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Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses.

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.

PLoS Biol. 2019 Mar 11;17(3):e2007050. doi: 10.1371/journal.pbio.2007050. eCollection 2019 Mar.


The genetic basis for adaptation of model-designed syntrophic co-cultures.

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.

PLoS Comput Biol. 2019 Mar 1;15(3):e1006213. doi: 10.1371/journal.pcbi.1006213. eCollection 2019 Mar.


Pseudogene repair driven by selection pressure applied in experimental evolution.

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.

Nat Microbiol. 2019 Mar;4(3):386-389. doi: 10.1038/s41564-018-0340-2. Epub 2019 Jan 28.


Reframing gene essentiality in terms of adaptive flexibility.

Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM.

BMC Syst Biol. 2018 Dec 17;12(1):143. doi: 10.1186/s12918-018-0653-z.


Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium.

Rugbjerg P, Feist AM, Sommer MOA.

Front Bioeng Biotechnol. 2018 Nov 12;6:166. doi: 10.3389/fbioe.2018.00166. eCollection 2018.


Identification of growth-coupled production strains considering protein costs and kinetic variability.

Dinh HV, King ZA, Palsson BO, Feist AM.

Metab Eng Commun. 2018 Oct 13;7:e00080. doi: 10.1016/j.mec.2018.e00080. eCollection 2018 Dec.


ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.

Phaneuf PV, Gosting D, Palsson BO, Feist AM.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1164-D1171. doi: 10.1093/nar/gky983.


Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Nat Commun. 2018 Sep 18;9(1):3796. doi: 10.1038/s41467-018-06219-9.


Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Front Microbiol. 2018 Aug 7;9:1793. doi: 10.3389/fmicb.2018.01793. eCollection 2018.


Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Appl Environ Microbiol. 2018 Sep 17;84(19). pii: e00823-18. doi: 10.1128/AEM.00823-18. Print 2018 Oct 1.


Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Metab Eng. 2018 Jul;48:233-242. doi: 10.1016/j.ymben.2018.06.005. Epub 2018 Jun 15.


Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Metab Eng. 2018 Jul;48:82-93. doi: 10.1016/j.ymben.2018.05.012. Epub 2018 May 26.


Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J.

Metab Eng. 2018 May;47:73-82. doi: 10.1016/j.ymben.2018.03.006. Epub 2018 Mar 10.


Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli.

Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.

Proc Natl Acad Sci U S A. 2018 Jan 2;115(1):222-227. doi: 10.1073/pnas.1716056115. Epub 2017 Dec 18.


Computational Methods to Assess the Production Potential of Bio-Based Chemicals.

Campodonico MA, Sukumara S, Feist AM, Herrgård MJ.

Methods Mol Biol. 2018;1671:97-116. doi: 10.1007/978-1-4939-7295-1_7.


Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.

Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM.

Microb Cell Fact. 2017 Nov 16;16(1):204. doi: 10.1186/s12934-017-0819-1.


iML1515, a knowledgebase that computes Escherichia coli traits.

Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO.

Nat Biotechnol. 2017 Oct 11;35(10):904-908. doi: 10.1038/nbt.3956. No abstract available.


Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring.

Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.

Metab Eng. 2017 Nov;44:100-107. doi: 10.1016/j.ymben.2017.09.012. Epub 2017 Sep 23.


Underground metabolism: network-level perspective and biotechnological potential.

Notebaart RA, Kintses B, Feist AM, Papp B.

Curr Opin Biotechnol. 2018 Feb;49:108-114. doi: 10.1016/j.copbio.2017.07.015. Epub 2017 Aug 29. Review.


Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.

Sandberg TE, Lloyd CJ, Palsson BO, Feist AM.

Appl Environ Microbiol. 2017 Jun 16;83(13). pii: e00410-17. doi: 10.1128/AEM.00410-17. Print 2017 Jul 1.


A Model for Designing Adaptive Laboratory Evolution Experiments.

LaCroix RA, Palsson BO, Feist AM.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03115-16. doi: 10.1128/AEM.03115-16. Print 2017 Apr 15.


Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion.

King ZA, O'Brien EJ, Feist AM, Palsson BO.

Metab Eng. 2017 Jan;39:220-227. doi: 10.1016/j.ymben.2016.12.004. Epub 2016 Dec 13.


Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.

Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT.

Metab Eng. 2017 Jan;39:141-150. doi: 10.1016/j.ymben.2016.11.008. Epub 2016 Nov 29.


Multi-omic data integration enables discovery of hidden biological regularities.

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.

Nat Commun. 2016 Oct 26;7:13091. doi: 10.1038/ncomms13091.


Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.

Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM.

Cell Syst. 2016 Sep 28;3(3):238-251.e12. doi: 10.1016/j.cels.2016.08.013. Epub 2016 Sep 22.


What do cells actually want?

Feist AM, Palsson BO.

Genome Biol. 2016 May 23;17(1):110. doi: 10.1186/s13059-016-0983-3.


Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.

Cell Syst. 2016 Apr 27;2(4):260-71. doi: 10.1016/j.cels.2016.04.003. Epub 2016 Apr 27.


Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications.

Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA.

Metab Eng Commun. 2016 Mar 19;3:84-96. doi: 10.1016/j.meteno.2016.03.003. eCollection 2016 Dec.


Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale.

McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.

Anal Chem. 2016 Apr 5;88(7):3844-52. doi: 10.1021/acs.analchem.5b04914. Epub 2016 Mar 24.


Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.

Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO.

PLoS One. 2016 Mar 10;11(3):e0151130. doi: 10.1371/journal.pone.0151130. eCollection 2016.


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.

McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.

Anal Chem. 2016 Jan 19;88(2):1362-70. doi: 10.1021/acs.analchem.5b03887. Epub 2015 Dec 24.


Do genome-scale models need exact solvers or clearer standards?

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.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


Next-generation genome-scale models for metabolic engineering.

King ZA, Lloyd CJ, Feist AM, Palsson BO.

Curr Opin Biotechnol. 2015 Dec;35:23-9. doi: 10.1016/j.copbio.2014.12.016. Epub 2015 Jan 7. Review.


Model-driven discovery of underground metabolic functions in Escherichia coli.

Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):929-34. doi: 10.1073/pnas.1414218112. Epub 2015 Jan 6.


Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium.

LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM.

Appl Environ Microbiol. 2015 Jan;81(1):17-30. doi: 10.1128/AEM.02246-14. Epub 2014 Oct 10.


Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R.

Microbiology. 2014 Dec;160(Pt 12):2780-93. doi: 10.1099/mic.0.082180-0. Epub 2014 Sep 22.


Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.

Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM.

BMC Syst Biol. 2014 Sep 18;8:110. doi: 10.1186/s12918-014-0110-6.


Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.

Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM.

Metab Eng. 2014 Sep;25:140-58. doi: 10.1016/j.ymben.2014.07.009. Epub 2014 Jul 28.


Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations.

Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM.

Mol Biol Evol. 2014 Oct;31(10):2647-62. doi: 10.1093/molbev/msu209. Epub 2014 Jul 10.


Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells.

Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM.

Mol Cell. 2014 Jul 17;55(2):253-63. doi: 10.1016/j.molcel.2014.05.008. Epub 2014 May 29.


Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae.

King ZA, Feist AM.

Metab Eng. 2014 Jul;24:117-28. doi: 10.1016/j.ymben.2014.05.009. Epub 2014 May 14.


Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K.

PLoS Comput Biol. 2014 Apr 24;10(4):e1003575. doi: 10.1371/journal.pcbi.1003575. eCollection 2014 Apr.


Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds.

Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN.

Proteins. 2014 Sep;82(9):1819-28. doi: 10.1002/prot.24536. Epub 2014 Mar 20.


Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.

Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25.


Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.

Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.

Nat Commun. 2013;4:2809. doi: 10.1038/ncomms3809.


A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent.

McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM.

Biotechnol Bioeng. 2014 Apr;111(4):803-15. doi: 10.1002/bit.25133. Epub 2013 Nov 19.


Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

McCloskey D, Palsson BØ, Feist AM.

Mol Syst Biol. 2013;9:661. doi: 10.1038/msb.2013.18. Review.


Working with Hispanic women who are deaf: recommendations from the literature.

Feist AM, Saladin SP, Hansmann S.

Am Ann Deaf. 2013 Winter;157(5):450-7. Review.


Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.

Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.

Biotechnol J. 2013 Sep;8(9):1070-9. doi: 10.1002/biot.201200266. Epub 2013 Mar 26.


Sulfide-driven microbial electrosynthesis.

Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K.

Environ Sci Technol. 2013 Jan 2;47(1):568-73. doi: 10.1021/es303837j. Epub 2012 Dec 19.


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