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Dynamic optimization elucidates optimal higher-level pathogenicity strategies of Pseudomonas aeruginosa
Research Square, 2024, June 20, preprint
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, ,
Mathematical modeling predicts that endemics by generalist insects are eradicated if nearly all plants produce constitutive defense
Sci. Rep., 2024, accepted
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, ,
How hosts and pathogens choose the strengths of defense and counter-defense. A game-theoretical view
arXiv:2409.04497, 2024, preprint
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, ,
Endemics by generalist insects are eradicated if nearly all plants produce constitutive defense. An explanation by mathematical modeling
Authorea, June 10, 2024, Preprint
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M. Sitina, ,
Optimal hematocrit theory – A review
Journal of Applied Physiology 137, 2024, 494-509
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, Z. He, ,
Comparing glutamine and glucose as fuels of energy metabolism in cancer and yeast cells: a linear optimization model
npj Syst. Biol. Appl. 10, 2024, 77
[ bibtex ]
,
Studying mixed-species biofilms of Candida albicans and Staphylococcus aureus using Evolutionary Game Theory
PLOS One 19(3), 2024, e0297307
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and
How plant toxins cause early larval mortality in herbivorous insects: An explanation by modeling the net energy curve
Toxins 16, 2024, 72
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, L. Scholz, J. M. Ziermann-Canabarro, ,
Constructing networks for comparison of collagen types
Journal of Integrative Bioinformatics 21, July, 2024, 2023.08.25.554753
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, G. Theißen,
Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content
Sci. Rep. 13, December, 2023, 22996
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, J. Gershenzon,
Selection pressure by specialist and generalist insect herbivores leads to optimal constitutive plant defense. A mathematical model
Ecology and Evolution 13, 2023, e10763
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, , , ,
Game-theoretical description of the go-or-grow dichotomy in tumor development for various settings and parameter constellations
Sci. Rep. 13, 2023, 16758
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,
Enumeration of saturated and unsaturated substituted N-heterocycles
arXiv:2309.02343, 2023, Preprint
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,
How plant toxins cause early larval mortality in herbivorous insects. An explanation by modeling the net-energy curve
Authorea, August 28, 2023, Preprint
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, J. Gershenzon,
Comparing two strategies of counter-defense against plant toxins: A modeling study on plant-herbivore interactions
Front. Ecol. Evol. 11, 2023, 1197757
[ bibtex | doi ]
Reinhart Heinrich: In memoriam of an exceptional scholar
BioSystems 231, 2023, 104965
[ bibtex ]
, J. Gerzhenzon,
Selection pressure by specialist and generalist insect herbivores leads to optimal constitutive plant defense. A mathematical model
Authorea March 10, 2023, preprint
[ bibtex | doi ]
, J. Gershenzon,
Comparing two strategies of counter-defence against plant toxins: A modeling study on plant-herbivore interactions
Authorea February 2, 2023, preprint
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, H. Zhang, ,
Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods
Intern. J. Molec. Sci. 23, 2022, 8692
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Andre Then, Jan Ewald, Natalie Söllner, Rebecca E. Cooper, Kirsten Küsel, Bashar Ibrahim, Stefan Schuster
Agent-based modeling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action
Royal Society Open Science 9, 2022, 211553
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D. de Bartolo, M. de Luca, G. Antonucci, , G. Morone, S. Paolucci, M. Iosa
The golden ratio as an ecological affordance leading to aesthetic attractiveness
PsyCh Journal 11 (5), 2022, 729-740, First published: 23 December 2021
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, P.M. Jansen, S. Brunke, D. Hiller, C.H. Luther, H. González-Díaz, M.T. Dittrich, A. Fleißner, B. Hube, ,
The landscape of toxic intermediates in the metabolic networks of pathogenic fungi reveals targets for antifungal drugs
bioRxiv, 2021, 2021-09
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S. Alseekh, A. Aharoni, Y. Brotman, K. Contrepois, J. D'Auria, , J.C. Ewald, P.D. Fraser, P. Giavalisco, R.D. Hall, M. Heinemann, H. Link, J. Luo, S. Neumann, J. Nielsen, L. Perez de Souza, K. Saito, U. Sauer, F.C. Schroeder, , G. Siuzdak, A. Skirycz, L.W. Sumner, M.P. Snyder, H. Tang, T. Tohge, Y. Wang, W. Wen, S. Wu, G. Xu, N. Zamboni, A.R. Fernie
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
Nature Methods 18 (7), 2021, 747-756
[ bibtex | doi | pdf | PudMed-ID: 34239102 ]
, F. Rivieccio, L. Radosa, , A.A. Brakhage, C. Kaleta
Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis
PLOS Comp. Biol. 17, 2021, e1009645
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S.Schuster, J.Ewald, C.Kaleta
Modeling the energy metabolism in immune cells
Current Opinion in Biotechnology 68, 2021, 282-291
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, ,
Influence of spatial structure on protein damage susceptibility: a bioinformatics approach
Sci. Rep. 11, 2021, 4938
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M. Sitina, ,
Calculating the optimal hematocrit under the constraint of constant cardiac power
Sci. Rep. 11, 2021, 3925
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, , A.T. Kovacs,
Modelling population dynamics in a unicellular social organism community using a minimal model and evolutionary game theory
Open Biology 10(11), 2020, 200206
[ bibtex | doi | PudMed-ID: 33142084 ]
A.Then, K.Mácha, B.Ibrahim, S.Schuster
A novel method for achieving an optimal classification of the proteinogenic amino acids
Scientific Reports 10, 2020, 15321
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E. Barth, , ,
Robustness during Aging — Molecular Biological and Physiological Aspects
Cells 9 (8), 2020, 1862
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S.Peter, F.Ghanim, P.Dittrich, B.Ibrahim
Organizations in reaction-diffusion systems: Effects of diffusion and boundary conditions
Ecological Complexity 43, 2020, 100855
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, ,
Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms
Sci. Rep. 10, 2020, 5579
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M. Sitina, ,
Calculating the optimal hematocrit under the constraint of constant cardiac power
bioRxiv, 2020, 2020.06.09.141374
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, ,
Influence of spatial structure on protein damage susceptibility – A bioinformatics approach
bioRxiv, 2020, 973099
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R.Garde, B.Ibrahim, Á.T.Kovács, S.Schuster
Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms
Royal Society Open Science 7, 2020, 190810
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, , , S.N. Lang, ,
Trends in mathematical modeling of host-pathogen interactions
Cell. Mol. Life Sci. Volume 77, Issue 3, 2020, pp 467–480
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, ,
Determination of scoring functions for protein damage susceptibility
BioSystems 187, 2020, 104035
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R.Garde, B.Ibrahim, Á.T.Kovács, S.Schuster
Differential equation based minimal model describing metabolic oscillations in Bacillus subtilis biofilms
bioRxiv, 2019, 775593
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*, E. Barth*, M. Marz
The landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues
bioRxiv February, 2019, 541417
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, , T. Dandekar,
Optimizing defence, counter-defence and counter-counter defence in parasitic and trophic interactions - A modelling study
arXiv:1907.04820, 2019,
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M.D. Egbert, G. Gruenert, , P. Dittrich
Combining Evolution and Self-organization to Find Natural Boolean Representations in Unconventional Computational Media
BioSystems 184, 2019, 104011
[ bibtex | abstract | doi | pdf | url ]
S. Peter, M. Hölzer, K. Lamkiewicz, P. di Fenizio, H. Al Hwaeer, M. Marz, , P. Dittrich,
Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis
Viruses 11(5), 2019, 449
[ bibtex | abstract | doi | pdf | url | PudMed-ID: 31100972 ]
R. Henze, G. Grünert, , P. Dittrich
Spatial Rule-Based Simulations: The SRSim Software
Hlavacek, William S., Series: Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, Humana Press, New York, NY , 2019, 231-249
[ bibtex | abstract | doi | pdf | url ]
S. Peter, P. Dittrich,
Chemical Organization Theory of Reaction-diffusion systems
In: IEEE (eds. Essaaidi M., Nemiche M.), Conference Location: Ouarzazate, Morocco, Morocco , 4th World Conference on Complex Systems (WCCS), 2019,
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R. Henze, C. Mu, M. Puljiz, N. Kamaleson, J. Huwald, J. Haslegrave, P. di Fenizio, D. Parker, C. Good, J. E. E. Rowe, , P. Dittrich
Multi-scale stochastic organizationoriented coarse-graining exemplified on the human mitotic checkpoint
Sci Reports 9, 2019, 3902
[ bibtex | abstract | doi | pdf | url | PudMed-ID: 30846816 ]
T. Weise, J.M. Reinecke, , M. Pfaff
Optimizing turbidostatic microalgal biomass productivity: A combined experimental and coarse-grained modelling approach
Algal Res. 39, 2019, 101439
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, , , C. Skerka, P. F. Zipfel,
Molecular crypsis by pathogenic fungi using human factor H - A numerical model
PLOS One 14, 2019, e0212187
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, G. Rozenberg, A. Salomaa, C. Zandron (Editors)
CMC2018 - Proceedings of the 19th International Conference on Membrane Computing
Series Lecture Notes in Computer Science, Springer Verlag, 2019, 288 p.
[ bibtex | url ]
K. G. V. Bondoc, C. Lembke, , , , W. Vyverman, G. Pohnert
Decision-making of the benthic diatom Seminavis robusta searching for inorganic nutrients and pheromones.
The ISME journal 13, 2019, 537-546
[ bibtex | abstract | doi | PudMed-ID: 30301945 ]
, , S. Fischer
Die Verteilung des Bindegewebes im Menschen
In: Kongressband 24. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen”. (eds. I. Dienstbühl, M. Stadler, H.-C. Scholle), Verlag Bussert & Stadeler (eds. I. Dienstbühl, M. Stadler, H.-C. Scholle), Verlag Bussert & Stadeler, 2018,
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, U. Dahmen
Computational modeling of oxidative stress in fatty livers elucidates the underlying mechanism of the increased susceptibility to ischemia/reperfusion injury
Computational and Structural Biotechnology Journal 16, 2018, 511-522
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, K. Voigt, P. Kämmer, S. Brunke, , J. Linde
Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion
Frontiers in Microbiology 9, 2018, 2313
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Stefan N. Lang, Sebastian Germerodt, Christina Glock, Christine Skerka, Peter F. Zipfel, Stefan Schuster
Molecular crypsis by pathogenic fungi using human factor H. A numerical model
bioRxiv, 2018, 250662, preprint, published in extended form in PLOS ONE in 2019
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, , , C. Hummert, C. Skerka, P.F. Zipfel, ,
Playing ’hide-and-seek’ with factor H: Game-theoretical analysis of a single nucleotide polymorphism
Journal of the Royal Society Interface 15, 2018, 20170963
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S. Peres, , P. Dague
Thermodynamic constraints for identifying the elementary flux modes
Biochemical Society Transactions 46(3), 2018, 641-647
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Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Computational Investigation of Environment-Noise Interaction in Single-Celled Organisms: The Merit of Expression Stochasticity Depends on the Quality of Environmental Fluctuations
Scientific Reports 8, 2018, 333
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P.Aramillo Irizar, S.Schäuble, D.Esser, M.Groth, C.Frahm, S.Priebe, M.Baumgart, N.Hartmann, S.Marthandan, U.Menzel, J.Müller, S.Schmidt, V.Ast, A.Caliebe, R.König, M.Krawczak, M.Ristow, S.Schuster, A.Cellerino, S.Diekmann, C.Englert, P.Hemmerich, J.Sühnel, R.Guthke, O.W.Witte, M.Platzer, E.Ruppin, C.Kaleta
Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly
Nature Communications 9, 2018, 327
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, X. Liu, , D. Boley
Linear programming model can explain respiration of fermentation products.
PloS one 13, 2018, e0191803
[ bibtex | doi | PudMed-ID: 29415045 ]
, T. Conrad, -Schnelle, M. Gustafsson, U. Dahmen, R. Guthke,
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks
Scientific Reports 8, 2018, 433
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, M. Platzer,
The definition of open reading frame revisited
Trends in Genetics 34, 2018, 167-170
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Thomas Hinze, Benjamin Förster
Event-based Life in a Nutshell: How Evaluation of Individual Life Cycles Can Reveal Statistical Inferences using Action-accumulating P Systems
Lecture Notes in Computer Science 10725, 2018, 129-150, In: M. Gheorghe, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 18th International Conference. ISBN 978-3-319-73358-6, Springer Verlag
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D. Ward, J. Trinogga, K. Wiegand, J. Du Toit, D. Okubamichael, S. Reinsch,
Large shrubs increase soil nutrients in a semi-arid savanna.
Geoderma 310, 2018, 153-162
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, , P. Arnold, B. Hesse, I. Mischewski, M. S. Fischer
Methoden zur Quantifizierung kollagenhaltiger Strukturen
In: Kongressband 23. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen”. (eds. I. Dienstbühl, M. Stadler, H.-C. Scholle), Verlag Bussert & Stadeler, 2017, 299-304
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, , C. Kaleta
Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli.
Scientific reports 7, 2017, 17213
[ bibtex | abstract | doi | PudMed-ID: 29222445 ]
Interview with Gheorghe Paun
Bulletin of the International Membrane Computing Society 4 (Dezember), 2017, 171-180
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B. Christ, U. Dahmen, K.l-H. Herrmann, M. König, J. R. Reichenbach, T. Ricken, , L. O. Schwen, S. Vlaic, N. Waschinsky
Computational Modeling in Liver Surgery
Frontiers in Physiology - Gastrointestinal Sciences 8, 2017, 906
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, U. Dahmen, R. Guthke,
Zonation of hepatic fat accumulation: insights from mathematical modelling of nutrient gradients and fatty acid uptake.
Journal of the Royal Society Interface 14, 2017, pii: 20170443
[ bibtex | abstract | doi | PudMed-ID: 28835543 ]
, ,
Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances
Biochemical Society Transactions 45 (4), 2017, 1-9
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, , , C. Kaleta, T. Dandekar and
Modelling the host–pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization
Journal of The Royal Society Interface 14 (132), 2017, 20170095
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A new solution concept for the ultimatum game leading to the Golden Ratio
Scientific Reports 7, 2017, 5642
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S. Klamt, G. Regensburger, M.P. Gerstl, C. Jungreuthmayer, , R. Mahadevan, J. Zanghellini, S. Müller
From Elementary Flux Modes to Elementary Flux Vectors: Metabolic Pathway Analysis with Arbitrary Linear Flux Constraints
PLOS Computational Biology 13 (4), 2017, e1005409
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, , T. Dandekar,
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
PLOS Computational Biology 13, 2017, e1005371
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S. Peres, M. Jolicoeur, C. Moulin, P. Dague,
How important is thermodynamics for identifying elementary flux modes?
PLOS One 12, 2017, e0171440
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, , S. Sasso
Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids
Scientific Reports 7, 2017, 39821
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K. Czakai, M. Dittrich, M. Kaltdorf, T. Müller, S. Krappmann, A. Schedler, M. Bonin, , , C. Speth, G. Rambach, H. Einsele, T. Dandekar, J. Löffler
Influence of platelet-rich plasma on the immune response of human monocyte-derived dendritic cells and macrophages simulated with Aspergillus fumigatus
International Journal of Medical Microbiology 307 (2), 2017, 95–107
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Coping with Dynamical Structures for Interdisciplinary Applications of Membrane Computing
Springer Series Lecture Notes in Computer Science 10105, 2017, 16-27
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S. Ellenberger, A. Burmester, , J. Wöstemeyer
Post-translational regulation by structural changes of 4-dihydromethyltrisporate dehydrogenase, a key enzyme in sexual and parasitic communication mediated by the trisporic acid pheromone system, of the fungal fusion parasite Parasitella parasitica
Journal of theoretical Biology 413, 2017, 50-57
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, K. Voigt,
The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenic aliphatic amino acids
Biochimica and Biophysica Acta - General Subjects 1861 ( 1, Part A), 2017, 3258-3269
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, L. Weber, U. Hatnik
Walking Membranes: Grid-exploring P Systems with Artificial Evolution for Multi-purpose Topological Optimisation of Cascaded Processes
Lecture Notes in Computer Science 10105 , 2017, 251-271
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, C. Kiefer, G. Coupland, L. E. Rose
Pinpointing genes underlying annual/perennial transitions with comparative genomics.
BMC genomics 17, 2016, 921
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M. Hölzer, V. Krähling ,F. Amman, E. Barth, S.H. Bernhart, V.A. Carmelo, M. Collatz, G. Doose , F. Eggenhofer, , J. Fallmann, L.M. Feldhahn , M. Fricke, , A.J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A.H. Sahyoun, S.J. Saunders, S.E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M.T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P.F. Stadler, S. Becker, M. Marz
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Scientific Reports 6: 34589, 2016,
[ bibtex | abstract | PudMed-ID: 27713552 ]
Hebecker B, , Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID
Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions.
Scientific Reports 6, 2016, 36055
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A. Dix, , R. Guthke, J. Linde
Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers.
Clinical Microbiology and Infection 22 (7), 2016, 600-606
[ bibtex | PudMed-ID: 27113568 ]
, , A. Lück, S. Pande, , , , C. Kost
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
PLOS Computational Biology 12 (6), 2016, e1004986
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J. Pollmächer, S. Timme, , A.A. Brakhage, P.F. Zipfel, M.T. Figge
Deciphering the counterplay of Aspergillus fumigatus infection and host inflammation by evolutionary games on graphs
Scientific Reports 6, 2016, Article number: 278072016
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, C. Gentsch, J. Mansfeld, K. Schmeißer, S. Waschina, S.Brandes, L. Klimmasch, N. Zamboni, K. Zarse, , M. Ristow, ,
A genome-scale database and reconstruction of Caenorhabditis elegans metabolism
Cell Systems 2 (5), 2016, 312-322
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T. Weise, , M. Pfaff
Bestimmung algenbiotechnologisch relevanter Parameter im kontinuierlichen Bioprozessregime: Ertrags- und Maintenance-Koeffizient
In: Tagungsband 17. NW-Konferenz der mittel- und ostdeutschen Hochschulen für angewandte Wissenschaften (eds. T. Seul), 2016, 30-35
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S. Ellenberger, L. Siegmund, , J. Wöstemeyer
Horizontal gene transfer between bacteria and protozoa: Gene-specific detection by combining different approaches in a new score-based algorithm
Endocytobiosis and Cell Research 27 (2), 2016, 36-46
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S. Widder, R. J. Allen, T. Pfeiffer, ..., , ...,O. S. Soyer
Challenges in microbial ecology: building predictive understanding of community function and dynamics
ISME Journal 10, 2016, 2557-2568
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, , K. Kirkici, Pa. Sauer, Pe. Sauer, S. Hayat
Passion to P for Polymorphic Processes in Practice
In: Multidisciplinary Creativity. Homage to Gheorghe Paun on His 65th Birthday (eds. M. Gheorghe, I. Petre, M.J. Perez-Jimenez, G. Rozenberg, A. Salomaa), ISBN 978-606-8401-63-8, Spandugino, 2016, ch. 7, 77-88
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, K. Kirkici, Pa. Sauer, Pe. Sauer,
Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential
Springer Lecture Notes in Computer Science 9504, 2016, 215-235
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S. Pande, F. Kaftan, S. Lang, A. Svatos, , C. Kost
Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments
ISME Journal 10, 2016, 1413-1423
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M. T. Prauße, , R. Guthke,
Computing the various pathways of penicillin synthesis and their molar yields.
Biotechnology and bioengineering 113 (1), 2016, 173-181
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A. Lopez Garcia de Lomana, , J. Valenzuela, S. Imam, W. Carter, D. D. Bilgin, C. B. Yohn, S. Turkarslan, D. J. Reiss, M. V. Orellana, N. D. Price, N. S. Baliga
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.
Biotechnology for biofuels 8, 2015, 207
[ bibtex | abstract | doi | PudMed-ID: 26633994 ]
J.Mansfeld, N.Urban, S.Priebe, M.Groth, C.Frahm, N.Hartmann, J.Gebauer, M.Ravichandran, A.Dommaschk, S.Schmeisser, D.Kuhlow, S.Monajembashi, S.Bremer-Streck, P.Hemmerich, M.Kiehntopf, N.Zamboni, C.Englert, R.Guthke, C.Kaleta, M.Platzer, J.Sühnel, O.W.Witte, K.Zarse, M.Ristow
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing
Nature Communications 6, 2015, 10043
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S. Imam, , J. Valenzuela, A. Lopez Garcia de Lomana, W. Carter, N. D. Price, N. S. Baliga
A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses.
The Plant journal : for cell and molecular biology 84 (6), 2015, 1239–1256
[ bibtex | abstract | doi | PudMed-ID: 26485611 ]
S. K. Ludwig, , , L. A. van Ginkel, H. Zhu, A. Ozcan, M. W. Nielen
Calling biomarkers in milk using a protein microarray on your smartphone
PloS one 10, 2015, e0134360
[ bibtex | abstract | doi | PudMed-ID: 26308444 ]
, D. Boley, , ,
Mathematical models for explaining the Warburg effect: A review focussed on ATP and biomass production
Biochemical Society Transactions 43 (6), 2015, 1187-1194
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, , R. König, S. Lorkowski,
Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types
Biochimie 118, 2015, 185-194
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, M. Pfaff, A. Ghallab, D. Driesch, S. G. Henkel, J. G. Hengstler, , , R. Gebhardt, S. Zellmer P. Li
Optimality in the zonation of ammonia detoxification in rodent liver
Archives of Toxicology 89 (11), 2015, 2069-2078
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, D. Boley, ,
A minimal model for explaining the higher ATP production in the Warburg effect
PeerJ PrePrints 3, 2015, e1309v1
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K. Kupczik, , R. Mundry, F.T. Neininger, T. Heidlauf, O. Röhrle
Reconstruction of muscle fascicle architecture from iodine-enhanced microCT images: A combined texture mapping and streamline approach
Journal of Theoretical Biology 382, 2015, 34-43
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P. Sauer, , P. Hofstedt
Dynamic Ad-hoc Topologies for Mobile Robot Navigation Based on Non-Uniform Grid Maps
International Journal of Mechanical and Mechatronics Engineering 2(6), 2015, 92-101
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, , C. Skerka, P. F. Zipfel, T. Dandekar,
Host-pathogen interactions between the human innate immune system and Candida albicans - Understanding and modeling defense and evasion strategies
Frontiers in Microbiology 6 (625), 2015,
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G.M.de Hijas-Liste, E.Balsa-Canto, , , P.Li, J.R.Banga,
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation
BMC Bioinformatics 16, 2015, 163
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T. Weise, , M. Pfaff
Mikroalgen- Kultivierung im tubulären Photobioreaktor: Biomasse-Produktivität von Nannochloropsis salina im dis- und semikontinuierlichen Bioprozessregime
In: Tagungsband 16. Nachwuchswissenschaftlerkonferenz der mittel- und ostdeutschen Hochschulen für angewandte Wissenschaften (eds. M. Knaut), 2015, 257-262
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, , ,
Footprints of Optimal Protein Assembly Strategies in the Operonic Structure of Prokaryotes
Metabolites 5 (2), 2015, 252-269
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J.A. Nyakatura,
Aberrant back muscle function correlates with intramuscular architecture of dorsovertebral muscles in two-toed sloths
Mammalian Biology - Zeitschrift für Säugetierkunde 80, 2015, 114-121
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The Golden Ratio as a proposed solution of the Ultimatum Game: An explanation by continued fractions
arXiv:1502.02552, 2015,
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Zonation of hepatic fatty acid metabolism - the diversity of its regulation and the benefit of modeling
BBA - Molecular and Cell Biology of Lipids 1851, 2015, 641-656
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J. Linde, S. Duggan, M. Weber, F. Horn, , D. Hellwig, K. Riege, M. Marz, R. Martin, R. Guthke, O. Kurzai
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Nucleic acids research 43, 2015, 1392-1406
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Lecture Notes in Computer Science 8961, 2015, 241-257
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Evolution 68, 2014, 2559-2570
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Evolutionary game theory: molecules as players
Molecular Biosystems 10 (12), 2014, 3066 - 3074
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Plos One 9 (1), 2014, e84837
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Commemorating the 1913 Michaelis-Menten paper Die Kinetik der Invertinwirkung: three perspectives
FEBS Journal 281, 2014, 435-463
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S. Pande, H. Merker, , M. Reichelt, , L.F. de Figueiredo, , C. Kost
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ISME Journal 8, 2014, 953–962
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What can we learn from Einstein and Arrhenius about the optimal flow of our blood?
Biochimica et Biophysica Acta - General Subjects 1840 (1), 2014, 271–276
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Fungal alternative splicing is associated with multicellular complexity and virulence - A genome-wide multi-species study
DNA Research 21, 2014, 37-39
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Quantification of the interaction between biomaterial surfaces and bacteria by 3-D modeling.
Acta Biomaterialia 10(1), 2014, 267-275
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A theoretical study of lipid accumulation in the liver - Implications for nonalcoholic fatty liver disease
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids 1841 (1), 2014, 62-69
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Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology
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Probandenspezifische Modellanpassungen für die Simulation ausgewählter Maßnahmen einer Wirbelsäulenstabilisierung
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In silico approaches and the role of ontologies in aging research
Rejuvenation Research 16 (6), 2013, 540-546
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The combinatorial multitude of fatty acids can be described by Fibonacci numbers
arXiv:1303.7189, 2013,
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International Journal of Foundations of Computer Science 24(5), 2013, 605-607
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A. K. Stavrum, , , P. Puntervoll, M. Ziegler
Model of Tryptophan Metabolism, Readily Scalable using Tissue-Specific Gene Expression Data.
Journal of Biological Chemistry 288, 2013, 34555-34566
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M. Bartl, , , P. Li,
Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes.
Nature Communications 4, 2013, 2243
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K. Schmeisser, J. Mansfeld, D. Kuhlow, S. Weimer, K. Zarse, S. Priebe, , M. Birringer, M. Groth, A Segref, C. Werner, S. Schmeisser, , A. Pfeiffer, R. Guthke, M. Platzer, T. Hoppe, H. Cohen, D. Sinclair, M. Ristow
Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide
Nature Chemical Biology 9, 2013, 693-700
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BioSystems 114, 2013, 31-38
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E ffect of substrate competition in kinetic models of metabolic networks
FEBS Letters 587, 2013, 2818-2824
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A. Rezola, J. Pey, L.F. de Figueiredo, A. Podhorski, , A. Rubio, F.J. Planes
Selection of human tissue-specific elementary flux modes using gene expression data
Bioinformatics 29 (16), 2013, 2009-2016
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Metabolic costs of amino acid and protein production in Escherichia coli
Biotechnology Journal 8, 2013, 1105-1114
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Quantitative Modeling of Fibrinogen Adsorption on Different Biomaterials
Cellular and Molecular Bioengineering 6 (2), 2013, 210-219
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Maintenance of Chronobiological Information by P System Mediated Assembly of Control Units for Oscillatory Waveforms and Frequency
In: Membrane Computing. 13th International Conference (eds. E. Csuhaj-Varju, M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, G. Vaszil), Vol. 7762, Springer Verlag, 2013, 208-227
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S. Ellenberger; ; J. Wöstemeyer
Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo
Journal of theoretical Biology 320, 2013, 66-75
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Intramuscular architecture of the autochthonous back muscles in humans.
Journal of Anatomy 222 (2), 2013, 214–222
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S. A. Shabalovskaya, , E. Heurich, M. Rettenmayr
Evaluation of wettability and surface energy of native Nitinol surfaces in relation to hemocompatibility
Materials Science & Engineering C-Materials for Biological Applications 33 (1), 2013, 127–132
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Metabolites 2, 2012, 940-958
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Out of (transcriptional) control? Design principles of the regulatory network controlling metabolic pathways in Escherichia coli
Proceedings of the German Conference on Bioinformatics 2012 , 2012,
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Stoffwechselanalyse: Neue Wege im Labyrinth entdecken
Laborwelt 4, 2012, 30-32
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N. Kottenhagen, L. Gramzow, F. Horn, and G. Theißen
Polyglutamine and polyalanine tracts are enriched in transcription factors of plants
In: Proceedings of the German Conference on Bioinformatics 2012 (eds. S. Böcker, F. Hufsky, K. Scheubert, J. Schleicher, S. Schuster), OASICS, 2012, 93-107
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Reply to Böning, Maassen, and Pries.
Journal of Applied Physiology 113, 2012, 1169
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GC content dependency of Open Reading Frame prediction via stop codon frequencies
Gene 511, 2012, 441-446
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Two new perspectives on NAD metabolism
In: Proceedings of the German Conference on Bioinformatics 2012 (eds. ), 2012, 5-8
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Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus
PLoS Computational Biology 8(9), 2012, e1002697
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On the evolutionary significance of the size and planarity of the proline ring
Naturwissenschaften 99, 2012, 789-799
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Intramuskuläre Architektur der menschlichen Rückenmuskulatur – Rekonstruktion, Modellierung & Simulation.
In: Kongressband 18. Erfurter Tage “Prävention von arbeitsbedingten Gesundheitsgefahren und Erkrankungen”. (eds. Grieshaber, R.; Stadler, M.; Scholle, H.-Ch.), Verlag Bussert & Stadeler, 2012,
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Detecting and investigating substrate cycles in a genome-scale human metabolic network
FEBS Journal 279, September, 2012, 3192–3202
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Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts.
PLoS ONE 7, 2012, e42150
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, A. Schroeter, C. Schimek, S. Vlaic, J. Wöstemeyer,
Model of the synthesis of trisporic acid in Mucorales showing bistability
IET Systems Biology 6, 2012, 207-214
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Comparison of various approaches to calculating the optimal hematocrit in vertebrates.
Journal of Applied Physiology 113, 2012, 355-367
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Temperature compensation and entrainment in circadian rhythms.
Physical Biology 9, 2012, 036011
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Unraveling Oscillating Structures by Means of P Systems
In: Research Topics in Membrane Computing (eds. M. Gheorghe, G. Paun, M.J. Perez-Jimenez), University of Sevilla, 2012, 39-42
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Agent-based modeling approach of immune defense against spores of opportunistic human pathogenic fungi
Frontiers in Microbial Immunology 3, 2012, 129
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Against the stream: Relevance of gluconeogenesis from fatty acids for natives of the arctic regions
International Journal of Circumpolar Health 71, 2012, 18436
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NAD biosynthesis and salvage - a phylogenetic perspective.
FEBS Journal 279 (18), September, 2012, 3355-3363
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Modelling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii
Journal of Biological Physics 38 (3), 2012, 449-464
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Chemical Analog Computers for Clock Frequency Control Based on P Modules
In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 182-202
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Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problems
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Detecting structural invariants in biological reaction networks.
Methods in Molecular Biology 804, 2012, 377-407
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I. Zevedei-Oancea,
Topological analysis of metabolic networks based on petri net theory.
Studies in health technology and informatics 162, 2011, 17-37
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M. Böl, N. Schilling,
Erratum to: Micromechanical modelling of skeletal muscles: from the single fibre to the whole muscle
Archive of Applied Mechanics 81, 2011, 1757-1757
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M. Böl, , N. Schilling
On a phenomenological model for fatigue effects in skeletal muscles.
J. Theor. Biol. 281, 2011, 122-132
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A. Göhler, Ö, Kökpinar, W. Schmidt-Heck, R. Geffers, R. Guthke, U. Rinas, , K. Jahreis,
More than just a metabolic regulator – elucidation and validation of new targets of PdhR in Escherichia coli
BMC Systems Biology 5 (197), 2011,
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Hands-on Metabolism Analysis of Complex Biochemical Networks Using Elementary Flux Modes.
Methods in Enzymology 500, 2011, 437-456
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F. Wessely, M. Bartl, R. Guthke, P. Li, ,
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.
Molecular Systems Biology 7, 2011, 515
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Calculating activation energies for temperature compensation in circadian rhythms
Physical Biology 8 (5), 2011, 056007
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Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii
Plos ONE 6 (8), 2011, e23026
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Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In-silico Study of Modules for Circadian Clock Systems.
Computational Intelligence and Neuroscience, vol. 2011, 2011, ID 262189
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L.F. de Figueiredo, T.I. Gossmann, M. Ziegler,
Pathway Analysis of NAD+ metabolism
Biochemical Journal 439 , 2011, 341–348
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In silico evidence for gluconeogenesis from fatty acids in humans
PLoS Computational Biology 7, 2011, e1002116
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Special issue: Integration of OMICs datasets into metabolic pathway analysis.
BioSystems 105, 2011, 107-108
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Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach
BioSystems 105, 2011, 147-153
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G. Beuster, K. Zarse, , R. Thierbach, M. Kiehntopf, P. Steinberg, , M. Ristow
Inhibition of alanine aminotransferase (ALAT) in silico and in vivo promotes mitochondrial metabolism to impair malignant growth
Journal of Biological Chemistry 286 (25), 2011, 22323-22330, Highlighted in Pädiatrix 6/2011 in the article "Stoffwechsel und Krebs – Krebs und Stoffwechsel" by Dr. Corinna Volz-Zang
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Y. Elhanati, , N. Brenner
Dynamic modeling of cooperative protein secretion in microorganism populations
Theoretical Population Biology 80 (1), 2011, 49-63
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R.H. Bortfeldt, , I. Koch
Exhaustive analysis of the modular structure of the spliceosomal assembly network – a Petri net approach.
Studies in Health Technology and Informatics 162, 2011, 244-278, Reprint of an article published in In Silico Biol. 10 (2010) 0007
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Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization
ERCIM News 85, 2011, 27-29
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A. Rezola, , M. Brock, J. Pey, A. Podhorski, C. Wittmann, , A. Bockmayr, F.J. Planes
Exploring metabolic pathways in genome-scale networks via generating flux modes.
Bioinformatics 27 (4), Feb, 2011, 534-540
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Topological Analysis of Metabolic and Regulatory Networks.
In: Modeling in Systems Biology – the Petri Net Approach (eds. I. Koch, W. Reisig, F. Schreiber), Springer-Verlag, 2011, ch. 10, 209-224
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Combinatorics of aliphatic amino acids
Naturwissenschaften 98 (1), 2011, 79-86
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Synchronisation of Biological Clock Signals: Capturing Coupled Repressilators from a Control Systems Perspective
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A novel method of studying fascicle architecture in relaxed and contracted muscles.
Journal of Biomechanics 43, 2010, 2897-2903
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Membrane Computing. Eleventh International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers.
M. Gheorghe, T. Hinze, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Series: Lecture Notes in Computer Science (Vol. 6501), Subseries: Theoretical Computer Science and General Issues , Springer Verlag, Heidelberg 2010, 393, ISBN: 978-3642181221
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Proceedings Compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC2010) and of the First Workshop on Applications of Membrane Computing, Concurrency, and Agent-based Modelling in Population Biology (AMCA-POP2010)
J. Behre, G. Escuela, T. Hinze (Eds.), ProBusiness Verlag, Berlin 2010, 238, ISBN: 978-3-86805-767-6
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G. Escuela, , P. Dittrich, , M. Moreno
Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems
In: Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS2010) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2010, 306-311, ISBN: 978-989-674-018-4
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R. H. Bortfeldt, , I. Koch
Exhaustive analysis of the modular structure of the spliceosomal assembly network - a Petri net approach
In Silico Biology 10, 2010, 0007
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Jensen's Inequality as a Tool for Explaining the Effect of Oscillations on the Average Cytosolic Calcium Concentration
Theory in Biosciences 129 (1), 2010, 25–38
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F. Centler, , P. Speroni di Fenizio, P. Dittrich
A parallel algorithm to compute chemical organizations in biological networks
Bioinformatics 26 (14), 2010, 1788-1789
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G. Grünert, B. Ibrahim, T. Lenser, M. Lohel, , P. Dittrich
Rule-based spatial modeling with diffusing, geometrically constrained molecules
BMC Bioinformatics 11, 2010, 307
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J. Decraene,
A Multidisciplinary Survey of Computational Techniques for the Modelling, Simulation and Analysis of Biochemical Networks
Journal of Universal Computer Science 16 (9), 2010, 1152-1175
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M. Sturm,
Verfahren zur Ausführung von mathematischen Operationen mittels eines DNA-Computers und DNA-Computer hierzu
Deutsches Patent, DE 101 59 886 B4, IPC G06N 3/00 patent, Deutsches Patentamt München, 2010, granted 2010
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G. Escuela, , P. Dittrich, , M. Moreno-Alvarez
Applying Membrane Systems in Food Engineering
In: Eight Brainstorming Week on Membrane Computing (eds. M.A. Martinez-del-Amor, G. Paun, I. Perez-Hurtado, A. Riscos-Nunez), Fenix Editora, Sevilla 2010, 109-121, ISBN: 978-84-614-2357-6
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H. Bordihn, R. Freund, , M. Holzer, M. Kutrib, F. Otto
Proceedings of the Second Workshop on Non-Classical Models for Automata and Applications - Vol. 263 (NCMA2)
Austrian Computer Society 2010, ISBN: 978-3-85403-263-2
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M. Gheorghe , G. Paun
Proceedings of the Eleventh International Conference on Membrane Computing (CMC11)
ProBusiness Verlag, Berlin 2010, ISBN: 978-3-86805-721-8
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M. Bartl, M. Pfaff,S. Toepfer, S. Zellmer, R. Gebhardt, , P. Li
Model-based Optimization to Explain Liver Zonation in Nitrogen Metabolism
In: Proceedings of the 55th International Scientific Colloquium (eds. ), Ilmenau, Germany 2010, 235-240
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M. Bartl, , , , P. Li
Just-in-time activation of a glycolysis inspired metabolic network - solution with a dynamic optimization approach
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CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
In: Proceedings of the 25th German Conference on Bioinformatics (eds. D. Schomburg, A. Grote), Gesellschaft f. Informatik, Bonn, 2010, 71-80, ISBN 978-3-88579-267-3
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Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
BMC Systems Biology 4, 2010, 116
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G. Gruenert, B. Ibrahim, T. Lenser, M. Lohel, , P. Dittrich
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BMC Bioinformatics 11, 2010, 307
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Towards a Unified Approach for the Modelling, Analysis, and Simulation of Cell Signalling Networks.
In: Sequence and Genome Analysis: Methods and Applications (eds. Z. Zhao), iConcept Press, 2010, ch. 13, 227-257
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Revisiting the thermodynamic theory of optimal ATP stoichiometries by analysis of various ATP-producing metabolic pathways
The Journal of Molecular Evolution 71, 2010, 346-355
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Fibrinogen adsorption on biomaterials - a numerical study
Macromol Biosci 10, 2010, 1216-1233
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Biochemical Society Transactions 38, 2010, 1202-1205
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Batman – The Dark Knight: A Game Theoretical Approach
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Game theoretical modelling of survival strategies of Candida albicans inside macrophages
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Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation
Physical Biology 7, 2010, 036009
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E. Ruppin, J.A. Papin, ,
Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
Current Opinion in Biotechnology 21, 2010, 502-510
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C. Gille, C. Bölling, A. Hoppe, S. Bulik, S. Hoffmann, K. Hübner, A. Karlstädt, R. Ganeshan, M. König, K. Rother, M. Weidlich, , H.G. Holzhütter
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Molecular Systems Biology 6, 2010, 411
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Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis
FEBS J 277, 2010, 1023-1034
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Cooperation and cheating in microbial exoenzyme production - Theoretical analysis for biotechnological applications
Biotechnology Journal 5, 2010, 751-758
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M. Bartl, P. Li,
Modelling the optimal timing in metabolic pathway activation-Use of Pontryagin's Maximum Principle and role of the Golden section
Biosystems 101, 2010, 67-77
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R. Sinha, T. Lenser, N. Jahn, U. Gausmann, , K. Szafranski, K. Huse, P. Rosenstiel, J. Hampe, , M. Hiller, R. Backofen, M. Platzer
TassDB2 - A comprehensive database of subtle alternative splicing events
BMC Bioinformatics 11, 2010, 216
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Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator
In: Proceedings of the 10th International Workshop on Membrane Computing (WMC) (eds. G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, A. Salomaa), Springer Verlag, 2010, 316-334
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R. Haberland,
Prolog-based XML processing for compact representation and deductive evaluation of biological reaction networks
In: Abstract Booklet, International Conference Biosystems Analysis and Engineering (BioSys) (eds. G. Antranikian, D. Chiu, F. Keil, A. Liese, T.Scheper, A.-P. Zeng), University of Technology Hamburg, 2009, 27
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Detecting Metabolic Conversions in Genome-Scale Metabolic Networks on the Basis of Elementary Flux Patterns in Subnetworks
In: Proceedings of the Vienna Conference on Mathematical Modelling 2009 - Vol. 2 of ARGESIM Reports (eds. I. Troch, F. Breitenecker), MathMod, Vienna 2009, 748-759
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Calculating the K-shortest elementary flux modes in metabolic networks
In: Proceedings of the Vienna Conference on Mathematical Modelling 2009 - Vol. 2 of ARGESIM Reports (eds. I. Troch, F.Breitenecker), MathMod, Vienna 2009, 736-747
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Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics
In: Proceedings Booklet Fifth Conference on Computability in Europe (CiE) (eds. K. Ambos-Spies, B. Löwe, W. Merkle), University of Heidelberg 2009, 186-195
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Modelling host-pathogen and pathogen-pathogen interactions of opportunistic fungal infections in humans: evolutionary game theory and individual-based modelling
Mycoses 52 (5), 2009, 425-425
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From Artificial Chemistry to Systems Biology: Software for Chemical Organization Theory
In: Artificial Life Models in Software - Vol. II (eds. A. Adamatzky, M. Komosinski), Springer, London, 2009, 319-342
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N. Matsumaru, , P. Dittrich
Organization-Oriented Chemical Programming of Distributed Artifacts
International Journal of Nanotechnology and Molecular Computation 1 (4), 2009, 54-70
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EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks
In: Proceedings of the 14th German Conference on Bioinformatics (GCB) (eds. I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler), Gesellschaft f. Informatik e.V., Bonn 2009, 180-190
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, A. Podhorski, A. Rubio, , J.E. Beasley, , F.J. Planes
Computing the shortest elementary flux modes in genome-scale metabolic networks
Bioinformatics 25, 2009, 3158-3165
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, , , D.A. Fell
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'
Bioinformatics 25, 2009, 3330-3331
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Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
Genome Research 19, 2009, 1872-1883
[ bibtex | abstract | PudMed-ID: 19541909 ]
, S. Richter, P. Dittrich
Using chemical organization theory for model checking
Bioinformatics 25, 2009, 1915-1922
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, R. Fassler, T. Lenser, P. Dittrich
Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled using Mass-Action Kinetics
International Journal of Foundations of Computer Science 20, 2009, 411-426
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, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich
Event-Driven Metamorphoses of P Systems
Lecture Notes in Computer Science 5391, 2009, 231-245
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Modeling signal transduction in enzyme cascades with the concept of elementary flux modes
J Comput Biol 16, 2009, 829-844
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, , , D.A. Fell
Can sugars be produced from fatty acids? A test case for pathway analysis tools (Erratum)
Bioinformatics 25, 2009, 152-158
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J. Kielbassa, R. Bortfeldt, , I. Koch
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry 33, 2009, 46-61
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, S. Textor, J. Gershenzon,
Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves
Phytochemistry Reviews 8, 2009, 39-51
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, J. U. Kreft, A. Schroeter, T. Pfeiffer
Use of game-theoretical methods in biochemistry and biophysics.
Journal of Biological Physics 34, 2008, 1-17
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, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks
In: Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, 2008, 162-169
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T. Lenser, N. Matsumaru, , P. Dittrich
Tracking the Evolution of Chemical Computing Networks
In: Proceedings of Artificial Life XI (eds. ), 2008, 343-350
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F. Centler, , Fenizio. PS. di, P. Dittrich
Computing chemical organizations in biological networks.
Bioinformatics 24, 2008, 1611-1618
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S. Hayat,
Toward integration of in vivo molecular computing devices: successes and challenges
HFSP Journal 2, 2008, 239-243
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K.S. Hilden, R. Bortfeldt, M. Hofrichter, A. Hatakka, T.K. Lundell
Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia
Microbiology 154, 2008, 2371-2379
[ bibtex | abstract | PudMed-ID: 18667569 ]
, , , DA. Fell
Can sugars be produced from fatty acids? A test case for pathway analysis tools.
Bioinformatics 24, 2008, 2615-2621
[ bibtex | PudMed-ID: 18806269 ]
D. Deutscher, I. Meilijson, , E. Ruppin
Can single knockouts accurately single out gene functions?
BMC Systems Biology 2, 2008, 50
[ bibtex | abstract | pdf | PudMed-ID: 18564419 ]
, F. Centler, Fenizio. PS. di, P. Dittrich
Phenotype prediction in regulated metabolic networks.
BMC Systems Biology 2, 2008, 1-15
[ bibtex | PudMed-ID: 18439260 ]
R. Bortfeldt, S. Schindler, K. Szafranski, , D. Holste
Comparative analysis of sequence features involved in the recognition of tandem splice sites
BMC Genomics 9, 2008, 202
[ bibtex | abstract | pdf | PudMed-ID: 18447903 ]
, T. Pfeiffer, D.A. Fell
Is maximization of molar yield in metabolic networks favoured by evolution?
Journal of Theoretical Biology 252, 2008, 497-504
[ bibtex | abstract | PudMed-ID: 18249414 ]
, T. Wilhelm, , E. Ruppin,
Structural robustness of metabolic networks with respect to multiple knockouts
Journal of Theoretical Biology 252, 2008, 433-441
[ bibtex | abstract | doi | PudMed-ID: 18023456 ]
, M. Marhl, M. Perc,
Equality of average and steady-state levels in some nonlinear models of biological oscillations
Theory in Biosciences 127, 2008, 1-14
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R. Bortfeldt, A. Herrmann, H. Pospisil,
Validation of human alternative splice forms using the EASED platform and multiple splice site discriminating features
In: Mathematical Modeling of Biological Systems - Vol. I (eds. A. Deutsch, L. Brusch, H. Byrne, G. de Vries,, H.-P. Herzel), Birkhäuser, Boston, 2007, 337-349
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, M. Marhl,
Selective Regulation of Protein Activity by Complex Ca2+Oscillations: A Theoretical Study
In: Mathematical Modeling of Biological Systems - Vol. I (eds. A. Deutsch, L. Brusch, H. Byrne, G. de Vries, H.-P. Herzel), Birkhäuser, Boston, 2007, 11-24
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, D.A. Fell
Modelling and simulating metabolic networks
In: Bioinformatics: From Genomes to Therapies (eds. T.Lengauer), Wiley-VCH, Weinheim, 2007, ch. 20, 755-805
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, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo
Series Lecture Notes in Computer Science 4860, 2007, 320-335
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Understanding the roadmap of metabolism by pathway analysis.
Methods in Molecular Biology 358, 2007, 199-226
[ bibtex | PudMed-ID: 17035688 ]
R. Schwarz, C. Liang, , M. Kuhnel, E. Hoffmann, S. Kuznetsov, M. Hecker, G. Griffiths, , T. Dandekar
Integrated network reconstruction, visualization and analysis using YANAsquare
BMC Bioinformatics 8, 2007, 313
[ bibtex | abstract | pdf | PudMed-ID: 17725829 ]
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Continuous model for the rock-scissors-paper game between bacteriocin producing bacteria
J of Mathematical Biology 54, 2007, 815-846
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M. Hiller, S. Nikolajewa, K. Huse, K. Szafranski, P. Rosenstiel, , R. Backofen, M. Platzer
TassDB: a database of alternative tandem splice sites
Nucleic Acids Research 35, 2007, D188-D192
[ bibtex | abstract | pdf | PudMed-ID: 17142241 ]
, T. Dandekar, J. Korbel, P. Bork,
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism
Gene 396, 2007, 215-225
[ bibtex | abstract | PudMed-ID: 17467928 ]
,
Modeling the rock - scissors - paper game between bacteriocin producing bacteria by Lotka-Volterra equations
Discrete and Continuous Dynamical Systems 8, 2007, 207-228
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, E. Klipp, M. Marhl
The predictive power of molecular network modelling - case studies of predictions with subsequent experimental verification
In: Discovering Biomolecular Mechanisms with Computational Biology (eds. F. Eisenhaber), Landes Bioscience, Georgetown 2006, 95-103
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T. Aho, T. Wilhelm, A. Beyer, , O. Yli-Harja
Finding infeasible reactions in metabolic networks: comparison of methods
In: Proceedings of the 4th TICSP Workshop on Computational Systems Biology (eds. P. Ruusuvuori et al.), WCSB 2006, Tampere 2006, 23-26
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, E. Klipp, M. Marhl
The Predictive Power of Molecular Network Modelling. Case Studies of Predictions with Subsequent Experimental Verification.
In: Discovering Biomolecular Mechanisms with Computational Biology (F. Eisenhaber, ed.) Landes Bioscience, 2006, 95-103
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, F. Centler, P. Dittrich
Analyzing molecular reaction networks: from pathways to chemical organizations.
Molecular Biotechnology 34, 2006, 117-123
[ bibtex | PudMed-ID: 17172657 ]
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Metatool 5.0: fast and flexible elementary modes analysis
Bioinformatics 22, 2006, 1930-1931
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, R. Eils, K. Prank
5th International Conference on Systems Biology (ICSB 2004), Heidelberg, October 9-13, 2004.
Biosystems 83, 2006, 71-74
[ bibtex | PudMed-ID: 16242837 ]
M. Marhl, M. Perc,
A minimal model for decoding of time-limited Ca2+ oscillations
Biophys Chem 120, 2006, 161-167
[ bibtex | abstract | PudMed-ID: 16338050 ]
A. Fajmut, M. Brumen,
Theoretical model of the interactions between Ca2+, calmodulin and myosin light chain kinase
FEBS Letters 579 (20), 2005, 4361-4366
[ bibtex | abstract | PudMed-ID: 16051224 ]
M. Marhl, M. Perc,
Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations
FEBS Letters 579, 2005, 5461-5465
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I. Zevedei-Oancea,
A theoretical framework for detecting signal transfer routes in signalling networks
Computers and Chemical Enginering 29, 2005, 597-617
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R. Schwarz, P. Musch, , B. Engels, H. Schirmer, , T. Dandekar
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
BMC Bioinformatics 6, 2005, 135
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Adenine and adenosine salvage pathways in erythrocytes and the role of S-adenosylhomocysteine hydrolase. A theoretical study using elementary flux modes
FEBS Journal 272, 2005, 5278-5290
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, , M. Marhl
Differential regulation of proteins by bursting calcium oscillations - a theoretical study
Biosystems 81, 2005, 49-63
[ bibtex | abstract | pdf | PudMed-ID: 15917128 ]
T. Pfeiffer,
Game-theoretical approaches to studying the evolution of biochemical systems
Trends in Biochemical Sciences 30, 2005, 20-25
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S. Klamt, J. Gagneur,
Algorithmic approaches for computing elementary modes in large biochemical reaction networks
Systems Biology (Stevenage) 152, 2005, 249-255
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, I. Zevedei-Oancea
Multifunctional enzymes and pathway modelling
In: Experimental Standard Conditions of Enzyme Characterizations (eds. M. G. Hicks, C. Kettner), Logos-Verlag, Berlin, 2004, 115-127
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T. Wilhelm, ,
Analysis of structural robustness of metabolic networks
Systems Biology (Stevenage) 1, 2004, 114-120
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J.A. Papin, J. Stelling, N.D. Price, S. Klamt, , B.O. Palsson
Comparison of network-based pathway analysis methods.
Trends in Biotechnology 22, 2004, 400-405
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W. Liebermeister, E. Klipp, , R. Heinrich
A theory of optimal differential gene expression
Biosystems 76, 2004, 261-278
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T. Frick,
An example of the prisoner's dilemma in biochemistry
Naturwissenschaften 90 (7), 2003, 327-331
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, S. Klamt, J. Stelling
Making predictions about robustness and flexibility from metabolic network structure
In: Proceedings of German Conference on Bioinformatics 2003 (eds. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer), Belleville Verlag, München 2003, 129-134
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Metabolic pathway analysis in biotechnology
In: Metabolic Engineering in the Post Genomic Era (eds. B.N. Kholodenko, H.V. Westerhoff), Horizon Scientific, Wymondham, 2003, 181-208
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I. Zevedei-Oancea,
Topological analysis of metabolic networks based on Petri net theory
In Silico Biology 3 (3), 2003, 323-345
[ bibtex | PudMed-ID: 12954094 ]
M. Marhl,
Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations.
Journal of Theoretical Biology 224 (4), 2003, 491-500
[ bibtex | PudMed-ID: 12957122 ]
T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram,
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.
Biosystems 70, 2003, 255-270
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, S. Klamt
Applying Metabolic Pathway Analysis to make good use of methanol (Commentary)
Trends in Biotechnology 20 (8), 2002, 322
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Mapping the combinatorial regulation by transcription factors (Commentary)
Trends in Biotechnology 20 (1), 2002, 5-6
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S. Klamt,
Calculating as many fluxes as possible in under determined metabolic networks
Molecular Biology Reports 29 (1-2), 2002, 243-248
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, S. Klamt, W. Weckwerth, F. Moldenhauer, T. Pfeiffer
Use of network analysis of metabolic systems in bioengineering
Bioproc. Biosyst. Eng. 24, 2002, 363-372
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J. Stelling, S. Klamt, K. Bettenbrock, , ED. Gilles
Metabolic network structure determines key aspects of functionality and regulation.
Nature 420 (6912), 2002, 190-193
[ bibtex | PudMed-ID: 12432396 ]
, C. Hilgetag, J.H. Woods, D.A. Fell
Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism
Journal of Mathematical Biology 45, 2002, 153-181
[ bibtex | abstract | doi | PudMed-ID: 12181603 ]
, I. Zevedei-Oancea
Treatment of multifunctional enzymes in metabolic pathway analysis
Biophysical Chemistry 99, 2002, 63-75
[ bibtex | abstract | doi | PudMed-ID: 12223240 ]
, M. Marhl, T. Höfer
Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling.
European Journal of Biochemistry 269, 2002, 1333-1355
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, S. Klamt, W. Weckwerth, F. Moldenhauer and T. Pfeiffer
Use of network analysis of metabolic systems in bioengineering.
Bioprocess and Biosystems Engineering 24, 2002, 363-372
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, T. Pfeiffer, F. Moldenhauer, I. Koch, T. Dandekar
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
Bioinformatics 18, 2002, 351-361
[ bibtex | abstract | PudMed-ID: 11847093 ]
S. Klamt,
Calculating as many fluxes as possible in underdetermined metabolic networks.
Molecular Biology Reports 29 (1-2), 2002, 243-248
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S. Klamt, , E.D. Gilles
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
Biotechnology and Bioengineering 77, 2002, 734-751
[ bibtex | abstract | PudMed-ID: 11835134 ]
Protons and sodium ions acting as intracellular carrier pigeons? (Commentary)
Trends in Biotechnology 19, 2001, 330
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T. Dandekar,
The Large-scale Organization of Metabolic Networks (Commentary)
Chemtracts 14, 2001, 137-141
[ bibtex ]
What can Silent Mutations Tell us? (Commentary)
Trends in Biotechnology 19, 2001, 242
[ bibtex ]
, M. Marhl
Bifurcation analysis of calcium oscillations: time-scale separation, canards, and frequency lowering.
Journal of Biological Systems 9, 2001, 291-314
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T. Pfeiffer, , S. Bonhoeffer
Cooperation and competition in the evolution of ATP-producing pathway
Science 292, 2001, 504-507
[ bibtex | abstract | PudMed-ID: 11283355 ]
Flux determination by isotopomer balancing - a successful application of theory to experiment (Commentary)
Trends in Biotechnology 19, 2000, 85
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, T. Pfeiffer, F. Moldenhauer, I. Koch, T. Dandekar
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma pneumoniae
In: Proceedings of the German Conference on Bioinformatics 2000 (eds. E. Bornberg-Bauer, U. Rost, J. Stoye, M. Vingron), Logos Verlag, Berlin 2000, 115-120
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Breeding of Escherichia coli Based on Colour (Commentary)
Trends in Biotechnology 8 (11), 2000, 442
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Biotechnology in silico. Metabolic Proteomics of Haemophilus influenzae (Commentary)
Trends in Biotechnology 18, 2000, 328
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T. Pfeiffer, T. Dandekar, F. Moldenhauer,
Topological Analysis of Metabolic Networks. Application to the Metabolism of Mycoplasma pneumoniae
In: BioThermoKinetics 2000, Animating the Cellular Map (eds. J.-H.S. Hofmeyr, J.M. Rohwer, J.L. Snoep), Stellenbosch University Press, Stellenbosch, 2000, 229-234
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, T. Dandekar, K. Mauch, M. Reuss, D.A. Fell
Recent Developments in Metabolic Pathway Analysis and Their Potential Implications for Biotechnology and Medicine
In: Technological and Medical Implications of Metabolic Control Analysis (eds. A. Cornish-Bowden, M.L. Cárdenas), Kluwer, Dordrecht, 2000, 57-66
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, B. N. Kholodenko, H. V. Westerhoff
Cellular information transfer regarded from a stoichiometry and control analysis perspective
Biosystems 55 (1-3), 2000, 73-81
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, DA. Fell, T. Dandekar
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
Nat Biotechnol 18, 2000, 326-332
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Pathway Analysis of Biochemical Reaction Networks
In: Proceedings of Workshop on Computation of Biochemical Pathways and Genetic Networks (eds. E. Bornberg-Bauer, A. de Beuckelaer, U. Kummer, U. Rost), Logos Verlag, Berlin, 1999, 117-121
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Studies on the Stoichiometric Structure of Enzymatic Reaction Systems
Theory in Biosciences 118 (2), 1999, 125-139
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Use and limitations of modular metabolic control analysis in medicine and biotechnology
Metabolic Engineering 1, 1999, 232-242
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, H.V. Westerhoff
Modular control analysis of slipping enzymes
Biosystems 49, 1999, 1-15
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, T. Dandekar, D.A. Fell
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
Trends in Biotechnology 17, 1999, 53-60
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C.H. Schilling, , B.O. Palsson, R. Heinrich
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era
Biotechnology Progress 15, 1999, 296-303
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T. Pfeiffer, I. Sánchez-Valdenebro, J.C. Nuño, F. Montero,
METATOOL: for studying metabolic networks
Bioinformatics 15, 1999, 251-257
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T. Dandekar, , B. Snel, M. Huynen, P. Bork
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Biochemical Journal 343, 1999, 115-124
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M. Marhl, , M. Brumen, R. Heinrich
Modelling Oscillations of Calcium and Endoplasmic Reticulum Transmembrane Potential. Role of the Signalling and Buffering Proteins and of the Size of the Ca2+ Sequestering ER Subcompartments
Bioelectrochemistry and Bioenergetics 46 (1), 1998, 79-90
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, R. Ouhabi, M. Rigoulet, J.-P. Mazat
Modelling the Interrelations between the Transmembrane Potential and pH Difference across Membranes with Electrogenic Proton Transport upon Build-up of the Proton-motive Force
Bioelectrochemistry and Bioenergetics 45 (2), 1998, 181-192
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R. Heinrich,
The Modelling of Metabolic Systems. Structure, Control and Optimality
Biosystems 47 (1-2), 1998, 61-77
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, D.A. Fell, T. Pfeiffer, T. Dandekar, P. Bork
Elementary Modes Analysis Illustrated with Human Red Cell Metabolism
In: BioThermoKinetics in the Post Genomic Era (eds. C. Larsson, I.-L. Pahlman, L. Gustafsson), Chalmers, Göteborg, 1998, 332-339
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, M. Marhl, M. Brumen, R. Heinrich
Influence of Calcium Binding to Proteins on Calcium Oscillations and ER Membrane Potential Oscillations. A Mathematical Model
In: Information Processing in Cells and Tissues (eds. R. Paton, M. Holcombe), Plenum Press, New York, 1998, 137-150
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R. Heinrich,
The modelling of metabolic systems. Structure, control and optimality
Biosystems 47, 1998, 61-77
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, R. Ouhabi, M. Rigoulet, J.-P. Mazat
Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force
Bioelectrochemistry and Bioenergetics 45, 1998, 181-192
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B. N. Kholodenko, , J. Garcia, H. V. Westerhoff, M. Cascante
Control analysis of metabolic systems involving quasi-equilibrium reactions
Biochimica et Biophysica Acta 1379 (3), 1998, 337-352
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M. Marhl, , M. Brumen
Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations
Biophysical Chemistry 71, 1998, 125-132
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M. Marhl, , M. Brumen, R. Heinrich
Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential: Role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments.
Bioelectrochemistry and Bioenergetics 46 (1), 1998, 79-90
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T. Wilhelm, , R. Heinrich
Kinetic and Thermodynamic Analyses of the Reversible Version of the Smallest Chemical Reaction System with Hopf Bifurcation
Nonlinear World 4, 1997, 295-321
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M. Marhl, , M. Brumen, R. Heinrich
Modeling the interrelations between the calcium oscillations and ER membrane potential oscillations.
Biophysical Chemistry 63 (2-3), 1997, 221-239
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The Regulation of Cellular Systems
R. Heinrich, S. Schuster, Chapman & Hall, New York (Springer; 1st edition, 1996), 1996, ISBN-10: 0412032619; ISBN-13: 978-0412032615
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Elementary Modes of Functioning in Biochemical Networks
In: Computation in Cellular and Molecular Biological Systems (eds. R. Cuthbertson, M. Holcombe, R. Paton), World Scientific, Singapore, 1996, 151-165
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Determining Elementary Modes of Functioning in Biochemical Reaction Networks at Steady State
In: Biomedical and Life Physics (eds. D.N. Ghista), Vieweg, Wiesbaden, 1996, 101-114
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Control Analysis in Terms of Generalized Variables Characterizing Metabolic Systems
Journal of Theoretical Biology 182 (3), 1996, 259-268
[ bibtex | doi | PudMed-ID: 8944157 ]
J. M. Rohwer, , H. V. Westerhoff
How to Recognize Monofunctional Units in a Metabolic System
Journal of Theoretical Biology 179 (3), 1996, 213-228
[ bibtex | doi | PudMed-ID: 8762334 ]
, R. Heinrich
Use of the Theories of Multi-criteria Optimization and of Linear Inequality Systems for the Steady-state Modelling of Biochemical Systems
In: Mathematical Population Dynamics: Analysis of Heterogeneity - Vol. 2 (eds. O. Arino et al.), Wuerz, Winnipeg, 1995, 35-48
[ bibtex ]
, C. Hilgetag
What Information about the Conserved-Moiety Structure of Chemical Reaction Systems Can be Derived from Their Stoichiometry?
Journal of Physical Chemistry 99 (20), 1995, 8017-8023
[ bibtex | abstract ]
B. N. Kholodenko, , J. M. Rohwer, M. Cascante, H. V. Westerhoff
Composite control of cell function: metabolic pathways behaving as single control units
FEBS Letters 368 (1), 1995, 1-4
[ bibtex | doi | PudMed-ID: 7615057 ]
B. N. Kholodenko, D. Molenaar, , R. Heinrich, H. V. Westerhoff
Defining control coefficients in non-ideal metabolic pathways
Biophysical Chemistry 56, 1995, 215-226
[ bibtex | doi | PudMed-ID: 17023325 ]
, C. Hilgetag
On Elementary Flux Modes in Biochemical Reaction Systems at Steady State
Journal of Biological Systems 2, 1994, 165-182
[ bibtex | abstract ]
, T. Höfer, C. Hilgetag, R. Schuster
Use of Convex Analysis for the Modelling of Biochemical Reaction Systems
In: Lecture Notes in Control and Information Sciences (eds. J. Henry, J.-P. Yvon), Springer, London, 1994, 365-374
[ bibtex ]
, C. Hilgetag, D.A. Fell
Detecting Elementary Modes of Functioning in Metabolic Networks
In: What is Controlling Life? (eds. E. Gnaiger, F.N. Gellerich, M. Wyss), Innsbruck University Press, Innsbruck, 1994, 103-105
[ bibtex ]
J.M. Rohwer, , H.V. Westerhoff
An Invariance Property of Coresponse Coefficients in Modular Metabolic Control and Regulation Analysis
In: What is Controlling Life? (eds. E. Gnaiger, F.N. Gellerich, M. Wyss), Innsbruck University Press, Innsbruck, 1994, 109-110
[ bibtex ]
, J.-P. Mazat
A Model Study on the Interrelation between the Transmembrane Potential and pH Difference Across the Mitochondrial Inner Membrane
In: Modern Trends in Biothermokinetics (eds. S. Schuster, M. Rigoulet, R. Ouhabi, J.-P. Mazat), Plenum Press, New York and London, 1993, 39-44
[ bibtex ]
, D. Kahn, H.V. Westerhoff
Modular analysis of the control of complex metabolic pathways
Biophysical Chemistry 48, 1993, 1-17
[ bibtex | abstract | PudMed-ID: 8257764 ]
R. Schuster,
Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed
Computer applications in the biosciences 9, 1993, 79-85
[ bibtex | PudMed-ID: 8435772 ]
, R. Schuster
Decomposition of biochemical reaction systems according to flux control insusceptibility
Journal De Chimie Physique Et De Physico-Chimie Biologique 89 (9), 1992, 1887-1910
[ bibtex ]
, R. Heinrich
The definitions of metabolic control analysis revisited
Biosystems 27, 1992, 1-15
[ bibtex ]
R. Schuster, , H.-G. Holzhütter
Simplification of Complex Kinetic Models used for the Quantitative Analysis of Nuclear Magnetic Resonance or Radioactive Tracer Studies
Journal of the Chemical Society-Faraday Transactions 88 (19), 1992, 2837-2844
[ bibtex | doi ]
R. Schuster,
Relationships between modal analysis andrapid-equilibrium approximation in the modeling of biochemicalnetworks
Systems Analysis Modelling Simulation 8 (8), 1991, 623-633
[ bibtex ]
, T. Höfer
Determining all extreme semi-positive conservation relations in chemical reaction systems: A test criterion for conservativity.
Journal of the Chemical Society-Faraday Transactions 87 (16), 1991, 2561-2566
[ bibtex | doi ]
, R. Schuster, R. Heinrich
Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks. II. Time hierarchy, enzymatic rate laws, and erythrocyte metabolism.
Journal of Mathematical Biology 29, 1991, 443-455
[ bibtex | abstract | PudMed-ID: 1875162 ]
, R. Heinrich
Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks - I. Theoretical analysis
Journal of Mathematical Biology 29, 1991, 425-442
[ bibtex | doi ]
R. Heinrich, , H.-G. Holzhuetter
Mathematical analysis of enzymic reaction systems using optimization principles
Eur J Biochem 201, 1991, 1-21
[ bibtex ]
R. Heinrich,
Is metabolic channelling the complicated solution to the easy problem of reducing transient times?
Journal of Theoretical Biology 152, 1991, 57-61
[ bibtex | doi | PudMed-ID: 1753768 ]
, R. Schuster
Detecting strictly detailed balanced subnetworks in open chemical reaction networks.
Journal of Mathematical Chemistry 6 (1), 1991, 17-40
[ bibtex | doi ]
, R. Schuster
A necessary and sufficient condition for
open chemically reacting systems endowed with a generalized mass
action kinetics to be detailed balanced
Z. phys. Chem. 271, 1990, 337-345
[ bibtex ]
, R. Schuster
A generalization of Wegschneiders condition. Implications for properties of steady states and for quasi-steady-state approximation
Journal of Mathematical Chemistry 3, 1989, 25-42
[ bibtex ]
, R. Heinrich
Time Hierarchy in Enzymatic Reaction Chains Resulting from Optimality Principles
Journal of Theoretical Biology 129, 1987, 189-209
[ bibtex | PudMed-ID: 3455462 ]
R. Heinrich, H.-G. Holzhuetter,
A theoretical approach to the evolution and structural design of enzymatic networks; linear enzymatic chains, branched pathways and glycolysis of erythrocytes
Bulletin of Mathematical Biology 49 (5), 1987, 539-595
[ bibtex | doi | PudMed-ID: 3435799 ]
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