| Year |
Citation |
Score |
| 2023 |
Goel N, Srivastav S, Patel A, Shirsath A, Panda TR, Patra M, Feist AM, Anand A. TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent . Microbiology Spectrum. e0222523. PMID 37855642 DOI: 10.1128/spectrum.02225-23 |
0.769 |
|
| 2023 |
Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, et al. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Reports. 42: 113105. PMID 37713311 DOI: 10.1016/j.celrep.2023.113105 |
0.827 |
|
| 2023 |
Sandberg TE, Wise KS, Dalldorf C, Szubin R, Feist AM, Glass JI, Palsson BO. Adaptive evolution of a minimal organism with a synthetic genome. Iscience. 26: 107500. PMID 37636038 DOI: 10.1016/j.isci.2023.107500 |
0.508 |
|
| 2023 |
Driessen JLSP, Johnsen J, Pogrebnyakov I, Mohamed ETT, Mussatto SI, Feist AM, Jensen SI, Nielsen AT. Adaptive laboratory evolution of to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Metabolic Engineering Communications. 16: e00223. PMID 37234932 DOI: 10.1016/j.mec.2023.e00223 |
0.326 |
|
| 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, ... ... Feist AM, 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 |
0.806 |
|
| 2022 |
Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhay A, Petzold CJ, Simmons BA, Singer SW. Revealing Oxidative Pentose Metabolism in New Pseudomonas putida Isolates. Environmental Microbiology. PMID 36465038 DOI: 10.1111/1462-2920.16296 |
0.73 |
|
| 2022 |
Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. Msystems. e0016522. PMID 36226969 DOI: 10.1128/msystems.00165-22 |
0.823 |
|
| 2022 |
Anand A, Patel A, Chen K, Olson CA, Phaneuf PV, Lamoureux C, Hefner Y, Szubin R, Feist AM, Palsson BO. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Nature Communications. 13: 3682. PMID 35760776 DOI: 10.1038/s41467-022-30877-5 |
0.817 |
|
| 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 |
0.764 |
|
| 2022 |
Mueller J, Willett H, Feist AM, Niu W. Engineering Pseudomonas putida for improved utilization of syringyl aromatics. Biotechnology and Bioengineering. PMID 35524438 DOI: 10.1002/bit.28131 |
0.332 |
|
| 2022 |
Lim HG, Rychel K, Sastry AV, Bentley GJ, Mueller J, Schindel HS, Larsen PE, Laible PD, Guss AM, Niu W, Johnson CW, Beckham GT, Feist AM, Palsson BO. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metabolic Engineering. PMID 35489688 DOI: 10.1016/j.ymben.2022.04.004 |
0.807 |
|
| 2021 |
Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. Acs Synthetic Biology. PMID 34762392 DOI: 10.1021/acssynbio.1c00337 |
0.804 |
|
| 2021 |
Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. Msphere. 6: e0044321. PMID 34431696 DOI: 10.1128/mSphere.00443-21 |
0.789 |
|
| 2021 |
Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular Systems Biology. 17: e10099. PMID 34288418 DOI: 10.15252/msb.202010099 |
0.825 |
|
| 2021 |
Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Communications Biology. 4: 793. PMID 34172889 DOI: 10.1038/s42003-021-02339-z |
0.779 |
|
| 2021 |
Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Cell Reports. 35: 108961. PMID 33826886 DOI: 10.1016/j.celrep.2021.108961 |
0.821 |
|
| 2021 |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, ... ... Feist AM, et al. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 10. PMID 33420779 DOI: 10.1093/gigascience/giaa156 |
0.77 |
|
| 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 |
0.599 |
|
| 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 |
0.658 |
|
| 2020 |
Heckmann D, Campeau A, Lloyd CJ, Phaneuf PV, Hefner Y, Carrillo-Terrazas M, Feist AM, Gonzalez DJ, Palsson BO. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. Proceedings of the National Academy of Sciences of the United States of America. PMID 32873645 DOI: 10.1073/Pnas.2001562117 |
0.816 |
|
| 2020 |
Phaneuf PV, Yurkovich JT, Heckmann D, Wu M, Sandberg TE, King ZA, Tan J, Palsson BO, Feist AM. Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. Bmc Genomics. 21: 514. PMID 32711472 DOI: 10.1186/S12864-020-06920-4 |
0.788 |
|
| 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, ... Feist AM, 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 |
0.797 |
|
| 2020 |
Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. Msystems. 5. PMID 32234776 DOI: 10.1128/mSystems.00828-19 |
0.747 |
|
| 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 |
0.706 |
|
| 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, ... Feist AM, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y |
0.801 |
|
| 2020 |
Lim HG, Fong B, Alarcon G, Magurudeniya HD, Eng T, Szubin R, Olson CA, Palsson BO, Gladden JM, Simmons BA, Mukhopadhyay A, Singer SW, Feist AM. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution Green Chemistry. 22: 5677-5690. DOI: 10.1039/D0Gc01663B |
0.489 |
|
| 2020 |
Liu Z, Feist AM, Dragone G, Mussatto SI. Lipid and carotenoid production from wheat straw hydrolysates by different oleaginous yeasts Journal of Cleaner Production. 249: 119308. DOI: 10.1016/J.Jclepro.2019.119308 |
0.312 |
|
| 2019 |
Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, ... ... Feist AM, et al. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Scientific Data. 6: 322. PMID 31848353 DOI: 10.1038/S41597-019-0331-Z |
0.785 |
|
| 2019 |
Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 31767748 DOI: 10.1073/Pnas.1909987116 |
0.806 |
|
| 2019 |
Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. High-quality genome-scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities. Environmental Microbiology. PMID 31657101 DOI: 10.1111/1462-2920.14843 |
0.825 |
|
| 2019 |
Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states. Molecular Biology and Evolution. PMID 31651953 DOI: 10.1093/Molbev/Msz251 |
0.817 |
|
| 2019 |
Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of under acid stress. Microbiology (Reading, England). PMID 31625833 DOI: 10.1099/Mic.0.000867 |
0.811 |
|
| 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 |
0.634 |
|
| 2019 |
Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. A defined minimal medium for systems analyses of reveals strain-specific metabolic requirements. Applied and Environmental Microbiology. PMID 31471305 DOI: 10.1128/Aem.01773-19 |
0.835 |
|
| 2019 |
Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metabolic Engineering. PMID 31401242 DOI: 10.1016/J.Ymben.2019.08.004 |
0.557 |
|
| 2019 |
Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, ... ... Feist AM, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116 |
0.746 |
|
| 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 |
0.664 |
|
| 2019 |
Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. Plos Computational Biology. 15: e1007066. PMID 31158228 DOI: 10.1371/Journal.Pcbi.1007066 |
0.817 |
|
| 2019 |
Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, ... ... Feist AM, et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data. 6: 43. PMID 31028276 DOI: 10.1038/S41597-019-0051-4 |
0.777 |
|
| 2019 |
Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Plos Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/Journal.Pcbi.1006971 |
0.815 |
|
| 2019 |
Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM. Enzyme promiscuity shapes adaptation to novel growth substrates. Molecular Systems Biology. 15: e8462. PMID 30962359 DOI: 10.15252/Msb.20188462 |
0.716 |
|
| 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 |
0.737 |
|
| 2019 |
Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. The genetic basis for adaptation of model-designed syntrophic co-cultures. Plos Computational Biology. 15: e1006213. PMID 30822347 DOI: 10.1371/Journal.Pcbi.1006213 |
0.807 |
|
| 2019 |
Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO. Pseudogene repair driven by selection pressure applied in experimental evolution. Nature Microbiology. PMID 30692668 DOI: 10.1038/S41564-018-0340-2 |
0.787 |
|
| 2018 |
Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM. Reframing gene essentiality in terms of adaptive flexibility. Bmc Systems Biology. 12: 143. PMID 30558585 DOI: 10.1186/S12918-018-0653-Z |
0.803 |
|
| 2018 |
Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7. PMID 30533692 DOI: 10.1128/MRA.00890-18 |
0.794 |
|
| 2018 |
Rugbjerg P, Feist AM, Sommer MOA. Enhanced Metabolite Productivity of Adapted to Glucose M9 Minimal Medium. Frontiers in Bioengineering and Biotechnology. 6: 166. PMID 30483499 DOI: 10.3389/Fbioe.2018.00166 |
0.389 |
|
| 2018 |
Dinh HV, King ZA, Palsson BO, Feist AM. Identification of growth-coupled production strains considering protein costs and kinetic variability. Metabolic Engineering Communications. 7: e00080. PMID 30370222 DOI: 10.1016/J.Mec.2018.E00080 |
0.548 |
|
| 2018 |
Phaneuf PV, Gosting D, Palsson BO, Feist AM. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Research. PMID 30357390 DOI: 10.1093/Nar/Gky983 |
0.789 |
|
| 2018 |
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nature Communications. 9: 3796. PMID 30228271 DOI: 10.1038/S41467-018-06219-9 |
0.821 |
|
| 2018 |
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Growth Adaptation of and Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Frontiers in Microbiology. 9: 1793. PMID 30131786 DOI: 10.3389/Fmicb.2018.01793 |
0.827 |
|
| 2018 |
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions. Applied and Environmental Microbiology. PMID 30054360 DOI: 10.1128/Aem.00823-18 |
0.828 |
|
| 2018 |
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metabolic Engineering. PMID 29906504 DOI: 10.1016/J.Ymben.2018.06.005 |
0.808 |
|
| 2018 |
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metabolic Engineering. PMID 29842925 DOI: 10.1016/J.Ymben.2018.05.012 |
0.833 |
|
| 2018 |
Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J. Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. Metabolic Engineering. PMID 29534903 DOI: 10.1016/J.Ymben.2018.03.006 |
0.737 |
|
| 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 |
0.627 |
|
| 2017 |
Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. PMID 29255023 DOI: 10.1073/Pnas.1716056115 |
0.606 |
|
| 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 |
0.608 |
|
| 2017 |
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/Nbt.3956 |
0.763 |
|
| 2017 |
Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Metabolic Engineering. PMID 28951266 DOI: 10.1016/J.Ymben.2017.09.012 |
0.6 |
|
| 2017 |
Notebaart RA, Kintses B, Feist AM, Papp B. Underground metabolism: network-level perspective and biotechnological potential. Current Opinion in Biotechnology. 49: 108-114. PMID 28837944 DOI: 10.1016/J.Copbio.2017.07.015 |
0.415 |
|
| 2017 |
Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Applied and Environmental Microbiology. PMID 28455337 DOI: 10.1128/Aem.00410-17 |
0.816 |
|
| 2017 |
LaCroix RA, Palsson BO, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Applied and Environmental Microbiology. PMID 28159796 DOI: 10.1128/Aem.03115-16 |
0.686 |
|
| 2016 |
Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA.
comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metabolic Engineering Communications. 3: 84-96. PMID 29468116 DOI: 10.1016/J.Meteno.2016.03.003 |
0.427 |
|
| 2016 |
King ZA, O'Brien EJ, Feist AM, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metabolic Engineering. PMID 27986597 DOI: 10.1016/J.Ymben.2016.12.004 |
0.769 |
|
| 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 |
0.792 |
|
| 2016 |
Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091 |
0.786 |
|
| 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 |
0.801 |
|
| 2016 |
Feist AM, Palsson BO. What do cells actually want? Genome Biology. 17: 110. PMID 27215675 DOI: 10.1186/S13059-016-0983-3 |
0.484 |
|
| 2016 |
Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/J.Cels.2016.04.004 |
0.818 |
|
| 2016 |
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Systems. 2: 260-271. PMID 27135538 DOI: 10.1016/J.Cels.2016.04.003 |
0.809 |
|
| 2016 |
McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM. A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale. Analytical Chemistry. PMID 26981784 DOI: 10.1021/Acs.Analchem.5B04914 |
0.799 |
|
| 2016 |
Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. Plos One. 11: e0151130. PMID 26964043 DOI: 10.1371/Journal.Pone.0151130 |
0.509 |
|
| 2015 |
McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM. MID Max: A LC-MS/MS method for measuring the precursor and product mass isotopomer distributions (MIDs) of metabolic intermediates and cofactors for metabolic flux analysis (MFA) applications. Analytical Chemistry. PMID 26666286 DOI: 10.1021/Acs.Analchem.5B03887 |
0.77 |
|
| 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 |
0.76 |
|
| 2015 |
Strucko T, Mohamed ETT, Feist A, Förster J. Development of an efficient glycerol utilizing Saccharomyces cerevisiae platform strain via adaptive laboratory evolution Yeast. 32. PMID 26358946 DOI: 10.1002/Yea.3092 |
0.702 |
|
| 2015 |
King ZA, Lloyd CJ, Feist AM, Palsson BO. Next-generation genome-scale models for metabolic engineering. Current Opinion in Biotechnology. 35: 23-29. PMID 25575024 DOI: 10.1016/J.Copbio.2014.12.016 |
0.817 |
|
| 2015 |
Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 112: 929-34. PMID 25564669 DOI: 10.1073/Pnas.1414218112 |
0.831 |
|
| 2015 |
LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Applied and Environmental Microbiology. 81: 17-30. PMID 25304508 DOI: 10.1128/Aem.02246-14 |
0.823 |
|
| 2015 |
McCloskey D, Gangoiti JA, Palsson BO, Feist AM. A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites Metabolomics. 11: 1338-1350. DOI: 10.1007/S11306-015-0790-Y |
0.487 |
|
| 2014 |
Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R. Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli. Microbiology (Reading, England). 160: 2780-93. PMID 25246670 DOI: 10.1099/Mic.0.082180-0 |
0.674 |
|
| 2014 |
Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. Bmc Systems Biology. 8: 110. PMID 25227965 DOI: 10.1186/S12918-014-0110-6 |
0.798 |
|
| 2014 |
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metabolic Engineering. 25: 140-58. PMID 25080239 DOI: 10.1016/J.Ymben.2014.07.009 |
0.569 |
|
| 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 |
0.826 |
|
| 2014 |
Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Molecular Cell. 55: 253-63. PMID 24882210 DOI: 10.1016/J.Molcel.2014.05.008 |
0.75 |
|
| 2014 |
King ZA, Feist AM. Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. Metabolic Engineering. 24: 117-28. PMID 24831709 DOI: 10.1016/J.Ymben.2014.05.009 |
0.369 |
|
| 2014 |
Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. Plos Computational Biology. 10: e1003575. PMID 24762737 DOI: 10.1371/Journal.Pcbi.1003575 |
0.709 |
|
| 2014 |
Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins. 82: 1819-28. PMID 24523134 DOI: 10.1002/Prot.24536 |
0.327 |
|
| 2014 |
McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnology and Bioengineering. 111: 803-15. PMID 24249002 DOI: 10.1002/Bit.25133 |
0.809 |
|
| 2014 |
McCloskey D, Utrilla J, Naviaux RK, Palsson BO, Feist AM. Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media Metabolomics. 11: 198-209. DOI: 10.1007/S11306-014-0686-2 |
0.46 |
|
| 2013 |
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proceedings of the National Academy of Sciences of the United States of America. 110: 20338-43. PMID 24277855 DOI: 10.1073/Pnas.1307797110 |
0.829 |
|
| 2013 |
Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nature Communications. 4: 2809. PMID 24264237 DOI: 10.1038/Ncomms3809 |
0.784 |
|
| 2013 |
McCloskey D, Palsson BØ, Feist AM. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Molecular Systems Biology. 9: 661. PMID 23632383 DOI: 10.1038/Msb.2013.18 |
0.809 |
|
| 2013 |
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnology Journal. 8: 1070-9. PMID 23420771 DOI: 10.1002/Biot.201200266 |
0.617 |
|
| 2013 |
Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K. Sulfide-driven microbial electrosynthesis. Environmental Science & Technology. 47: 568-73. PMID 23252645 DOI: 10.1021/Es303837J |
0.757 |
|
| 2013 |
King ZA, Feist AM. Optimizing cofactor specificity of oxidoreductase enzymes for the generation of microbial production strains - OptSwap Industrial Biotechnology. 9: 236-246. DOI: 10.1089/Ind.2013.0005 |
0.392 |
|
| 2012 |
Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BØ. Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor. Journal of Biotechnology. 161: 242-9. PMID 22796827 DOI: 10.1016/J.Jbiotec.2012.07.004 |
0.454 |
|
| 2011 |
Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. Bmc Systems Biology. 5: 180. PMID 22041191 DOI: 10.1186/1752-0509-5-180 |
0.806 |
|
| 2011 |
Lee DH, Feist AM, Barrett CL, Palsson BØ. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. Plos One. 6: e26172. PMID 22028828 DOI: 10.1371/Journal.Pone.0026172 |
0.527 |
|
| 2011 |
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Molecular Systems Biology. 7: 535. PMID 21988831 DOI: 10.1038/Msb.2011.65 |
0.835 |
|
| 2011 |
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/Nprot.2011.308 |
0.804 |
|
| 2011 |
Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234 |
0.744 |
|
| 2010 |
Feist AM, Palsson BO. The biomass objective function. Current Opinion in Microbiology. 13: 344-9. PMID 20430689 DOI: 10.1016/J.Mib.2010.03.003 |
0.512 |
|
| 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 |
0.805 |
|
| 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 |
0.762 |
|
| 2009 |
Feist AM, Thiele I, Palsson B. Genome-scale reconstruction, modeling, and simulation of E. coli's metabolic network Systems Biology and Biotechnology of Escherichia Coli. 149-176. DOI: 10.1007/978-1-4020-9394-4_9 |
0.651 |
|
| 2008 |
Lee J, Yun H, Feist AM, Palsson BØ, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Applied Microbiology and Biotechnology. 80: 849-62. PMID 18758767 DOI: 10.1007/S00253-008-1654-4 |
0.593 |
|
| 2008 |
Feist AM, Palsson BØ. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature Biotechnology. 26: 659-67. PMID 18536691 DOI: 10.1038/Nbt1401 |
0.561 |
|
| 2007 |
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology. 3: 121. PMID 17593909 DOI: 10.1038/Msb4100155 |
0.796 |
|
| 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 |
0.819 |
|
| 2006 |
Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular Systems Biology. 2: 2006.0004. PMID 16738551 DOI: 10.1038/Msb4100046 |
0.591 |
|
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