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Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.  2017.  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.
Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.  2017.  Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring.. Metab Eng.
Mohamed ET, Wang S, Lennen RM, Herrgard MJ, Simmons BA, Singer SW, Feist AM.  2017.  Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.. Microb Cell Fact. 16(1):204.
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H et al..  2017.  iML1515, a knowledgebase that computes Escherichia coli traits.. Nat Biotechnol. 35(10):904-908.
Sandberg TE, Lloyd CJ, Palsson BO, Feist AM.  2017.  Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.. Appl Environ Microbiol.
LaCroix RA, Palsson BO, Feist AM.  2017.  A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol.
Notebaart RA, Kintses álint, Feist AM, Papp ázs.  2017.  Underground metabolism: network-level perspective and biotechnological potential. Current Opinion in Biotechnology. 49:108-114.
Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO.  2016.  Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.. PLoS One. 11(3):e0151130.
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.  2016.  Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.. Cell Syst. 2(4):260-71.
Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT.  2016.  Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.. Metab Eng. 39:141-150.
King ZA, O'Brien EJ, Feist AM, Palsson BO.  2016.  Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion.. Metab Eng.
McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM.  2016.  A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale.. Anal Chem.
Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A et al..  2016.  Multi-omic data integration enables discovery of hidden biological regularities.. Nat Commun. 7:13091.
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JMiguel, Palsson BO, Herrgard MJ, Feist AM.  2016.  Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.. Cell Syst.
Feist AM, Palsson BO.  2016.  What do cells actually want? Genome Biol. 17(1):110.
Geertz-Hansen HMarcus, Blom N, Feist AM, Brunak S, Petersen TNordahl.  2014.  Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds.. Proteins.
Feist AM, Nagarajan H, Rotaru A-E, Tremblay P-L, Zhang T, Nevin KP, Lovley DR, Zengler K.  2014.  Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575.
LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM.  2014.  Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution.. Appl Environ Microbiol.
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM.  2014.  Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.. Mol Biol Evol.
McCloskey DM, Utrilla J, Naviaux RK, Palsson BO, Feist AM.  2014.  Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media. Metabolomics. 10(10.1007/s11306-014-0686-2)
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM.  2014.  Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.. Metab Eng. 25C:140-158.
Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R.  2014.  The Metabolic Impact of a NADH-producing Glucose-6-phosphate Dehydrogenase in Escherichia coli.. Microbiology.
King ZA, Feist AM.  2014.  Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae.. Metab Eng. 24C:117-128.
Liu JK, Brien EJO, Lerman JA, Zengler K, Palsson BO, Feist AM.  2014.  Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.. BMC Syst Biol. 8(1):110.
Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Heiden MGVander, Metallo CM.  2014.  Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells.. Mol Cell.
McCloskey D, Palsson BØ, Feist AM.  2013.  Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661.
Nagarajan H, Embree M, Rotaru A-E, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.  2013.  Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.  2013.  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.. Proc Natl Acad Sci U S A.
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.. Biotechnol J.
McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM.  2013.  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.
King ZA, Feist AM.  2013.  Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap. Industrial Biotechnology. 9(4):236-246.
Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K.  2013.  Sulfide-driven microbial electrosynthesis.. Environ Sci Technol. 47(1):568-573.



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