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Parizad Babaei
Researcher at Chalmers University of Technology
Publications - 12
Citations - 717
Parizad Babaei is an academic researcher from Chalmers University of Technology. The author has contributed to research in topics: Gut flora & Internal medicine. The author has an hindex of 9, co-authored 10 publications receiving 460 citations. Previous affiliations of Parizad Babaei include Technical University of Denmark & University of Tehran.
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Journal ArticleDOI
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven,Moritz Emanuel Beber,Brett G. Olivier,Frank Bergmann,Meriç Ataman,Parizad Babaei,Jennifer A. Bartell,Lars M. Blank,Siddharth Chauhan,Kevin Correia,Christian Diener,Christian Diener,Andreas Dräger,Birgitta E. Ebert,Birgitta E. Ebert,Janaka N. Edirisinghe,José P. Faria,Adam M. Feist,Adam M. Feist,Georgios Fengos,Ronan M. T. Fleming,Beatriz García-Jiménez,Beatriz García-Jiménez,Vassily Hatzimanikatis,Wout van Helvoirt,Wout van Helvoirt,Christopher S. Henry,Henning Hermjakob,Markus J. Herrgård,Ali Kaafarani,Hyun Uk Kim,Zachary A. King,Steffen Klamt,Edda Klipp,Jasper J. Koehorst,Matthias König,Meiyappan Lakshmanan,Dong-Yup Lee,Dong-Yup Lee,Sang Yup Lee,Sang Yup Lee,Sunjae Lee,Sunjae Lee,Nathan E. Lewis,Filipe Liu,Hongwu Ma,Daniel Machado,Radhakrishnan Mahadevan,Paulo Maia,Adil Mardinoglu,Adil Mardinoglu,Gregory L. Medlock,Jonathan M. Monk,Jens Nielsen,Jens Nielsen,Lars K. Nielsen,Lars K. Nielsen,Juan Nogales,Intawat Nookaew,Intawat Nookaew,Bernhard O. Palsson,Bernhard O. Palsson,Jason A. Papin,Kiran Raosaheb Patil,Mark G. Poolman,Nathan D. Price,Osbaldo Resendis-Antonio,Anne Richelle,Isabel Rocha,Isabel Rocha,Benjamin Sanchez,Benjamin Sanchez,Peter J. Schaap,Rahuman S. Malik Sheriff,Saeed Shoaie,Saeed Shoaie,Nikolaus Sonnenschein,Bas Teusink,Paulo Vilaça,Jon Olav Vik,Judith A. H. Wodke,Joana C. Xavier,Qianqian Yuan,Maksim Zakhartsev,Cheng Zhang +84 more
TL;DR: A community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality, and advocate adoption of the latest version of the Systems Biology Markup Language level 3 flux balance constraints (SBML3FBC) package as the primary description and exchange format.
Journal ArticleDOI
Human gut microbiota and healthy aging: Recent developments and future prospective
TL;DR: This work has shown that genome-scale metabolic modeling can help to explore the connections between diet, microbes, and host as well as to expand the understanding of the metabolic capability of each species in the gut microbiota.
Journal ArticleDOI
Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome
TL;DR: The equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.
Journal ArticleDOI
Gut Microbiota Dysbiosis is Associated with Malnutrition and Reduced Plasma Amino Acid Levels: Lessons from Genome-Scale Metabolic Modeling
Manish Kumar,Boyang Ji,Parizad Babaei,Promi Das,Dimitra Lappa,Girija Ramakrishnan,Todd E. Fox,Rashidul Haque,William A. Petri,Fredrik Bäckhed,Jens Nielsen +10 more
TL;DR: In this article, the authors applied genome-scale metabolic modeling to model the gut microbial species, which were selected from healthy and malnourished children from three low-income countries.
Posted ContentDOI
Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
Christian Lieven,Moritz Emanuel Beber,Brett G. Olivier,Frank Bergmann,Meriç Ataman,Parizad Babaei,Jennifer A. Bartell,Lars M. Blank,Siddharth Chauhan,Kevin Correia,Christian Diener,Andreas Dräger,Birgitta E. Ebert,Janaka N. Edirisinghe,José P. Faria,Adam M. Feist,Georgios Fengos,Ronan M. T. Fleming,Beatriz García-Jiménez,Vassily Hatzimanikatis,Wout van Helvoirt,Christopher S. Henry,Henning Hermjakob,Markus J. Herrgård,Hyun Uk Kim,Zachary A. King,Jasper J. Koehorst,Steffen Klamt,Edda Klipp,Meiyappan Lakshmanan,Nicolas Le Novère,Dong-Yup Lee,Sang Yup Lee,Sunjae Lee,Nathan E. Lewis,Hongwu Ma,Daniel Machado,Radhakrishnan Mahadevan,Paulo Maia,Adil Mardinoglu,Greg L Medlock,Jonathan M. Monk,Jens Nielsen,Lars K. Nielsen,Juan Nogales,Intawat Nookaew,Osbaldo Resendis,Bernhard O. Palsson,Jason A. Papin,Kiran Raosaheb Patil,Nathan D. Price,Anne Richelle,Isabel Rocha,Benjamin Sanchez,Peter J. Schaap,Rahuman S. Malik Sheriff,Saeed Shoaie,Nikolaus Sonnenschein,Bas Teusink,Paulo Vilaça,Jon Olav Vik,Judith A. H. Wodke,Joana C. Xavier,Qianqian Yuan,Maksim Zakhartsev,Cheng Zhang +65 more
TL;DR: For example, Memote as mentioned in this paper is an open-source software containing a community-maintained, standardized set of metabolic model tests, which can be extended to include experimental datasets for automatic model validation.