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CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks.
Bioinformatics. 2022 Feb 7;38(5):1467-1469. doi: 10.1093/bioinformatics/btab828.
Bioinformatics. 2022.
PMID: 34878104
Free PMC article.
Automatic construction of metabolic models with enzyme constraints.
Bekiaris PS, Klamt S.
Bekiaris PS, et al.
BMC Bioinformatics. 2020 Jan 14;21(1):19. doi: 10.1186/s12859-019-3329-9.
BMC Bioinformatics. 2020.
PMID: 31937255
Free PMC article.
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Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
Bekiaris PS, Klamt S.
Bekiaris PS, et al.
PLoS Comput Biol. 2021 Jun 15;17(6):e1009093. doi: 10.1371/journal.pcbi.1009093. eCollection 2021 Jun.
PLoS Comput Biol. 2021.
PMID: 34129600
Free PMC article.
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StrainDesign: a comprehensive Python package for computational design of metabolic networks.
Schneider P, Bekiaris PS, von Kamp A, Klamt S.
Schneider P, et al. Among authors: bekiaris ps.
Bioinformatics. 2022 Oct 31;38(21):4981-4983. doi: 10.1093/bioinformatics/btac632.
Bioinformatics. 2022.
PMID: 36111857
Free PMC article.
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Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions.
Bekiaris PS, Klamt S.
Bekiaris PS, et al.
Nat Commun. 2023 Aug 3;14(1):4660. doi: 10.1038/s41467-023-40297-8.
Nat Commun. 2023.
PMID: 37537166
Free PMC article.
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Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.
Bekiaris PS, Tekath T, Staiger D, Danisman S.
Bekiaris PS, et al.
PLoS One. 2018 Jan 3;13(1):e0190421. doi: 10.1371/journal.pone.0190421. eCollection 2018.
PLoS One. 2018.
PMID: 29298348
Free PMC article.
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