| Year |
Citation |
Score |
| 2023 |
Donati S, Mattanovich M, Hjort P, Jacobsen SAB, Blomquist SD, Mangaard D, Gurdo N, Pastor FP, Maury J, Hanke R, Herrgård MJ, Wulff T, Jakočiūnas T, Nielsen LK, McCloskey D. An automated workflow for multi-omics screening of microbial model organisms. Npj Systems Biology and Applications. 9: 14. PMID 37208327 DOI: 10.1038/s41540-023-00277-6 |
0.698 |
|
| 2023 |
Peluso AA, Lundgaard AT, Babaei P, Mousovich-Neto F, Rocha AL, Damgaard MV, Bak EG, Gnanasekaran T, Dollerup OL, Trammell SAJ, Nielsen TS, Kern T, Abild CB, Sulek K, Ma T, et al. Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans. Npj Aging. 9: 7. PMID 37012386 DOI: 10.1038/s41514-023-00106-4 |
0.669 |
|
| 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, 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 |
0.782 |
|
| 2022 |
Yang L, Malla S, Özdemir E, Kim SH, Lennen R, Christensen HB, Christensen U, Munro LJ, Herrgård MJ, Kell DB, Palsson BØ. Identification and Engineering of Transporters for Efficient Melatonin Production in . Frontiers in Microbiology. 13: 880847. PMID 35794920 DOI: 10.3389/fmicb.2022.880847 |
0.754 |
|
| 2022 |
Radi MS, SalcedoSora JE, Kim SH, Sudarsan S, Sastry AV, Kell DB, Herrgård MJ, Feist AM. Membrane transporter identification and modulation via adaptive laboratory evolution. Metabolic Engineering. PMID 35598887 DOI: 10.1016/j.ymben.2022.05.004 |
0.749 |
|
| 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 |
0.727 |
|
| 2020 |
Dahlin J, Holkenbrink C, Marella ER, Wang G, Liebal U, Lieven C, Weber D, McCloskey D, Wang HL, Ebert BE, Herrgård MJ, Blank LM, Borodina I. Corrigendum: Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts and . Frontiers in Genetics. 11: 637738. PMID 33505441 DOI: 10.3389/fgene.2020.637738 |
0.679 |
|
| 2020 |
Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Analytical Chemistry. PMID 33269929 DOI: 10.1021/acs.analchem.0c03421 |
0.667 |
|
| 2020 |
Hansen ASL, Dunham MJ, Arsovska D, Zhang J, Keasling JD, Herrgard MJ, Jensen MK. Dietary Change Enables Robust Growth-Coupling of Heterologous Methyltransferase Activity in Yeast. Acs Synthetic Biology. PMID 33179905 DOI: 10.1021/acssynbio.0c00348 |
0.423 |
|
| 2020 |
Pereira R, Mohamed ET, Radi MS, Herrgård MJ, Feist AM, Nielsen J, Chen Y. Elucidating aromatic acid tolerance at low pH in using adaptive laboratory evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 33106428 DOI: 10.1073/pnas.2013044117 |
0.59 |
|
| 2020 |
Mohamed ET, Werner AZ, Salvachúa D, Singer CA, Szostkiewicz K, Rafael Jiménez-Díaz M, Eng T, Radi MS, Simmons BA, Mukhopadhyay A, Herrgård MJ, Singer SW, Beckham GT, Feist AM. Adaptive laboratory evolution of KT2440 improves -coumaric and ferulic acid catabolism and tolerance. Metabolic Engineering Communications. 11: e00143. PMID 32963959 DOI: 10.1016/J.Mec.2020.E00143 |
0.631 |
|
| 2020 |
Landberg J, Wright NR, Wulff T, Herrgård MJ, Nielsen AT. CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. Biotechnology and Bioengineering. PMID 32808670 DOI: 10.1002/Bit.27536 |
0.371 |
|
| 2020 |
Luo H, Schneider K, Christensen U, Lei Y, Herrgard M, Palsson BØ. Microbial Synthesis of Human-Hormone Melatonin at Gram Scales. Acs Synthetic Biology. PMID 32501000 DOI: 10.1021/Acssynbio.0C00065 |
0.524 |
|
| 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 |
0.706 |
|
| 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, 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 |
0.781 |
|
| 2020 |
Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in . Acs Synthetic Biology. PMID 32149495 DOI: 10.1021/Acssynbio.9B00488 |
0.682 |
|
| 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, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y |
0.782 |
|
| 2019 |
Kristjansdottir T, Bosma EF, Branco Dos Santos F, Özdemir E, Herrgård MJ, França L, Ferreira B, Nielsen AT, Gudmundsson S. A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Microbial Cell Factories. 18: 186. PMID 31665018 DOI: 10.1186/S12934-019-1229-3 |
0.436 |
|
| 2019 |
Pereira R, Wei Y, Mohamed E, Radi M, Malina C, Herrgård MJ, Feist AM, Nielsen J, Chen Y. Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae. Metabolic Engineering. PMID 31550508 DOI: 10.1016/J.Ymben.2019.09.008 |
0.622 |
|
| 2019 |
Dahlin J, Holkenbrink C, Marella ER, Wang G, Liebal U, Lieven C, Weber D, McCloskey D, Ebert BE, Herrgård MJ, Blank LM, Borodina I. Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts and . Frontiers in Genetics. 10: 747. PMID 31543895 DOI: 10.3389/Fgene.2019.00747 |
0.716 |
|
| 2019 |
Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Feuvre RL, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, et al. Author Correction: Building a global alliance of biofoundries. Nature Communications. 10: 3132. PMID 31296848 DOI: 10.1038/S41467-019-10862-1 |
0.48 |
|
| 2019 |
Mohamed ET, Mundhada H, Landberg J, Cann I, Mackie RI, Nielsen AT, Herrgård MJ, Feist AM. Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Microbial Cell Factories. 18: 116. PMID 31255177 DOI: 10.1186/S12934-019-1165-2 |
0.654 |
|
| 2019 |
Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Le Feuvre R, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, et al. Building a global alliance of biofoundries. Nature Communications. 10: 2040. PMID 31068573 DOI: 10.1038/S41467-019-10079-2 |
0.462 |
|
| 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 |
0.707 |
|
| 2019 |
Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ, Palsson BO. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. Plos Biology. 17: e2007050. PMID 30856169 DOI: 10.1371/Journal.Pbio.2007050 |
0.715 |
|
| 2019 |
Kang K, Bergdahl B, Machado D, Dato L, Han TL, Li J, Villas-Boas S, Herrgård MJ, Förster J, Panagiotou G. Linking genetic, metabolic and phenotypic diversity among S. cerevisiae strains using multi-omics associations. Gigascience. PMID 30715293 DOI: 10.1093/Gigascience/Giz015 |
0.799 |
|
| 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 |
0.759 |
|
| 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 |
0.756 |
|
| 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 |
0.73 |
|
| 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 |
0.748 |
|
| 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 |
0.748 |
|
| 2018 |
Shepelin D, Hansen ASL, Lennen R, Luo H, Herrgård MJ. Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes. Genes. 9. PMID 29751691 DOI: 10.3390/Genes9050249 |
0.744 |
|
| 2018 |
McCloskey D, Xu J, Schrübbers L, Christensen HB, Herrgård MJ. RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli. Metabolic Engineering. PMID 29702276 DOI: 10.1016/J.Ymben.2018.04.009 |
0.739 |
|
| 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 |
0.701 |
|
| 2018 |
Campodonico MA, Sukumara S, Feist AM, Herrgård MJ. Computational Methods to Assess the Production Potential of Bio-Based Chemicals. Methods in Molecular Biology (Clifton, N.J.). 1671: 97-116. PMID 29170955 DOI: 10.1007/978-1-4939-7295-1_7 |
0.619 |
|
| 2017 |
Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microbial Cell Factories. 16: 204. PMID 29145855 DOI: 10.1186/S12934-017-0819-1 |
0.775 |
|
| 2017 |
Baumgarten T, Schlegel S, Wagner S, Löw M, Eriksson J, Bonde I, Herrgård MJ, Heipieper HJ, Nørholm MH, Slotboom DJ, de Gier JW. Isolation and characterization of the E. coli membrane protein production strain Mutant56(DE3). Scientific Reports. 7: 45089. PMID 28338018 DOI: 10.1038/Srep45089 |
0.319 |
|
| 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 |
0.811 |
|
| 2016 |
Mundhada H, Miguel JS, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT. Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution. Metabolic Engineering. PMID 27908688 DOI: 10.1016/J.Ymben.2016.11.008 |
0.787 |
|
| 2016 |
Machado D, Herrgård MJ, Rocha I. Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. Plos Computational Biology. 12: e1005140. PMID 27711110 DOI: 10.1371/Journal.Pcbi.1005140 |
0.408 |
|
| 2016 |
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems. PMID 27667363 DOI: 10.1016/J.Cels.2016.08.013 |
0.795 |
|
| 2016 |
Kildegaard KR, Jensen NB, Schneider K, Czarnotta E, Özdemir E, Klein T, Maury J, Ebert BE, Christensen HB, Chen Y, Kim IK, Herrgård MJ, Blank LM, Forster J, Nielsen J, et al. Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microbial Cell Factories. 15: 53. PMID 26980206 DOI: 10.1186/S12934-016-0451-5 |
0.671 |
|
| 2016 |
Maury J, Germann SM, Baallal Jacobsen SA, Jensen NB, Kildegaard KR, Herrgård MJ, Schneider K, Koza A, Forster J, Nielsen J, Borodina I. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae. Plos One. 11: e0150394. PMID 26934490 DOI: 10.1371/Journal.Pone.0150394 |
0.724 |
|
| 2015 |
Machado D, Herrgård MJ. Co-evolution of strain design methods based on flux balance and elementary mode analysis. Metabolic Engineering Communications. 2: 85-92. PMID 34150512 DOI: 10.1016/j.meteno.2015.04.001 |
0.303 |
|
| 2015 |
Jensen SI, Lennen RM, Herrgård MJ, Nielsen AT. Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Scientific Reports. 5: 17874. PMID 26643270 DOI: 10.1038/Srep17874 |
0.751 |
|
| 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 |
0.739 |
|
| 2015 |
Herrgård M, Sukumara S, Campodonico M, Zhuang K. A multi-scale, multi-disciplinary approach for assessing the technological, economic and environmental performance of bio-based chemicals. Biochemical Society Transactions. 43: 1151-6. PMID 26614653 DOI: 10.1042/Bst20150144 |
0.361 |
|
| 2015 |
Machado D, Herrgård MJ, Rocha I. Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. Frontiers in Bioengineering and Biotechnology. 3: 154. PMID 26501058 DOI: 10.3389/Fbioe.2015.00154 |
0.405 |
|
| 2015 |
Lennen RM, Nilsson Wallin AI, Pedersen M, Bonde M, Luo H, Herrgård MJ, Sommer MO. Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects. Nucleic Acids Research. PMID 26496947 DOI: 10.1093/Nar/Gkv1090 |
0.752 |
|
| 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, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.709 |
|
| 2015 |
Zhuang KH, Herrgård MJ. Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production. Metabolic Engineering. 31: 1-12. PMID 26116515 DOI: 10.1016/J.Ymben.2015.05.007 |
0.423 |
|
| 2015 |
Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nature Communications. 6: 7101. PMID 26055627 DOI: 10.1038/Ncomms8101 |
0.777 |
|
| 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 |
0.725 |
|
| 2015 |
Jako?i?nas T, Bonde I, Herrgård M, Harrison SJ, Kristensen M, Pedersen LE, Jensen MK, Keasling JD. Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metabolic Engineering. 28: 213-22. PMID 25638686 DOI: 10.1016/J.Ymben.2015.01.008 |
0.584 |
|
| 2015 |
Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgård MJ, Rosenstand I, Öberg F, Forster J, Nielsen J. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metabolic Engineering. 27: 57-64. PMID 25447643 DOI: 10.1016/J.Ymben.2014.10.003 |
0.695 |
|
| 2015 |
Machado D, Herrgård MJ. Co-evolution of strain design methods based on flux balance and elementary mode analysis Metabolic Engineering Communications. 2: 85-92. DOI: 10.1016/J.Meteno.2015.04.001 |
0.436 |
|
| 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 |
0.803 |
|
| 2014 |
Lennen RM, Herrgård MJ. Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Applied and Environmental Microbiology. 80: 6223-42. PMID 25085490 DOI: 10.1128/Aem.01542-14 |
0.77 |
|
| 2014 |
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Molecular Biology and Evolution. 31: 2647-62. PMID 25015645 DOI: 10.1093/Molbev/Msu209 |
0.81 |
|
| 2014 |
Machado D, Herrgård M. Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. Plos Computational Biology. 10: e1003580. PMID 24762745 DOI: 10.1371/Journal.Pcbi.1003580 |
0.383 |
|
| 2014 |
Lennen R, Bonde I, Koza A, Herrgård M. Library sequencing strategies for comparative analysis of stress resistance mechanisms in Escherichia coli strains New Biotechnology. 31: S86. DOI: 10.1016/J.Nbt.2014.05.1811 |
0.737 |
|
| 2013 |
Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Frontiers in Microbiology. 4: 106. PMID 23761787 DOI: 10.3389/Fmicb.2013.00106 |
0.309 |
|
| 2013 |
Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Frontiers in Microbiology. 4: 84. PMID 23755042 DOI: 10.3389/Fmicb.2013.00084 |
0.304 |
|
| 2013 |
Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Frontiers in Microbiology. 4: 95. PMID 23720654 DOI: 10.3389/Fmicb.2013.00095 |
0.36 |
|
| 2013 |
Inskeep WP, Jay ZJ, Tringe SG, Herrgård MJ, Rusch DB. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Frontiers in Microbiology. 4: 67. PMID 23653623 DOI: 10.3389/Fmicb.2013.00067 |
0.369 |
|
| 2013 |
Zhuang K, Bakshi BR, Herrgård MJ. Multi-scale modeling for sustainable chemical production. Biotechnology Journal. 8: 973-84. PMID 23520143 DOI: 10.1002/Biot.201200272 |
0.405 |
|
| 2013 |
Harrison SJ, Herrgard MJ. The uses and future prospects of metabolomics and targeted metabolite profiling in cell factory development Industrial Biotechnology. 9: 196-202. DOI: 10.1089/Ind.2013.0008 |
0.376 |
|
| 2012 |
Herrgard M, Panagiotou G. Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology" Computational and Structural Biotechnology Journal. 3. DOI: 10.5936/Csbj.201210012 |
0.393 |
|
| 2010 |
Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. Plos One. 5: e9773. PMID 20333304 DOI: 10.1371/Journal.Pone.0009773 |
0.332 |
|
| 2010 |
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Metabolic Engineering. 12: 173-186. PMID 19840862 DOI: 10.1016/J.Ymben.2009.10.003 |
0.795 |
|
| 2009 |
Mo ML, Palsson BO, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. Bmc Systems Biology. 3: 37. PMID 19321003 DOI: 10.1186/1752-0509-3-37 |
0.778 |
|
| 2009 |
Barrett CL, Herrgard MJ, Palsson B. Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. Bmc Systems Biology. 3: 30. PMID 19267928 DOI: 10.1186/1752-0509-3-30 |
0.509 |
|
| 2009 |
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. Reconstruction of biochemical networks in microorganisms. Nature Reviews. Microbiology. 7: 129-43. PMID 19116616 DOI: 10.1038/Nrmicro1949 |
0.754 |
|
| 2008 |
Portnoy VA, Herrgård MJ, Palsson BØ. Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Applied and Environmental Microbiology. 74: 7561-9. PMID 18952873 DOI: 10.1128/Aem.00880-08 |
0.802 |
|
| 2008 |
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/Nbt1492 |
0.746 |
|
| 2008 |
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nature Biotechnology. 26: 1003-10. PMID 18711341 DOI: 10.1038/Nbt.1487 |
0.503 |
|
| 2008 |
Applebee MK, Herrgård MJ, Palsson BØ. Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. Journal of Bacteriology. 190: 5087-94. PMID 18487343 DOI: 10.1128/Jb.01976-07 |
0.777 |
|
| 2007 |
Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BØ, Sharan R, Ruppin E. Systematic condition-dependent annotation of metabolic genes. Genome Research. 17: 1626-33. PMID 17895423 DOI: 10.1101/Gr.6678707 |
0.807 |
|
| 2007 |
Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Current Opinion in Biotechnology. 18: 360-4. PMID 17719767 DOI: 10.1016/J.Copbio.2007.07.002 |
0.54 |
|
| 2007 |
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols. 2: 727-38. PMID 17406635 DOI: 10.1038/nprot.2007.99 |
0.806 |
|
| 2006 |
Herrgård MJ, Fong SS, Palsson BØ. Identification of genome-scale metabolic network models using experimentally measured flux profiles. Plos Computational Biology. 2: e72. PMID 16839195 DOI: 10.1371/Journal.Pcbi.0020072 |
0.725 |
|
| 2006 |
Herrgård MJ, Lee BS, Portnoy V, Palsson BØ. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Research. 16: 627-35. PMID 16606697 DOI: 10.1101/Gr.4083206 |
0.809 |
|
| 2005 |
Herrgård MJ, Palsson BØ. Untangling the web of functional and physical interactions in yeast. Journal of Biology. 4: 5. PMID 15982410 DOI: 10.1186/Jbiol26 |
0.432 |
|
| 2004 |
Duarte NC, Herrgård MJ, Palsson BØ. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research. 14: 1298-309. PMID 15197165 DOI: 10.1101/Gr.2250904 |
0.568 |
|
| 2004 |
Herrgård MJ, Palsson BØ. Flagellar biosynthesis in silico: building quantitative models of regulatory networks. Cell. 117: 689-90. PMID 15186769 DOI: 10.1016/J.Cell.2004.05.020 |
0.492 |
|
| 2004 |
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 429: 92-6. PMID 15129285 DOI: 10.1038/Nature02456 |
0.775 |
|
| 2004 |
Herrgård MJ, Covert MW, Palsson BØ. Reconstruction of microbial transcriptional regulatory networks. Current Opinion in Biotechnology. 15: 70-7. PMID 15102470 DOI: 10.1016/J.Copbio.2003.11.002 |
0.72 |
|
| 2003 |
Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. Journal of Bacteriology. 185: 6392-9. PMID 14563874 DOI: 10.1128/Jb.185.21.6392-6399.2003 |
0.699 |
|
| 2003 |
Herrgård MJ, Covert MW, Palsson BØ. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Research. 13: 2423-34. PMID 14559784 DOI: 10.1101/Gr.1330003 |
0.693 |
|
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