Adam Feist

Title(s)RES-FY-B/E/E-NON REP, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440. Metab Eng. 2024 Jun 25. Bleem AC, Kuatsjah E, Johnsen J, Mohamed ET, Alexander WG, Kellermyer ZA, Carroll AL, Rossi R, Schlander IB, Peabody V GL, Guss AM, Feist AM, Beckham GT. PMID: 38936762.
      View in: PubMed   Mentions:    Fields:    
    2. Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. Nat Commun. 2024 Apr 30; 15(1):3338. Kim HS, Noh MH, White EM, Kandefer MV, Wright AF, Datta D, Lim HG, Smiggs E, Locklin JJ, Rahman MA, Feist AM, Pokorski JK. PMID: 38688899; PMCID: PMC11061138.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nat Commun. 2024 Mar 15; 15(1):2356. Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO. PMID: 38490991; PMCID: PMC10943186.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    4. TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent Escherichia coli. Microbiol Spectr. 2023 Dec 12; 11(6):e0222523. Goel N, Srivastav S, Patel A, Shirsath A, Panda TR, Patra M, Feist AM, Anand A. PMID: 37855642; PMCID: PMC10715208.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    5. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep. 2023 09 26; 42(9):113105. 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, Palsson BO. PMID: 37713311; PMCID: PMC10591938.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    6. Adaptive evolution of a minimal organism with a synthetic genome. iScience. 2023 Sep 15; 26(9):107500. Sandberg TE, Wise KS, Dalldorf C, Szubin R, Feist AM, Glass JI, Palsson BO. PMID: 37636038; PMCID: PMC10448532.
      View in: PubMed   Mentions: 5  
    7. Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments. Metab Eng Commun. 2023 Dec; 17:e00227. Carpenter AC, Feist AM, Harrison FSM, Paulsen IT, Williams TC. PMID: 37538933; PMCID: PMC10393799.
      View in: PubMed   Mentions: 2  
    8. Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Metab Eng Commun. 2023 Jun; 16:e00223. Driessen JLSP, Johnsen J, Pogrebnyakov I, Mohamed ETT, Mussatto SI, Feist AM, Jensen SI, Nielsen AT. PMID: 37234932; PMCID: PMC10206485.
      View in: PubMed   Mentions: 1  
    9. Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metab Eng. 2023 03; 76:179-192. 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, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM. PMID: 36738854.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    10. Understanding Functional Redundancy and Promiscuity of Multidrug Transporters in E. coli under Lipophilic Cation Stress. Membranes (Basel). 2022 Dec 14; 12(12). Radi MS, Munro LJ, Salcedo-Sora JE, Kim SH, Feist AM, Kell DB. PMID: 36557171.
      View in: PubMed   Mentions: 2  
    11. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol. 2023 02; 25(2):493-504. Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW. PMID: 36465038; PMCID: PMC10107873.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    12. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. mSystems. 2022 Oct 13; e0016522. Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. PMID: 36226969.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    13. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Nat Commun. 2022 06 27; 13(1):3682. Anand A, Patel A, Chen K, Olson CA, Phaneuf PV, Lamoureux C, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 35760776; PMCID: PMC9237125.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    14. Membrane transporter identification and modulation via adaptive laboratory evolution. Metab Eng. 2022 07; 72:376-390. Radi MS, SalcedoSora JE, Kim SH, Sudarsan S, Sastry AV, Kell DB, Herrgård MJ, Feist AM. PMID: 35598887.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    15. Engineering Pseudomonas putida for improved utilization of syringyl aromatics. Biotechnol Bioeng. 2022 09; 119(9):2541-2550. Mueller J, Willett H, Feist AM, Niu W. PMID: 35524438; PMCID: PMC9378539.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    16. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metab Eng. 2022 07; 72:297-310. 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. PMID: 35489688.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    17. Selection for Cell Yield Does Not Reduce Overflow Metabolism in Escherichia coli. Mol Biol Evol. 2022 01 07; 39(1). Rabbers I, Gottstein W, Feist AM, Teusink B, Bruggeman FJ, Bachmann H. PMID: 34893866; PMCID: PMC8789295.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    18. Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. ACS Synth Biol. 2021 12 17; 10(12):3379-3395. 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. PMID: 34762392; PMCID: PMC8870144.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    19. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. mSphere. 2021 08 25; 6(4):e0044321. Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B. PMID: 34431696; PMCID: PMC8386450.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    20. Genome-scale metabolic modeling reveals key features of a minimal gene set. Mol Syst Biol. 2021 07; 17(7):e10099. Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. PMID: 34288418; PMCID: PMC8290834.
      View in: PubMed   Mentions: 12     Fields:    
    21. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Commun Biol. 2021 06 25; 4(1):793. Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM. PMID: 34172889; PMCID: PMC8233327.
      View in: PubMed   Mentions: 11  Translation:HumansCells
    22. Compensatory evolution of Pseudomonas aeruginosa's slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis. Nat Commun. 2021 05 27; 12(1):3186. La Rosa R, Rossi E, Feist AM, Johansen HK, Molin S. PMID: 34045458; PMCID: PMC8160344.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    23. Adaptive laboratory evolution of Rhodosporidium toruloides to inhibitors derived from lignocellulosic biomass and genetic variations behind evolution. Bioresour Technol. 2021 Aug; 333:125171. Liu Z, Radi M, Mohamed ETT, Feist AM, Dragone G, Mussatto SI. PMID: 33894448.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    24. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Cell Rep. 2021 04 06; 35(1):108961. Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO. PMID: 33826886; PMCID: PMC8489512.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    25. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 2021 01 09; 10(1). 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, Pogliano J, Nizet V, Feist AM, Palsson BO. PMID: 33420779; PMCID: PMC7794652.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    26. Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution. Proc Natl Acad Sci U S A. 2020 11 10; 117(45):27954-27961. Pereira R, Mohamed ET, Radi MS, Herrgård MJ, Feist AM, Nielsen J, Chen Y. PMID: 33106428; PMCID: PMC7668050.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    27. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. Proc Natl Acad Sci U S A. 2020 09 15; 117(37):23182-23190. Heckmann D, Campeau A, Lloyd CJ, Phaneuf PV, Hefner Y, Carrillo-Terrazas M, Feist AM, Gonzalez DJ, Palsson BO. PMID: 32873645; PMCID: PMC7502767.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    28. Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metab Eng Commun. 2020 Dec; 11:e00143. 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. PMID: 32963959; PMCID: PMC7490845.
      View in: PubMed   Mentions: 25  
    29. Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. BMC Genomics. 2020 Jul 25; 21(1):514. Phaneuf PV, Yurkovich JT, Heckmann D, Wu M, Sandberg TE, King ZA, Tan J, Palsson BO, Feist AM. PMID: 32711472; PMCID: PMC7382830.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    30. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 Apr; 38(4):504. 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, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32265554; PMCID: PMC7138757.
      View in: PubMed   Mentions: 3     Fields:    
    31. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. mSystems. 2020 Mar 31; 5(2). Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM. PMID: 32234776; PMCID: PMC7112963.
      View in: PubMed   Mentions: 4     Fields:    
    32. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli. ACS Synth Biol. 2020 03 20; 9(3):494-499. Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ. PMID: 32149495.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    33. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. Mol Biol Evol. 2020 03 01; 37(3):660-667. Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. PMID: 31651953; PMCID: PMC7038661.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    34. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 03; 38(3):272-276. 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, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32123384; PMCID: PMC7082222.
      View in: PubMed   Mentions: 173     Fields:    
    35. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data. 2019 12 17; 6(1):322. 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, Nizet V, Palsson BO, Feist AM, Pogliano J. PMID: 31848353; PMCID: PMC6917727.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    36. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proc Natl Acad Sci U S A. 2019 12 10; 116(50):25287-25292. 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. PMID: 31767748; PMCID: PMC6911176.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    37. High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environ Microbiol. 2020 01; 22(1):255-269. Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. PMID: 31657101; PMCID: PMC7078882.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    38. Adaptive laboratory evolution of Escherichia coli under acid stress. Microbiology (Reading). 2020 02; 166(2):141-148. 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. PMID: 31625833; PMCID: PMC7273327.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    39. Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. Appl Environ Microbiol. 2019 11 01; 85(21). Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. PMID: 31471305; PMCID: PMC6803309.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    40. Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae. Metab Eng. 2019 12; 56:130-141. Pereira R, Wei Y, Mohamed E, Radi M, Malina C, Herrgård MJ, Feist AM, Nielsen J, Chen Y. PMID: 31550508.
      View in: PubMed   Mentions: 31     Fields:    Translation:Animals
    41. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng. 2019 12; 56:1-16. Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. PMID: 31401242; PMCID: PMC6944292.
      View in: PubMed   Mentions: 130     Fields:    
    42. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proc Natl Acad Sci U S A. 2019 07 09; 116(28):14368-14373. 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, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO. PMID: 31270234; PMCID: PMC6628673.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    43. Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Microb Cell Fact. 2019 Jun 29; 18(1):116. Mohamed ET, Mundhada H, Landberg J, Cann I, Mackie RI, Nielsen AT, Herrgård MJ, Feist AM. PMID: 31255177; PMCID: PMC6599523.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    44. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLoS Comput Biol. 2019 06; 15(6):e1007066. Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA. PMID: 31158228; PMCID: PMC6564042.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    45. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. 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, Nizet V, Palsson BO, Feist AM. PMID: 31028276; PMCID: PMC6486602.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    46. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput Biol. 2019 04; 15(4):e1006971. Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. PMID: 31009451; PMCID: PMC6497307.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    47. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol. 2019 04 08; 15(4):e8462. 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. PMID: 30962359; PMCID: PMC6452873.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    48. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. PLoS Biol. 2019 03; 17(3):e2007050. 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. PMID: 30856169; PMCID: PMC6411097.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    49. The genetic basis for adaptation of model-designed syntrophic co-cultures. PLoS Comput Biol. 2019 03; 15(3):e1006213. 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. PMID: 30822347; PMCID: PMC6415869.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    50. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol. 2019 03; 4(3):386-389. 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. PMID: 30692668.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    51. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 2019 01 08; 47(D1):D1164-D1171. Phaneuf PV, Gosting D, Palsson BO, Feist AM. PMID: 30357390; PMCID: PMC6323966.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    52. Reframing gene essentiality in terms of adaptive flexibility. BMC Syst Biol. 2018 12 17; 12(1):143. Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM. PMID: 30558585; PMCID: PMC6296033.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    53. Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium. Front Bioeng Biotechnol. 2018; 6:166. Rugbjerg P, Feist AM, Sommer MOA. PMID: 30483499; PMCID: PMC6240765.
      View in: PubMed   Mentions: 8  
    54. Identification of growth-coupled production strains considering protein costs and kinetic variability. Metab Eng Commun. 2018 Dec; 7:e00080. Dinh HV, King ZA, Palsson BO, Feist AM. PMID: 30370222; PMCID: PMC6199775.
      View in: PubMed   Mentions: 5  
    55. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiol Resour Announc. 2018 Oct; 7(13). Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. PMID: 30533692; PMCID: PMC6256561.
      View in: PubMed   Mentions: 2  
    56. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun. 2018 09 18; 9(1):3796. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30228271; PMCID: PMC6143558.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    57. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018 10 01; 84(19). McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30054360; PMCID: PMC6146989.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    58. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30131786; PMCID: PMC6090065.
      View in: PubMed   Mentions: 15  
    59. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018 07; 48:233-242. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29906504.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    60. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng. 2018 07; 48:82-93. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29842925.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    61. Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. Metab Eng. 2018 05; 47:73-82. Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J. PMID: 29534903.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    62. Computational Methods to Assess the Production Potential of Bio-Based Chemicals. Methods Mol Biol. 2018; 1671:97-116. Campodonico MA, Sukumara S, Feist AM, Herrgård MJ. PMID: 29170955.
      View in: PubMed   Mentions: 2     Fields:    
    63. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Proc Natl Acad Sci U S A. 2018 01 02; 115(1):222-227. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. PMID: 29255023; PMCID: PMC5776819.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    64. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact. 2017 Nov 16; 16(1):204. Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM. PMID: 29145855; PMCID: PMC5691611.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    65. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 10 11; 35(10):904-908. Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. PMID: 29020004; PMCID: PMC6521705.
      View in: PubMed   Mentions: 200     Fields:    Translation:Cells
    66. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Metab Eng. 2017 11; 44:100-107. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. PMID: 28951266; PMCID: PMC5845443.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    67. Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol. 2018 02; 49:108-114. Notebaart RA, Kintses B, Feist AM, Papp B. PMID: 28837944.
      View in: PubMed   Mentions: 20     Fields:    
    68. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 07 01; 83(13). Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. PMID: 28455337; PMCID: PMC5478979.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    69. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 04 15; 83(8). LaCroix RA, Palsson BO, Feist AM. PMID: 28159796; PMCID: PMC5377496.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    70. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2017 01; 39:220-227. King ZA, O'Brien EJ, Feist AM, Palsson BO. PMID: 27986597.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    71. Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution. Metab Eng. 2017 01; 39:141-150. Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT. PMID: 27908688.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    72. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 10 26; 7:13091. 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. PMID: 27782110; PMCID: PMC5095171.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    73. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst. 2016 09 28; 3(3):238-251.e12. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. PMID: 27667363; PMCID: PMC5058344.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    74. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. Feist AM, Palsson BO. PMID: 27215675; PMCID: PMC4877762.
      View in: PubMed   Mentions: 10     Fields:    
    75. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 05 25; 2(5):335-46. 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, Keasling JD, Palsson BO, Lee TS. PMID: 27211860; PMCID: PMC4882250.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    76. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016 04 27; 2(4):260-71. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. PMID: 27135538; PMCID: PMC4853925.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    77. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 05; 88(7):3844-52. McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. PMID: 26981784.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    78. Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metab Eng Commun. 2016 Dec; 3:84-96. Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA. PMID: 29468116; PMCID: PMC5779729.
      View in: PubMed   Mentions: 14  
    79. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One. 2016; 11(3):e0151130. Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. PMID: 26964043; PMCID: PMC4786092.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    80. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications. Anal Chem. 2016 Jan 19; 88(2):1362-70. McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. PMID: 26666286.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    81. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. 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, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. PMID: 26467284; PMCID: PMC4631202.
      View in: PubMed   Mentions: 32     Fields:    
    82. Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 35:23-9. King ZA, Lloyd CJ, Feist AM, Palsson BO. PMID: 25575024.
      View in: PubMed   Mentions: 51     Fields:    Translation:Humans
    83. Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):929-34. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. PMID: 25564669; PMCID: PMC4311852.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    84. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol. 2015 Jan; 81(1):17-30. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. PMID: 25304508; PMCID: PMC4272732.
      View in: PubMed   Mentions: 117     Fields:    Translation:Cells
    85. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. PMID: 25227965; PMCID: PMC4177180.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    86. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng. 2014 Sep; 25:140-58. Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM. PMID: 25080239.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    87. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol Biol Evol. 2014 Oct; 31(10):2647-62. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. PMID: 25015645; PMCID: PMC4166923.
      View in: PubMed   Mentions: 85     Fields:    Translation:Cells
    88. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Mol Cell. 2014 Jul 17; 55(2):253-63. Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM. PMID: 24882210; PMCID: PMC4106038.
      View in: PubMed   Mentions: 308     Fields:    Translation:HumansCells
    89. Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. Metab Eng. 2014 Jul; 24:117-28. King ZA, Feist AM. PMID: 24831709.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    90. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PLoS Comput Biol. 2014 Apr; 10(4):e1003575. Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. PMID: 24762737; PMCID: PMC3998878.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    91. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins. 2014 Sep; 82(9):1819-28. Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN. PMID: 24523134.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    92. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10; 110(50):20338-43. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. PMID: 24277855; PMCID: PMC3864276.
      View in: PubMed   Mentions: 139     Fields:    Translation:Cells
    93. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnol Bioeng. 2014 Apr; 111(4):803-15. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM. PMID: 24249002.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    94. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J. 2013 Sep; 8(9):1070-9. Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. PMID: 23420771.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    95. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat Commun. 2013; 4:2809. Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. PMID: 24264237.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    96. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol. 2013; 9:661. McCloskey D, Palsson BØ, Feist AM. PMID: 23632383; PMCID: PMC3658273.
      View in: PubMed   Mentions: 128     Fields:    Translation:Cells
    97. Sulfide-driven microbial electrosynthesis. Environ Sci Technol. 2013 Jan 02; 47(1):568-73. Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K. PMID: 23252645.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    98. Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor. J Biotechnol. 2012 Oct 31; 161(3):242-9. Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BØ. PMID: 22796827.
      View in: PubMed   Mentions: 25     Fields:    Translation:Animals
    99. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol. 2011 Oct 31; 5:180. Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I. PMID: 22041191; PMCID: PMC3219569.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansCells
    100. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. PLoS One. 2011; 6(10):e26172. Lee DH, Feist AM, Barrett CL, Palsson BØ. PMID: 22028828; PMCID: PMC3196513.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    101. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol. 2011 Oct 11; 7:535. Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. PMID: 21988831; PMCID: PMC3261703.
      View in: PubMed   Mentions: 465     Fields:    Translation:Cells
    102. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011 Aug 04; 6(9):1290-307. 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. PMID: 21886097; PMCID: PMC3319681.
      View in: PubMed   Mentions: 586     Fields:    
    103. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. Feist AM, Palsson BO. PMID: 20430689; PMCID: PMC2912156.
      View in: PubMed   Mentions: 244     Fields:    Translation:AnimalsCells
    104. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010 May; 12(3):173-86. Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. PMID: 19840862; PMCID: PMC3125152.
      View in: PubMed   Mentions: 87     Fields:    Translation:Cells
    105. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009 Feb; 7(2):129-43. Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. PMID: 19116616; PMCID: PMC3119670.
      View in: PubMed   Mentions: 312     Fields:    Translation:Cells
    106. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol. 2008 Oct; 80(5):849-62. Lee J, Yun H, Feist AM, Palsson BØ, Lee SY. PMID: 18758767.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    107. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol. 2008 Jun; 26(6):659-67. Feist AM, Palsson BØ. PMID: 18536691; PMCID: PMC3108568.
      View in: PubMed   Mentions: 214     Fields:    Translation:Cells
    108. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol. 2007; 3:121. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. PMID: 17593909; PMCID: PMC1911197.
      View in: PubMed   Mentions: 579     Fields:    Translation:Cells
    109. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc. 2007; 2(3):727-38. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. PMID: 17406635.
      View in: PubMed   Mentions: 326     Fields:    Translation:Cells
    110. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006; 2:2006.0004. Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. PMID: 16738551; PMCID: PMC1681478.
      View in: PubMed   Mentions: 106     Fields:    Translation:Cells
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