOI: 10.1111/tpj.16352
Contributors: Nima P. Saadat; Marvin van Aalst; Alejandro Brand; Oliver Ebenhöh; Alain Tissier; Anna B. Matuszyńska
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Crossref

What controls carbon sequestration in plants under which conditions?

Biosystems
2023-09 | Journal article
DOI: 10.1016/j.biosystems.2023.104968
Contributors: Tim Nies; Marvin van Aalst; Nima Saadat; Josha Ebeling; Oliver Ebenhöh
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Crossref

A mathematical model of photoinhibition: exploring the impact of quenching processes

2023-09-12 | Preprint
DOI: 10.1101/2023.09.12.557336
Contributors: Tim Nies; Shizue Matsubara; Oliver Ebenhöh
Source: check_circle
Crossref

Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803

2023-06-30 | Preprint
DOI: 10.1101/2023.06.30.547186
Contributors: Tobias Pfennig; Elena Kullmann; Tomáš Zavřel; Andreas Nakielski; Oliver Ebenhöh; Jan Červený; Gábor Bernát; Anna Barbara Matuszyńska
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Crossref

Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

PLOS Computational Biology
2023-06-06 | Journal article
DOI: 10.1371/journal.pcbi.1011156
Contributors: Hugo Dourado; Pedro Mendes; Wolfram Liebermeister; Oliver Ebenhöh; Martin J. Lercher
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Crossref

Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme

PLOS Computational Biology
2023-05-19 | Journal article
DOI: 10.1371/journal.pcbi.1010694
Contributors: Yvan Rousset; Mark Alber; Oliver Ebenhöh; Adélaïde Raguin
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Crossref

Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies

2023-05-05 | Preprint
DOI: 10.1101/2023.05.04.539293
Contributors: Ellen Oldenburg; Ovidiu Popa; Matthias Wietz; Wilken-Jon von Appen; Sinhue Torres-Valdes; Christina Bienhold; Oliver Ebenhöh; Katja Metfies
Source: check_circle
Crossref

What controls carbon sequestration in plants under which conditions?

2023-04-21 | Preprint
DOI: 10.1101/2023.04.20.537672
Contributors: Tim Nies; Marvin van Aalst; Nima Saadat; Josha Ebeling; Oliver Ebenhöh
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Crossref

Helixer–de novoPrediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model

2023-02-06 | Preprint
DOI: 10.1101/2023.02.06.527280
Contributors: Felix Holst; Anthony Bolger; Christopher Günther; Janina Maß; Sebastian Triesch; Felicitas Kindel; Niklas Kiel; Nima Saadat; Oliver Ebenhöh; Björn Usadel et al.
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Crossref

Approximating carbon fixation - how important is the Calvin-Benson cycle steady-state assumption?

2022-11-20 | Preprint
DOI: 10.1101/2022.11.18.517021
Contributors: Marvin van Aalst; Oliver Ebenhöh; Berkley J. Walker
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Crossref

Manipulation of Topoisomerase Expression Inhibits Cell Division but not Growth, and Reveals A Distinctive Promoter Structure in Synechocystis.

2022-11-10 | Other
DOI: 10.1093/nar/gkac1132
Contributors: Anna Behle; Maximilian Dietsch; Louis Goldschmidt; Wandana Murugathas; Lutz Berwanger; Jonas Burmester; Lun Yao; David Brandt; Oliver Ebenhöh; Ilka Axmann et al.
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Crossref

Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme

2022-11-01 | Preprint
DOI: 10.1101/2022.10.31.514469
Contributors: Yvan Rousset; Oliver Ebenhöh; Adélaïde Raguin
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Crossref

Growth Mechanics: General principles of optimal cellular resource allocation in balanced growth

2022-10-28 | Preprint
DOI: 10.1101/2022.10.27.514082
Contributors: Hugo Dourado; Wolfram Liebermeister; Oliver Ebenhöh; Martin J. Lercher
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Crossref

Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes

2022-09-30 | Preprint
DOI: 10.1101/2022.09.29.510054
Contributors: Nima P. Saadat; Marvin van Aalst; Alejandro Brand; Oliver Ebenhöh; Alain Tissier; Anna B. Matuszyńska
Source: check_circle
Crossref

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

2022-07-11 | Preprint
DOI: 10.1101/2022.07.11.499575
Contributors: St. Elmo Wilken; Mathieu Besançon; Miroslav Kratochvíl; Chilperic Armel Foko Kuate; Christophe Trefois; Wei Gu; Oliver Ebenhöh
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Crossref

Network Reconstruction and Modelling Made Reproducible with moped

Metabolites
2022-03 | Journal article | Author
DOI: 10.3390/metabo12040275
Contributors: Nima Philipp Saadat; Marvin van Aalst; Oliver Ebenhöh
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Multidisciplinary Digital Publishing Institute
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COBREXA.jl: constraint-based reconstruction and exascale analysis

Bioinformatics
2022-01-27 | Journal article
DOI: 10.1093/bioinformatics/btab782
Contributors: Miroslav Kratochvíl; Laurent Heirendt; St Elmo Wilken; Taneli Pusa; Sylvain Arreckx; Alberto Noronha; Marvin van Aalst; Venkata P Satagopam; Oliver Ebenhöh; Reinhard Schneider et al.
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The view of microbes as energy converters illustrates the trade-off between growth rate and yield

Biochemical Society Transactions
2021-08-27 | Journal article
DOI: 10.1042/BST20200977
Contributors: St. Elmo Wilken; Victor Vera Frazão; Nima P. Saadat; Oliver Ebenhöh
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Crossref

Uncoupling of the Diurnal Growth Program by Artificial Genome Relaxation in Synechocystis sp. PCC 6803

2021-07-27 | Other
DOI: 10.1101/2021.07.26.453758
Contributors: Anna Behle; Maximilian Dietsch; Louis Goldschmidt; Wandana Murugathas; David Brandt; Tobias Busche; Jörn Kalinowski; Oliver Ebenhöh; Ilka M. Axmann; Rainer Machné
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Crossref

COBREXA.jl: constraint-based reconstruction and exascale analysis

2021-06-07 | Other
DOI: 10.1101/2021.06.04.447038
Contributors: Miroslav Kratochvíl; Laurent Heirendt; St. Elmo Wilken; Taneli Pusa; Sylvain Arreckx; Alberto Noronha; Marvin van Aalst; Venkata P Satagopam; Oliver Ebenhöh; Reinhard Schneider et al.
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Crossref

Chlorophyll fluorescence: How the quality of information about PAM instrument parameters may affect our research

2021-05-13 | Other
DOI: 10.1101/2021.05.12.443801
Contributors: Tim Nies; Yuxi Niu; Oliver Ebenhöh; Shizue Matsubara; Anna Matuszyńska
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Crossref

The view of microbes as energy converters illustrates the trade-off between growth rate and yield

2021-04-18 | Other
DOI: 10.1101/2021.04.16.440103
Contributors: St. Elmo Wilken; Victor Vera Frazão; Nima P. Saadat; Oliver Ebenhöh
Source: check_circle
Crossref

From sequence to information

Philosophical Transactions of the Royal Society B: Biological Sciences
2020-12-21 | Journal article
DOI: 10.1098/rstb.2019.0448
Contributors: Ovidiu Popa; Ellen Oldenburg; Oliver Ebenhöh
Source: check_circle
Crossref

Network reconstruction and modelling made reproducible with moped

2020-12-06 | Preprint
DOI: 10.1101/2020.12.04.411512
Contributors: Nima P Saadat; Marvin van Aalst; Oliver Ebenhöh
Source: check_circle
Crossref

Constructing and analysing dynamic models with modelbase v1.0 - a software update

2020-10-02 | Preprint
DOI: 10.1101/2020.09.30.321380
Contributors: Marvin van Aalst; Oliver Ebenhöh; Anna Matuszyńska
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Crossref

Thermodynamic Limits and Optimality of Microbial Growth

Entropy
2020-02-28 | Journal article
DOI: 10.3390/e22030277
Contributors: Nima Saadat; Tim Nies; Yvan Rousset; Oliver Ebenhöh
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Crossref
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Are Microbes Thermodynamically Optimised Self-Reproducing Machines?

2019-12-19 | Other
DOI: 10.20944/preprints201912.0245.v1
Contributors: Nima P. Saadat; Tim Nies; Yvan Rousset; Oliver Ebenhöh
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Crossref
grade
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From Sequence to Information

2019-11-22 | Other
DOI: 10.20944/preprints201911.0252.v1
Contributors: Ovidiu Popa; Ellen Oldenburg; Oliver Ebenhöh
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grade
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An integrative approach to investigate natural variation in the accumulation of aliphatic glucosinolates in Arabidopsis thaliana

2019-11-13 | Other
DOI: 10.1101/838227
Contributors: Suraj Sharma; Ovidiu Popa; Stanislav Kopriva; Oliver Ebenhoeh
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Crossref

Optimal efficiency of the Q-cycle mechanism around physiological temperatures from an open quantum systems approach

Scientific Reports
2019-11-13 | Journal article
DOI: 10.1038/s41598-019-52842-x
Contributors: Francesco Tacchino; Antonella Succurro; Oliver Ebenhöh; Dario Gerace
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Crossref

Balancing energy supply during photosynthesis – a theoretical perspective

Physiologia Plantarum
2019-05 | Journal article
DOI: 10.1111/ppl.12962
Contributors: Anna Matuszyńska; Nima P. Saadat; Oliver Ebenhöh
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Crossref

A single-input binary counting module based on serine integrase site-specific recombination

Nucleic Acids Research
2019-05-21 | Journal article
DOI: 10.1093/nar/gkz245
Contributors: Jia Zhao; Alexandra Pokhilko; Oliver Ebenhöh; Susan J Rosser; Sean D Colloms
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Crossref

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

mSystems
2019-02-26 | Journal article
DOI: 10.1128/msystems.00230-18
Contributors: Antonella Succurro; Daniel Segrè; Oliver Ebenhöh; Sarah Glaven
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Crossref

Building Mathematical Models of Biological Systems with modelbase

Journal of Open Research Software
2018-11-16 | Journal article
DOI: 10.5334/jors.236
Contributors: Oliver Ebenhöh; Marvin van Aalst; Nima P. Saadat; Tim Nies; Anna Matuszyńska
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Crossref

The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling

Scientific Reports
2018-08-21 | Journal article
DOI: 10.1038/s41598-018-30884-x
Contributors: Thomas Pfau; Nils Christian; Shyam K. Masakapalli; Lee J. Sweetlove; Mark G. Poolman; Oliver Ebenhöh
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Mathematical model of a serine integrase-controlled toggle switch with a single input

Journal of The Royal Society Interface
2018-06-30 | Journal article
DOI: 10.1098/rsif.2018.0160
Contributors: Alexandra Pokhilko; Oliver Ebenhöh; W. Marshall Stark; Sean D. Colloms
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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
2018-05-31 | Journal article
DOI: 10.1098/rsif.2017.0965
Contributors: Stefano Magni; Antonella Succurro; Alexander Skupin; Oliver Ebenhöh
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Crossref

Review and perspective on mathematical modeling of microbial ecosystems

Biochemical Society Transactions
2018-04-17 | Journal article
DOI: 10.1042/BST20170265
Contributors: Antonella Succurro; Oliver Ebenhöh
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Peer review (43 reviews for 23 publications/grants)

Review activity for Agronomy. (1)
Review activity for Applied statistics. (1)
Review activity for Biochemical Society transactions. (1)
Review activity for Biosystems. (2)
Review activity for Biotechnology for biofuels (1)
Review activity for BMC evolutionary biology. (2)
Review activity for Communications biology. (1)
Review activity for eLife (1)
Review activity for European journal of biochemistry. (2)
Review activity for Faculty Opinions (4)
Review activity for FEBS letters. (1)
Review activity for Journal of experimental botany. (1)
Review activity for Journal of mathematical biology. (1)
Review activity for Journal of plant research. (1)
Review activity for Journal of the Royal Society interface : (7)
Review activity for Microorganisms. (1)
Review activity for Molecular systems biology. (1)
Review activity for MSystems. (2)
Review activity for Nature (1)
Review activity for Philosophical transactions. (1)
Review activity for PLoS computational biology. (7)
Review activity for Proceedings of the National Academy of Sciences of the United States of America. (1)
Review activity for Theory in biosciences. (2)
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