MEMOTE for standardized genome-scale metabolic model testing

Nat Biotechnol. 2020 Mar;38(3):272-276. doi: 10.1038/s41587-020-0446-y.

Authors

Christian Lieven^#¹, Moritz E Beber^#¹, Brett G Olivier², Frank T Bergmann³, Meric Ataman⁴, Parizad Babaei¹, Jennifer A Bartell¹, Lars M Blank⁵, Siddharth Chauhan⁶, Kevin Correia⁷, Christian Diener^{8

9}, Andreas Dräger^{10

11

12}, Birgitta E Ebert^{5

13}, Janaka N Edirisinghe¹⁴, José P Faria¹⁴, Adam M Feist^{1

6}, Georgios Fengos⁴, Ronan M T Fleming¹⁵, Beatriz García-Jiménez^{16

17}, Vassily Hatzimanikatis⁴, Wout van Helvoirt^{18

19}, Christopher S Henry¹⁴, Henning Hermjakob²⁰, Markus J Herrgård¹, Ali Kaafarani¹, Hyun Uk Kim²¹, Zachary King⁶, Steffen Klamt²², Edda Klipp²³, Jasper J Koehorst²⁴, Matthias König²³, Meiyappan Lakshmanan²⁵, Dong-Yup Lee^{25

26}, Sang Yup Lee^{1

21}, Sunjae Lee^{27

28}, Nathan E Lewis^{6

29}, Filipe Liu¹⁴, Hongwu Ma³⁰, Daniel Machado³¹, Radhakrishnan Mahadevan^{7

32}, Paulo Maia³³, Adil Mardinoglu^{27

28}, Gregory L Medlock³⁴, Jonathan M Monk⁶, Jens Nielsen^{1

35}, Lars Keld Nielsen^{1

13}, Juan Nogales¹⁶, Intawat Nookaew^{35

36}, Bernhard O Palsson^{1

6}, Jason A Papin³⁴, Kiran R Patil³¹, Mark Poolman³⁷, Nathan D Price⁹, Osbaldo Resendis-Antonio⁸, Anne Richelle²⁹, Isabel Rocha^{38

39}, Benjamín J Sánchez^{1

35}, Peter J Schaap²⁴, Rahuman S Malik Sheriff²⁰, Saeed Shoaie^{27

28}, Nikolaus Sonnenschein⁴⁰, Bas Teusink², Paulo Vilaça³³, Jon Olav Vik¹⁸, Judith A H Wodke²³, Joana C Xavier⁴¹, Qianqian Yuan³⁰, Maksim Zakhartsev¹⁸, Cheng Zhang²⁷

Affiliations

¹ Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
² Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
³ BioQUANT/COS, Heidelberg University, Heidelberg, Germany.
⁴ Ecole Polytechnique Fédérale de Lausanne, Laboratory of Computational Systems Biotechnology, Lausanne, Switzerland.
⁵ iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany.
⁶ Department of Bioengineering, University of California, La Jolla, CA, USA.
⁷ Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
⁸ Human Systems Biology Laboratory, Instituto Nacional de Medicina Genomica & Coordinación de la Investigación Científica-Red de Apoyo a la Investigación, UNAM, Mexico City, Mexico.
⁹ Institute for Systems Biology, Seattle, WA, USA.
¹⁰ Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), Tübingen, Germany.
¹¹ Department of Computer Science, University of Tübingen, Tübingen, Germany.
¹² German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
¹³ Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
¹⁴ Argonne National Laboratory, Lemont, IL, USA.
¹⁵ Analytical Biosciences, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands.
¹⁶ Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
¹⁷ Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
¹⁸ Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
¹⁹ Hanze University of Applied Sciences, Groningen, the Netherlands.
²⁰ European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
²¹ Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, BioInformatics Research Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
²² Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany.
²³ Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
²⁴ Department of Agrotechnology and Food Sciences, Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
²⁵ Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
²⁶ School of Chemical Engineering Sungkyunkwan University, Jangan-gu Suwon, Gyeonggi-do, Republic of Korea.
²⁷ Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
²⁸ Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.
²⁹ Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego School of Medicine, La Jolla, CA, USA.
³⁰ Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, P.R. China.
³¹ Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
³² Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.
³³ SilicoLife Lda., Braga, Portugal.
³⁴ Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.
³⁵ Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Göteborg, Sweden.
³⁶ Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA.
³⁷ Oxford Brookes University, Oxford, UK.
³⁸ Centre of Biological Engineering, University of Minho, Braga, Portugal.
³⁹ Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
⁴⁰ Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark. niso@biosustain.dtu.dk.
⁴¹ Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.

^# Contributed equally.

No abstract available

Publication types

Letter
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / methods*
Genome
Metabolic Networks and Pathways*
Models, Biological
Molecular Sequence Annotation
Workflow

Publication types

MeSH terms

Grants and funding