G
German Preciat
Researcher at Leiden University
Publications - 6
Citations - 880
German Preciat is an academic researcher from Leiden University. The author has contributed to research in topics: Microbiome & Computer science. The author has an hindex of 3, co-authored 5 publications receiving 542 citations. Previous affiliations of German Preciat include University of Luxembourg.
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Journal ArticleDOI
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt,Sylvain Arreckx,Thomas Pfau,Sebastián N. Mendoza,Anne Richelle,Almut Heinken,Hulda S. Haraldsdóttir,Jacek Wachowiak,Sarah M. Keating,Vanja Vlasov,Stefania Magnusdottir,Chiam Yu Ng,German Preciat,Alise Žagare,Siu Hung Joshua Chan,Maike K. Aurich,Catherine M. Clancy,Jennifer Modamio,John T. Sauls,Alberto Noronha,Aarash Bordbar,Benjamin Cousins,Diana C. El Assal,Luis Vitores Valcárcel,Iñigo Apaolaza,Susan Ghaderi,Masoud Ahookhosh,Marouen Ben Guebila,Andrejs Kostromins,Nicolas Sompairac,Hoai M. Le,Ding Ma,Yuekai Sun,Lin Wang,James T. Yurkovich,Miguel A.P. Oliveira,Phan Tu Vuong,Lemmer P. El Assal,Inna Kuperstein,Andrei Zinovyev,H. Scott Hinton,William A. Bryant,Francisco J. Aragón Artacho,Francisco J. Planes,Egils Stalidzans,Alejandro Maass,Santosh Vempala,Michael Hucka,Michael A. Saunders,Costas D. Maranas,Nathan E. Lewis,Thomas Sauter,Bernhard O. Palsson,Bernhard O. Palsson,Ines Thiele,Ronan M. T. Fleming,Ronan M. T. Fleming +56 more
TL;DR: This protocol provides an overview of all new features of the COBRA Toolbox and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios.
Posted Content
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.
Laurent Heirendt,Sylvain Arreckx,Thomas Pfau,Sebastián N. Mendoza,Anne Richelle,Almut Heinken,Hulda S. Haraldsdóttir,Jacek Wachowiak,Sarah M. Keating,Vanja Vlasov,Stefania Magnusdottir,Chiam Yu Ng,German Preciat,Alise Žagare,Siu Hung Joshua Chan,Maike K. Aurich,Catherine M. Clancy,Jennifer Modamio,John T. Sauls,Alberto Noronha,Aarash Bordbar,Benjamin Cousins,Diana C. El Assal,Luis Vitores Valcárcel,Iñigo Apaolaza,Susan Ghaderi,Masoud Ahookhosh,Marouen Ben Guebila,Andrejs Kostromins,Nicolas Sompairac,Hoai M. Le,Ding Ma,Yuekai Sun,Lin Wang,James T. Yurkovich,Miguel A.P. Oliveira,Phan Tu Vuong,Lemmer P. El Assal,Inna Kuperstein,Andrei Zinovyev,H. Scott Hinton,William A. Bryant,Francisco J. Aragón Artacho,Francisco J. Planes,Egils Stalidzans,Alejandro Maass,Santosh Vempala,Michael Hucka,Michael A. Saunders,Costas D. Maranas,Nathan E. Lewis,Thomas Sauter,Bernhard O. Palsson,Ines Thiele,Ronan M. T. Fleming +54 more
TL;DR: This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios and is an update to the COBRA Toolbox 1.0 and 2.0.
Posted ContentDOI
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Almut Heinken,Acharya G,Dmitry A. Ravcheev,Johannes Hertel,Nyga M,Okpala Oe,Hogan M,Stefania Magnusdottir,Filippo Martinelli,German Preciat,Janaka N. Edirisinghe,Janaka N. Edirisinghe,Christopher S. Henry,Ronan M. T. Fleming,Ines Thiele +14 more
TL;DR: This analysis reveals that some drug activation capabilities are present in only a subset of individuals, moreover, drug conversion potential correlate with clinical parameters, and paves the way towards personalised, predictive analysis of host-drug-microbiome interactions.
Journal ArticleDOI
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
Almut Heinken,Johannes Hertel,Geeta Acharya,Dmitry A. Ravcheev,M. Nyga,Onyedika Emmanuel Okpala,Marcus Hogan,Stefania Magnusdottir,Filippo Martinelli,Bram Nap,German Preciat,Janaka N. Edirisinghe,Christopher S. Henry,Ronan M. T. Fleming,Ines Thiele +14 more
TL;DR: AGORA2 as discussed by the authors is a genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version, which includes 7,302 strains and includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs.
Posted ContentDOI
XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models
German Preciat,Agnieszka B. Wegrzyn,Ines Thiele,Thomas Hankemeier,Ronan M. T. Fleming,Ronan M. T. Fleming +5 more
TL;DR: XomicsToModel as mentioned in this paper is a semi-automated pipeline that integrates bibliomic, transcriptomic, proteomic, and metabolomic data with a generic genome-scale metabolic reconstruction, or model.