Nikolaus Sonnenschein

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Markus HerrgardCTO, BioInnovation InstituteVerified email at bii.dk
Jens NielsenProfessor in Systems Biology, Chalmers University of Technology, SwedenVerified email at chalmers.se
Christian LievenNovo Nordisk Foundation Center for BiosustainabilityVerified email at biosustain.dtu.dk
Bernhard PalssonUCSDVerified email at eng.ucsd.edu
Moritz Emanuel BeberUnseen Bio ApSVerified email at unseenbio.com
Andreas DrägerJuniorprofessor for Computational Systems Biology of Infection and Antimicrobial-ResistanceVerified email at uni-tuebingen.de
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Zachary A. KingVerified email at ucsd.edu
Ali EbrahimUniversity of California, San DiegoVerified email at ucsd.edu
Irina BorodinaThe Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkVerified email at biosustain.dtu.dk
Rebecca M LennenSenior Researcher, Novo Nordisk Foundation Center for Biosustainability, Technical University ofVerified email at biosustain.dtu.dk
Aarash BordbarSinopia BiosciencesVerified email at sinopiabio.com
Daniel C. ZielinskiProject Scientist, University of California San DiegoVerified email at ucsd.edu
Douglas McCloskeyVerified email at eng.ucsd.edu
Jay KeaslingProfessor of Chemical & Biomolecular Engineering and of Bioengineering, University of CaliforniaVerified email at lbl.gov
Jie ZhangNovo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkVerified email at biosustain.dtu.dk
Michael Krogh JensenGroup leader, Novo-Nordisk Foundation Center for BiosustainabilityVerified email at biosustain.dtu.dk
Georgi MuskhelishviliJacobs University BremenVerified email at jacobs-university.de
Svetlana GalkinaSaint-Petersburg State University, Biological faculty, Department of Genetics and BiotechnologyVerified email at spbu.ru
Henning RedestigData scientist, Genencor InternationalVerified email at iff.com

Nikolaus Sonnenschein

Ginkgo Bioworks

Verified email at ginkgobioworks.com

Biotechnology


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A community-driven global reconstruction of human metabolism I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ... Nature biotechnology 31 (5), 419-425, 2013	1120	2013
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways ZA King, A Dräger, A Ebrahim, N Sonnenschein, NE Lewis, BO Palsson PLoS computational biology 11 (8), e1004321, 2015	320	2015
MEMOTE for standardized genome-scale metabolic model testing C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... Nature biotechnology 38 (3), 272-276, 2020	238	2020
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism H Lu, F Li, BJ Sánchez, Z Zhu, G Li, I Domenzain, S Marcišauskas, ... Nature Communications 10 (1), 1-13, 2019	183	2019
Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics A Bordbar, D McCloskey, DC Zielinski, N Sonnenschein, N Jamshidi, ... Cell Systems 1 (4), 283-292, 2015	103	2015
Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance KR Kildegaard, BM Hallström, TH Blicher, N Sonnenschein, NB Jensen, ... Metabolic engineering 26, 57-66, 2014	86	2014
Engineering an NADPH/NADP⁺ Redox Biosensor in Yeast J Zhang, N Sonnenschein, TPB Pihl, KR Pedersen, MK Jensen, ... ACS synthetic biology 5 (12), 1546-1556, 2016	66	2016
Improving reproducibility in synthetic biology MM Jessop-Fabre, N Sonnenschein Frontiers in Bioengineering and Biotechnology 7, 18, 2019	65	2019
Analog regulation of metabolic demand N Sonnenschein, M Geertz, G Muskhelishvili, MT Hütt BMC systems biology 5 (1), 40, 2011	62	2011
Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories JGR Cardoso, K Jensen, C Lieven, AS Lærke Hansen, S Galkina, ... ACS synthetic biology 7 (4), 1163-1166, 2018	60	2018
Do genome‐scale models need exact solvers or clearer standards? A Ebrahim, E Almaas, E Bauer, A Bordbar, AP Burgard, RL Chang, ... Molecular Systems Biology 11 (10), 831, 2015	58	2015
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production … MJ Massaiu, I., Pasotti, L., Sonnenschein, N., Rama, E., Cavaletti, M ... Microbial Cell Factories 18 (3), 2019	57	2019
Systems biology solutions for biochemical production challenges ASL Hansen, RM Lennen, N Sonnenschein, MJ Herrgård Current Opinion in Biotechnology 45, 85-91, 2017	49	2017
A genome-scale metabolic model for Methylococcus capsulatus (Bath) suggests reduced efficiency electron transfer to the particulate methane monooxygenase C Lieven, LAH Petersen, SB Jørgensen, KV Gernaey, MJ Herrgard, ... Frontiers in microbiology 9, 2947, 2018	43	2018
Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks ME Beber, C Fretter, S Jain, N Sonnenschein, M Müller-Hannemann, ... Journal of The Royal Society Interface, 2012	41	2012
Analysis of genetic variation and potential applications in genome-scale metabolic modeling JGR Cardoso, MR Andersen, MJ Herrgård, N Sonnenschein Frontiers in bioengineering and biotechnology 3, 13, 2015	37	2015
Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies IE Elsemman, A Rodriguez Prado, P Grigaitis, M Garcia Albornoz, ... Nature Communications 13 (1), 1-12, 2022	35	2022
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0 I Domenzain, B Sánchez, M Anton, EJ Kerkhoven, A Millán-Oropeza, ... Nature Communications 13, 2022	34	2022
OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs K Jensen, V Broeken, ASL Hansen, N Sonnenschein, MJ Herrgård Metabolic engineering communications 8, e00087, 2019	33	2019
Genome-Wide CRISPRi-Based Identification of Targets for Decoupling Growth from Production S Li, CB Jendresen, J Landberg, LE Pedersen, N Sonnenschein, ... ACS Synthetic Biology 9 (5), 1030-1040, 2020	24	2020

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