Meriç Ataman
Meriç Ataman
Post-doctoral Research Fellow University of Basel
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Cited by
Cited by
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering
M Morales, M Ataman, S Badr, S Linster, I Kourlimpinis, ...
Energy & Environmental Science 9 (9), 2794-2805, 2016
Heading in the right direction: thermodynamics-based network analysis and pathway engineering
M Ataman, V Hatzimanikatis
Current opinion in biotechnology 36, 176-182, 2015
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
P Salvy, G Fengos, M Ataman, T Pathier, KC Soh, V Hatzimanikatis
Bioinformatics 35 (1), 167-169, 2019
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
M Ataman, DF Hernandez Gardiol, G Fengos, V Hatzimanikatis
PLoS computational biology 13 (7), e1005444, 2017
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
A Chiappino-Pepe, S Tymoshenko, M Ataman, D Soldati-Favre, ...
PLoS computational biology 13 (3), e1005397, 2017
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
BioRxiv, 350991, 2018
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases
SIB Swiss Institute of Bioinformatics Members
Nucleic acids research 44 (D1), D27-D37, 2016
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
B Borer, M Ataman, V Hatzimanikatis, D Or
PLoS computational biology 15 (6), e1007127, 2019
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
M Ataman, V Hatzimanikatis
PLoS computational biology 13 (7), e1005513, 2017
Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
T Hameri, G Fengos, M Ataman, L Miskovic, V Hatzimanikatis
Metabolic engineering 52, 29-41, 2019
Discovery and evaluation of biosynthetic pathways for the production of five methyl ethyl ketone precursors
M Tokic, N Hadadi, M Ataman, D Neves, BE Ebert, LM Blank, L Miskovic, ...
ACS synthetic biology 7 (8), 1858-1873, 2018
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
M Masid, M Ataman, V Hatzimanikatis
Nature communications 11 (1), 2821, 2020
Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas
MA Islam, N Hadadi, M Ataman, V Hatzimanikatis, G Stephanopoulos
Metabolic engineering 41, 173-181, 2017
Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites
N Hadadi, M Ataman, V Hatzimanikatis, C Panayiotou
Physical Chemistry Chemical Physics 17 (16), 10438-10453, 2015
Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses
A Chiappino-Pepe, V Pandey, M Ataman, V Hatzimanikatis
Current Opinion in Systems Biology 2, 59-66, 2017
Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach
C Panayiotou, S Mastrogeorgopoulos, M Ataman, N Hadadi, ...
Physical Chemistry Chemical Physics 18 (47), 32570-32592, 2016
CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis
S Ghosh, M Ataman, M Bak, A Börsch, A Schmidt, K Buczak, G Martin, ...
Nucleic acids research 50 (6), 3096-3114, 2022
Constraint-based metabolic control analysis for rational strain engineering
S Tsouka, M Ataman, T Hameri, L Miskovic, V Hatzimanikatis
Metabolic Engineering 66, 191-203, 2021
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
E Vayena, A Chiappino-Pepe, H MohammadiPeyhani, Y Francioli, ...
Proceedings of the National Academy of Sciences 119 (46), e2211197119, 2022
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