M
Maksim Zakhartsev
Researcher at Norwegian University of Life Sciences
Publications - 10
Citations - 399
Maksim Zakhartsev is an academic researcher from Norwegian University of Life Sciences. The author has contributed to research in topics: Test suite & Metabolic network. The author has an hindex of 4, co-authored 10 publications receiving 254 citations. Previous affiliations of Maksim Zakhartsev include University of Hohenheim.
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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.
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.
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,B. 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,Ali Kaafarani,Hyun Uk Kim,Zachary A. King,Steffen Klamt,Edda Klipp,Jasper J. Koehorst,Matthias König,Meiyappan Lakshmanan,Dong-Yup Lee,Sang Yup Lee,Sunjae Lee,Nathan E. Lewis,Filipe Liu,Hongwu Ma,Daniel Machado,Radhakrishnan Mahadevan,Paulo Maia,Adil Mardinoglu,Gregory L. Medlock,Jonathan M. Monk,Jens Nielsen,Lars K. Nielsen,Juan Nogales,Intawat Nookaew,Osbaldo Resendis-Antonio,Bernhard O. Palsson,Jason A. Papin,Kiran Raosaheb Patil,Mark G. Poolman,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 +68 more
TL;DR: Memote is presented, an open-source software containing a community-maintained, standardized set of metabolic model tests that provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.
Journal ArticleDOI
Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium.
Sergey N. Gavrilov,D. G. Zavarzina,Ivan M. Elizarov,Tamara V. Tikhonova,N. I. Dergousova,Vladimir Popov,Vladimir Popov,Jonathan R. Lloyd,David Knight,Mohamed Y. El-Naggar,Sahand Pirbadian,Kar Man Leung,Frank T. Robb,Maksim Zakhartsev,Orianna Bretschger,Elizaveta A. Bonch-Osmolovskaya,Elizaveta A. Bonch-Osmolovskaya +16 more
TL;DR: In this paper, the authors describe EET channels in the thermophilic Gram-positive bacterium Carboxydothermus ferrireducens that drive exoelectrogenesis and rapid conversion of amorphous mineral ferrihydrite to large magnetite crystals.
Journal ArticleDOI
Introduction to the 9th Young Scientists School on Systems Biology and Bioinformatics (SBB'2017).
TL;DR: This special issue presents materials from the 9th International Young Scientists School on Systems Biology and Bioinformatics (SBB' 2017), organized in June 2017 in Yalta, Russia, and the works of Belyaev Conference-2017 and SBB'2017 School on computational biology were recently covered in special issues of several international journals.