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Adam Feist

TitleAssociate Project Scientist
InstitutionUniversity of California San Diego
DepartmentBioengineering
Address9500 Gilman Drive #0412
La Jolla CA 92093
Phone858-534-9592
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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.
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    1. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist A, Palsson BO. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018 Jun 12. PMID: 29906504.
      View in: PubMed
    2. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist A, 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. Metab Eng. 2018 May 26. PMID: 29842925.
      View in: PubMed
    3. Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist A, Jouhten P, Patil KR, Forster J. Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. Metab Eng. 2018 Mar 10; 47:73-82. PMID: 29534903.
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    4. Campodonico MA, Sukumara S, Feist A, Herrgård MJ. Computational Methods to Assess the Production Potential of Bio-Based Chemicals. Methods Mol Biol. 2018; 1671:97-116. PMID: 29170955.
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    5. Long CP, Gonzalez JE, Feist A, Palsson BO, Antoniewicz MR. 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 Jan 02; 115(1):222-227. PMID: 29255023.
      View in: PubMed
    6. Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist A. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact. 2017 Nov 16; 16(1):204. PMID: 29145855.
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    7. Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist A, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 Oct 11; 35(10):904-908. PMID: 29020004.
      View in: PubMed
    8. Long CP, Gonzalez JE, Feist A, Palsson BO, Antoniewicz MR. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Metab Eng. 2017 Nov; 44:100-107. PMID: 28951266.
      View in: PubMed
    9. Notebaart RA, Kintses B, Feist A, Papp B. Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol. 2018 Feb; 49:108-114. PMID: 28837944.
      View in: PubMed
    10. Sandberg TE, Lloyd CJ, Palsson BO, Feist A. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 07 01; 83(13). PMID: 28455337.
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    11. LaCroix RA, Palsson BO, Feist A. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 04 15; 83(8). PMID: 28159796.
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    12. King ZA, O'Brien EJ, Feist A, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2017 01; 39:220-227. PMID: 27986597.
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    13. Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist A, Nielsen AT. Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution. Metab Eng. 2017 01; 39:141-150. PMID: 27908688.
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    14. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist A, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 Oct 26; 7:13091. PMID: 27782110.
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    15. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist A. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst. 2016 Sep 28; 3(3):238-251.e12. PMID: 27667363.
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    16. Feist A, Palsson BO. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. PMID: 27215675.
      View in: PubMed
    17. 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. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 May 25; 2(5):335-46. PMID: 27211860; PMCID: PMC4882250 [Available on 05/25/17].
    18. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist A, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016 Apr 27; 2(4):260-71. PMID: 27135538; PMCID: PMC4853925 [Available on 04/27/17].
    19. McCloskey D, Young JD, Xu S, Palsson BO, Feist A. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 05; 88(7):3844-52. PMID: 26981784.
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    20. Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist A, Asenjo JA. 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. PMID: 29468116.
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    21. Sandberg TE, Long CP, Gonzalez JE, Feist A, Antoniewicz MR, Palsson BO. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One. 2016; 11(3):e0151130. PMID: 26964043; PMCID: PMC4786092.
    22. McCloskey D, Young JD, Xu S, Palsson BO, Feist A. 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. PMID: 26666286.
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    23. Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist A, 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. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. PMID: 26467284; PMCID: PMC4631202.
    24. King ZA, Lloyd CJ, Feist A, Palsson BO. Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 35:23-9. PMID: 25575024.
      View in: PubMed
    25. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist A. Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):929-34. PMID: 25564669; PMCID: PMC4311852.
    26. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist A. 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. PMID: 25304508; PMCID: PMC4272732.
    27. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist A. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. PMID: 25227965; PMCID: PMC4177180.
    28. Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist A. 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. PMID: 25080239.
      View in: PubMed
    29. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist A. 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. PMID: 25015645; PMCID: PMC4166923.
    30. Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist A, Vander Heiden MG, Metallo CM. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Mol Cell. 2014 Jul 17; 55(2):253-63. PMID: 24882210; PMCID: PMC4106038.
    31. King ZA, Feist A. Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. Metab Eng. 2014 Jul; 24:117-28. PMID: 24831709.
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    32. Feist A, 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 Comput Biol. 2014 Apr; 10(4):e1003575. PMID: 24762737; PMCID: PMC3998878.
    33. Geertz-Hansen HM, Blom N, Feist A, Brunak S, Petersen TN. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins. 2014 Sep; 82(9):1819-28. PMID: 24523134.
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    34. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist A, Palsson BØ. 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. PMID: 24277855; PMCID: PMC3864276.
    35. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist A. 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. PMID: 24249002.
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    36. Gonnerman MC, Benedict MN, Feist A, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J. 2013 Sep; 8(9):1070-9. PMID: 23420771.
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    37. Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist A, Palsson BØ, Lovley DR, Zengler K. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat Commun. 2013; 4:2809. PMID: 24264237.
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    38. McCloskey D, Palsson BØ, Feist A. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol. 2013; 9:661. PMID: 23632383; PMCID: PMC3658273.
    39. Gong Y, Ebrahim A, Feist A, Embree M, Zhang T, Lovley D, Zengler K. Sulfide-driven microbial electrosynthesis. Environ Sci Technol. 2013 Jan 02; 47(1):568-73. PMID: 23252645.
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    40. Fu W, Gudmundsson O, Feist A, Herjolfsson G, Brynjolfsson S, Palsson BØ. 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. PMID: 22796827.
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    41. Bordbar A, Feist A, 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 Syst Biol. 2011 Oct 31; 5:180. PMID: 22041191; PMCID: PMC3219569.
    42. Lee DH, Feist A, Barrett CL, Palsson BØ. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. PLoS One. 2011; 6(10):e26172. PMID: 22028828; PMCID: PMC3196513.
    43. Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist A, Palsson BØ. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol. 2011 Oct 11; 7:535. PMID: 21988831; PMCID: PMC3261703.
    44. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist A, 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. Nat Protoc. 2011 Aug 04; 6(9):1290-307. PMID: 21886097; PMCID: PMC3319681.
    45. Feist A, Palsson BO. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689; PMCID: PMC2912156.
    46. Feist A, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010 May; 12(3):173-86. PMID: 19840862; PMCID: PMC3125152.
    47. Feist A, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009 Feb; 7(2):129-43. PMID: 19116616; PMCID: PMC3119670.
    48. Lee J, Yun H, Feist A, Palsson BØ, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol. 2008 Oct; 80(5):849-62. PMID: 18758767.
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    49. Feist A, Palsson BØ. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol. 2008 Jun; 26(6):659-67. PMID: 18536691; PMCID: PMC3108568.
    50. Feist A, 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. Mol Syst Biol. 2007; 3:121. PMID: 17593909; PMCID: PMC1911197.
    51. Becker SA, Feist A, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc. 2007; 2(3):727-38. PMID: 17406635.
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    52. Feist A, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006; 2:2006.0004. PMID: 16738551; PMCID: PMC1681478.