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    Adam Feist

    Address9500 Gilman Drive #0412
    CA La Jolla 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. 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 Sep 23. PMID: 28951266.
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      2. Notebaart RA, Kintses B, Feist A, Papp B. Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol. 2017 Aug 21; 49:108-114. PMID: 28837944.
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      3. 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 Jul 01; 83(13). PMID: 28455337.
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      4. LaCroix RA, Palsson BO, Feist A. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 Apr 15; 83(8). PMID: 28159796.
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      5. 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 Jan; 39:220-227. PMID: 27986597.
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      6. 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 Jan; 39:141-150. PMID: 27908688.
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      7. 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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      8. 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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      9. Feist A, Palsson BO. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. PMID: 27215675; PMCID: PMC4877762.
      10. 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].
      11. 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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      12. 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.
      13. 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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      14. 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.
      15. 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.
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      16. 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.
      17. 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.
      18. Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist A, Cabrera R. Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli. Microbiology. 2014 Dec; 160(Pt 12):2780-93. PMID: 25246670.
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      19. 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.
      20. 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.
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      21. 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.
      22. 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.
      23. 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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      24. 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.
      25. 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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      26. 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.
      27. 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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      28. 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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      29. 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.
      30. 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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      31. 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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      32. 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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      33. 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.
      34. 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.
      35. 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.
      36. 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.
      37. Feist A, Palsson BO. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689; PMCID: PMC2912156.
      38. 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.
      39. 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.
      40. 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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      41. 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.
      42. 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.
      43. 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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      44. 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.