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Items: 1 to 20 of 49

1.

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.

PMID:
29255023
2.

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.

PMID:
29170955
3.

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.

4.

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.

PMID:
29020004
5.

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.

PMID:
28951266
6.

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.

PMID:
28837944
7.

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.

8.

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.

9.

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.

PMID:
27986597
10.

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.

PMID:
27908688
11.

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.

12.

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.

13.

What do cells actually want?

Feist AM, Palsson BO.

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

14.

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.

15.

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.

PMID:
26981784
16.

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.

17.

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.

PMID:
26666286
18.

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.

19.

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.

PMID:
25575024
20.

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.

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