| Year |
Citation |
Score |
| 2023 |
Carrasco Muriel J, Long C, Sonnenschein N. Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO. Microbiology Spectrum. e0170523. PMID 37931133 DOI: 10.1128/spectrum.01705-23 |
0.406 |
|
| 2023 |
Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, ... Sonnenschein N, et al. Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metabolic Engineering. PMID 36738854 DOI: 10.1016/j.ymben.2023.01.012 |
0.755 |
|
| 2022 |
Domenzain I, Sánchez B, Anton M, Kerkhoven EJ, Millán-Oropeza A, Henry C, Siewers V, Morrissey JP, Sonnenschein N, Nielsen J. Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. Nature Communications. 13: 3766. PMID 35773252 DOI: 10.1038/s41467-022-31421-1 |
0.393 |
|
| 2022 |
He B, Cai C, McCubbin T, Muriel JC, Sonnenschein N, Hu S, Yuan Z, Marcellin E. A Genome-Scale Metabolic Model of : Assessing Bioenergetics and Thermodynamic Feasibility. Metabolites. 12. PMID 35448501 DOI: 10.3390/metabo12040314 |
0.371 |
|
| 2022 |
Elsemman IE, Rodriguez Prado A, Grigaitis P, Garcia Albornoz M, Harman V, Holman SW, van Heerden J, Bruggeman FJ, Bisschops MMM, Sonnenschein N, Hubbard S, Beynon R, Daran-Lapujade P, Nielsen J, Teusink B. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nature Communications. 13: 801. PMID 35145105 DOI: 10.1038/s41467-022-28467-6 |
0.384 |
|
| 2021 |
Mol V, Bennett M, Sánchez BJ, Lisowska BK, Herrgård MJ, Nielsen AT, Leak DJ, Sonnenschein N. Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metabolic Engineering. PMID 33753231 DOI: 10.1016/j.ymben.2021.03.002 |
0.706 |
|
| 2020 |
Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J. Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications. 11: 5443. PMID 33093448 DOI: 10.1038/s41467-020-19358-9 |
0.762 |
|
| 2020 |
Wright NR, Wulff T, Palmqvist EA, Jørgensen TR, Workman CT, Sonnenschein N, Rønnest NP, Herrgård MJ. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of S. cerevisiae. Biotechnology and Bioengineering. PMID 32277712 DOI: 10.1002/Bit.27353 |
0.612 |
|
| 2020 |
Li S, Jendresen CB, Landberg J, Pedersen LE, Sonnenschein N, Jensen SI, Nielsen AT. Genome-wide CRISPRi-based identification of targets for decoupling growth from production. Acs Synthetic Biology. PMID 32268068 DOI: 10.1021/Acssynbio.9B00143 |
0.313 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Sonnenschein N, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4 |
0.767 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Sonnenschein N, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y |
0.77 |
|
| 2019 |
Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications. 10: 3586. PMID 31395883 DOI: 10.1038/S41467-019-11581-3 |
0.803 |
|
| 2019 |
Jensen K, Broeken V, Hansen ASL, Sonnenschein N, Herrgård MJ. OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs. Metabolic Engineering Communications. 8: e00087. PMID 30956947 DOI: 10.1016/J.Mec.2019.E00087 |
0.601 |
|
| 2019 |
Jensen PR, Matos MRA, Sonnenschein N, Meier S. Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells. Analytical Chemistry. PMID 30896922 DOI: 10.1021/Acs.Analchem.9B00660 |
0.78 |
|
| 2019 |
Massaiu I, Pasotti L, Sonnenschein N, Rama E, Cavaletti M, Magni P, Calvio C, Herrgård MJ. 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 strains. Microbial Cell Factories. 18: 3. PMID 30626384 DOI: 10.1186/S12934-018-1052-2 |
0.729 |
|
| 2018 |
Lieven C, Petersen LAH, Jørgensen SB, Gernaey KV, Herrgard MJ, Sonnenschein N. A Genome-Scale Metabolic Model for (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. Frontiers in Microbiology. 9: 2947. PMID 30564208 DOI: 10.3389/Fmicb.2018.02947 |
0.833 |
|
| 2018 |
D'Arrigo I, Cardoso JGR, Rennig M, Sonnenschein N, Herrgård MJ, Long KS. Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling. Environmental Microbiology Reports. PMID 30298597 DOI: 10.1111/1758-2229.12704 |
0.683 |
|
| 2018 |
Cardoso JGR, Zeidan AA, Jensen K, Sonnenschein N, Neves AR, Herrgård MJ. MARSI: metabolite analogues for rational strain improvement. Bioinformatics (Oxford, England). 34: 2319-2321. PMID 29949953 DOI: 10.1093/Bioinformatics/Bty108 |
0.693 |
|
| 2018 |
Lieven C, Herrgård MJ, Sonnenschein N. Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology. Biotechnology Journal. PMID 29917330 DOI: 10.1002/Biot.201800011 |
0.825 |
|
| 2018 |
Cardoso J, Jensen K, Lieven C, Hansen ASL, Galkina S, Beber ME, Özdemir E, Herrgard M, Redestig H, Sonnenschein N. Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories. Acs Synthetic Biology. PMID 29558112 DOI: 10.1021/Acssynbio.7B00423 |
0.786 |
|
| 2017 |
Hansen AS, Lennen RM, Sonnenschein N, Herrgård MJ. Systems biology solutions for biochemical production challenges. Current Opinion in Biotechnology. 45: 85-91. PMID 28319856 DOI: 10.1016/J.Copbio.2016.11.018 |
0.68 |
|
| 2017 |
Dräger A, King ZA, Yurkovich JT, Blessing C, Khandelwa D, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Visualization and creation of biochemical networks with Escher F1000research. 6. DOI: 10.7490/F1000Research.1114756.1 |
0.727 |
|
| 2016 |
Zhang J, Sonnenschein N, Pihl TP, Pedersen KR, Jensen MK, Keasling JD. Engineering an NADPH/NADP+ redox biosensor in yeast. Acs Synthetic Biology. PMID 27419466 DOI: 10.1021/Acssynbio.6B00135 |
0.478 |
|
| 2016 |
Dräger A, King ZA, Lu JS, Ebrahim A, Sonnenschein N, Miller PC, Lerman JA, Palsson BO, Lewis NE. New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher F1000research. 5. DOI: 10.7490/F1000Research.1112788.1 |
0.765 |
|
| 2015 |
Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 1: 283-292. PMID 27136057 DOI: 10.1016/J.Cels.2015.10.003 |
0.783 |
|
| 2015 |
Machado D, Zhuang KH, Sonnenschein N, Herrgård MJ. Editorial: Current Challenges in Modeling Cellular Metabolism. Frontiers in Bioengineering and Biotechnology. 3: 193. PMID 26636080 DOI: 10.3389/Fbioe.2015.00193 |
0.743 |
|
| 2015 |
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, ... ... Sonnenschein N, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.662 |
|
| 2015 |
King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. Plos Computational Biology. 11: e1004321. PMID 26313928 DOI: 10.1371/Journal.Pcbi.1004321 |
0.778 |
|
| 2015 |
Cardoso JG, Andersen MR, Herrgård MJ, Sonnenschein N. Analysis of genetic variation and potential applications in genome-scale metabolic modeling. Frontiers in Bioengineering and Biotechnology. 3: 13. PMID 25763369 DOI: 10.3389/Fbioe.2015.00013 |
0.655 |
|
| 2015 |
Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics Cell Systems. 1: 283-292. DOI: 10.1016/j.cels.2015.10.003 |
0.819 |
|
| 2014 |
Kildegaard KR, Hallström BM, Blicher TH, Sonnenschein N, Jensen NB, Sherstyk S, Harrison SJ, Maury J, Herrgård MJ, Juncker AS, Forster J, Nielsen J, Borodina I. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metabolic Engineering. 26: 57-66. PMID 25263954 DOI: 10.1016/J.Ymben.2014.09.004 |
0.755 |
|
| 2013 |
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, ... ... Sonnenschein N, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488 |
0.794 |
|
| 2012 |
Sonnenschein N, Marr C, Hütt MT. A topological characterization of medium-dependent essential metabolic reactions. Metabolites. 2: 632-47. PMID 24957651 DOI: 10.3390/Metabo2030632 |
0.653 |
|
| 2012 |
Beber ME, Fretter C, Jain S, Sonnenschein N, Müller-Hannemann M, Hütt MT. Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks. Journal of the Royal Society, Interface. 9: 3426-35. PMID 22896565 DOI: 10.1098/Rsif.2012.0490 |
0.627 |
|
| 2012 |
Sonnenschein N, Golib Dzib JF, Lesne A, Eilebrecht S, Boulkroun S, Zennaro MC, Benecke A, Hütt MT. A network perspective on metabolic inconsistency. Bmc Systems Biology. 6: 41. PMID 22583819 DOI: 10.1186/1752-0509-6-41 |
0.667 |
|
| 2011 |
Sonnenschein N, Geertz M, Muskhelishvili G, Hütt MT. Analog regulation of metabolic demand. Bmc Systems Biology. 5: 40. PMID 21406074 DOI: 10.1186/1752-0509-5-40 |
0.627 |
|
| 2009 |
Sonnenschein N, Hütt MT, Stoyan H, Stoyan D. Ranges of control in the transcriptional regulation of Escherichia coli. Bmc Systems Biology. 3: 119. PMID 20034377 DOI: 10.1186/1752-0509-3-119 |
0.597 |
|
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