Enforced ATP wasting as a general design principle to rationally engineer microbial cell factories

Publikacje

Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks

Autorzy: Steffen Klamt; Axel von Kamp
Opublikowane w: Metabolites, Numer 22181989, 2022, Strona(/y) 585, ISSN 2218-1989
Wydawca: MDPI
DOI: 10.3390/metabo12070585

StrainDesign: a comprehensive Python package for computational design of metabolic networks

Autorzy: Philipp Schneider; Pavlos Stephanos Bekiaris; Axel von Kamp; Steffen Klamt
Opublikowane w: Bioinformatics, Numer 13674803, 2022, Strona(/y) 4981–4983, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac632

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

Autorzy: Philipp Schneider, Axel von Kamp, Steffen Klamt
Opublikowane w: PLOS Computational Biology, Numer 16/7, 2020, Strona(/y) e1008110, ISSN 1553-7358
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1008110

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks

Autorzy: Sven Thiele; Axel von Kamp; Pavlos Stephanos Bekiaris; Philipp Schneider; Steffen Klamt
Opublikowane w: Bioinformatics, Numer 38, 2022, Strona(/y) 1467-1469, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab828

Automatic construction of metabolic models with enzyme constraints

Autorzy: Bekiaris, Pavlos Stephanos; Klamt, Steffen
Opublikowane w: BMC Bioinformatics, Numer 21, 2020, Strona(/y) 19, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-019-3329-9

Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks

Autorzy: Steffen Klamt; Radhakrishnan Mahadevan; Axel von Kamp
Opublikowane w: BMC Bioinformatics, Numer 21, 2020, Strona(/y) 510, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-020-03837-3

Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink

Autorzy: Simon Boecker; Sebastián Espinel-Ríos; Katja Bettenbrock; Steffen Klamt
Opublikowane w: Metabolic Engineering, Numer 10967176, 2022, Strona(/y) 50-57, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2022.05.006

Maximizing batch fermentation efficiency by constrained model‐based optimization and predictive control of adenosine triphosphate turnover

Autorzy: Sebastián Espinel Ríos; Katja Bettenbrock; Steffen Klamt; Rolf Findeisen
Opublikowane w: AIChE-Journal, Numer 68, 2022, Strona(/y) e17555, ISSN 1547-5905
Wydawca: American Institute of Chemical Engineers
DOI: 10.1002/aic.17555

Deciphering the physiological response of Escherichia coli under high ATP demand

Autorzy: Simon Boecker; Giulia Slaviero; Thorben Schramm; Witold Szymanski; Ralf Steuer; Hannes Link; Steffen Klamt
Opublikowane w: Molecular Systems Biology, Numer 17, 2021, Strona(/y) e10504, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.202110504

Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli

Autorzy: Björn-Johannes Harder, Katja Bettenbrock, Steffen Klamt
Opublikowane w: Biotechnology and Bioengineering, Numer 115/1, 2018, Strona(/y) 156-164, ISSN 0006-3592
Wydawca: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.26446

When Do Two-Stage Processes Outperform One-Stage Processes?

Autorzy: Steffen Klamt, Radhakrishnan Mahadevan, Oliver Hädicke
Opublikowane w: Biotechnology Journal, Numer 13/2, 2018, Strona(/y) 1700539, ISSN 1860-6768
Wydawca: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201700539

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

Autorzy: Axel von Kamp, Steffen Klamt
Opublikowane w: Nature Communications, Numer 8, 2017, Strona(/y) 15956, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms15956

A mathematical framework for yield ( vs. rate) optimization in constraint-based modeling and applications in metabolic engineering

Autorzy: Steffen Klamt, Stefan Müller, Georg Regensburger, Jürgen Zanghellini
Opublikowane w: Metabolic Engineering, Numer 47, 2018, Strona(/y) 153-169, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2018.02.001

Use of CellNetAnalyzer in biotechnology and metabolic engineering

Autorzy: Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt
Opublikowane w: Journal of Biotechnology, Numer 261, 2017, Strona(/y) 221-228, ISSN 0168-1656
Wydawca: Elsevier BV
DOI: 10.1016/j.jbiotec.2017.05.001

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

Autorzy: Oliver Hädicke, Axel von Kamp, Timur Aydogan, Steffen Klamt
Opublikowane w: PLOS Computational Biology, Numer 14/9, 2018, Strona(/y) e1006492, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1006492

Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli

Autorzy: Simon Boecker, Ahmed Zahoor, Thorben Schramm, Hannes Link, Steffen Klamt
Opublikowane w: Biotechnology Journal, Numer 14/9, 2019, Strona(/y) 1800438, ISSN 1860-6768
Wydawca: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201800438

Characterizing and ranking computed metabolic engineering strategies

Autorzy: Philipp Schneider, Steffen Klamt
Opublikowane w: Bioinformatics, Numer 35/17, 2019, Strona(/y) 3063-3072, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/bty1065

MoVE identifies metabolic valves to switch between phenotypic states

Autorzy: Naveen Venayak, Axel von Kamp, Steffen Klamt, Radhakrishnan Mahadevan
Opublikowane w: Nature Communications, Numer 9/1, 2018, Strona(/y) 5332, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-07719-4

Systematizing the different notions of growth-coupled product synthesis and a single framework for computing corresponding strain designs.

Autorzy: Philipp Schneider; Radhakrishnan Mahadevan; Steffen Klamt
Opublikowane w: Biotechnology Journal, Numer 16, 2021, Strona(/y) e2100236, ISSN 1860-7314
Wydawca: Wiley-VCH GmbH
DOI: 10.1002/biot.202100236

Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli

Autorzy: Simon Boecker; Björn-Johannes Harder; Regina Kutscha; Stefan Pflügl; Steffen Klamt
Opublikowane w: Microbial Cell Factories, Numer 20, 2021, Strona(/y) 63, ISSN 1475-2859
Wydawca: BioMed Central
DOI: 10.1186/s12934-021-01554-x

ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production

Autorzy: Ahmed Zahoor, Katrin Messerschmidt, Simon Boecker, Steffen Klamt
Opublikowane w: Biotechnology for Biofuels, Numer 13/1, 2020, ISSN 1754-6834
Wydawca: BioMed Central
DOI: 10.1186/s13068-020-01822-9

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