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2019
 

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Pereira, Rui ; Wei, Yongjun ; Mohamed, Elsayed Tharwat Tolba ; Radi, Mohammad ; Malina, Carl ; Herrgård, Markus J. ; Feist, Adam M. ; Nielsen, Jens ; Chen, Yun
in: Metabolic Engineering, vol: 56, pages: 130-141

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2019.09.008

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Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

Phaneuf, Patrick V. ; Gosting, Dennis ; Palsson, Bernhard O. ; Feist, Adam M.
in: Nucleic acids research, vol: 47, issue: D1, pages: D1164-D1171

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky983

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, Jean Christophe ; Lloyd, Colton J. ; Monk, Jonathan M. ; Yang, Laurence ; Sastry, Anand V. ; Seif, Yara ; Palsson, Bernhard O. ; Rodrigue, Sébastien ; Feist, Adam M. ; King, Zachary A. ; Jacques, Pierre Étienne
in: PLOS Computational Biology, vol: 15, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1006971

 

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Yang, Laurence ; Mih, Nathan ; Anand, Amitesh ; Park, Joon Ho ; Tan, Justin ; Yurkovich, James T. ; Monk, Jonathan M. ; Lloyd, Colton J. ; Sandberg, Troy E. ; Seo, Sang Woo ; Kim, Donghyuk ; Sastry, Anand V. ; Phaneuf, Patrick ; Gao, Ye ; Broddrick, Jared T. ; Chen, Ke ; Heckmann, David ; Szubin, Richard ; Hefner, Ying ; Feist, Adam M. ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 116, issue: 28, pages: 14368-14373

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1073/pnas.1905039116

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Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

Poudel, Saugat ; Tsunemoto, Hannah ; Meehan, Michael ; Szubin, Richard ; Olson, Connor A. ; Lamsa, Anne ; Seif, Yara ; Dillon, Nicholas ; Vrbanac, Alison ; Sugie, Joseph ; Dahesh, Samira ; Monk, Jonathan M. ; Dorrestein, Pieter C. ; Pogliano, Joseph ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Scientific Data, vol: 6, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41597-019-0051-4

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Enzyme promiscuity shapes adaptation to novel growth substrates

Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; de Raad, Markus ; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M.
in: Molecular Systems Biology, vol: 15, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.15252/msb.20188462

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Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, Elsayed Tharwat Tolba ; Mundhada, Hemanshu ; Landberg, Jenny Marie ; Cann, Isaac ; Mackie, Roderick I. ; Nielsen, Alex Toftgaard ; Herrgard, Markus J. ; Feist, Adam M.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1165-2

 

Pseudogene repair driven by selection pressure applied in experimental evolution

Anand, Amitesh ; Olson, Connor A. ; Yang, Laurence ; Sastry, Anand V. ; Catoiu, Edward ; Choudhary, Kumari Sonal ; Phaneuf, Patrick V. ; Sandberg, Troy E. ; Xu, Sibei ; Hefner, Ying ; Szubin, Richard ; Feist, Adam ; Palsson, Bernhard
in: Nature Microbiology, vol: 4, issue: 3, pages: 386-389

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41564-018-0340-2

 

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

Machado, Henrique ; Weng, Liam L. ; Dillon, Nicholas ; Seif, Yara ; Holland, Michelle ; Pekar, Jonathan E. ; Monk, Jonathan M. ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Applied and Environmental Microbiology, vol: 85, issue: 21, pages: 1-13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1128/aem.01773-19

 

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

Sandberg, Troy E. ; Salazar, Michael J ; Weng, Liam L ; Palsson, Bernhard O ; Feist, Adam M
in: Metabolic Engineering

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2019.08.004

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

Lloyd, Colton J. ; King, Zachary A. ; Sandberg, Troy E. ; Hefner, Ying ; Olson, Connor A. ; Phaneuf, Patrick V. ; O'Brien, Edward J. ; Sanders, Jon G. ; Salido, Rodolfo A. ; Sanders, Karenina ; Brennan, Caitriona ; Humphrey, Gregory ; Knight, Rob ; Feist, Adam M.
in: PLOS Computational Biology, vol: 15, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1006213

2018
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Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Metabolic Engineering, vol: 48, pages: 82-93

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.05.012

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

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Metabolic Engineering, vol: 48, pages: 233-242

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.06.005

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Bacterial cells with improved tolerance to diacids

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2018091525 , Date: 2018-05-24

Type: Patent

Status: Published     |    Year: 2018

 

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

Campodonico, Miguel A ; Sukumara, Sumesh ; Feist, Adam M. ; Herrgård, Markus J.
part of: Synthetic Metabolic Pathways, pages: 97-116, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_7

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

Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam M. ; Palsson, Bernhard O. ; Antoniewicz, Maciek R.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 1, pages: 222-227

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1716056115

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

Rugbjerg, Peter ; Feist, Adam M. ; Sommer, Morten Otto Alexander
in: Frontiers in Bioengineering and Biotechnology, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3389/fbioe.2018.00166

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

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41467-018-06219-9

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

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3389/fmicb.2018.01793

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

Dinh, Hoang V. ; King, Zachary A. ; Palsson, Bernhard O. ; Feist, Adam M.
in: Metabolic Engineering Communications, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.mec.2018.e00080

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

Strucko, Tomas ; Zirngibl, Katharina ; Pereira, Filipa ; Kafkia, Eleni ; Mohamed, Elsayed T. ; Rettel, Mandy ; Stein, Frank ; Feist, Adam M ; Jouhten, Paula ; Patil, Kiran Raosaheb ; Forster, Jochen
in: Metabolic Engineering, vol: 47, pages: 73-82

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.03.006

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

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Applied and Environmental Microbiology, vol: 84, issue: 19

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1128/AEM.00823-18

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Reframing gene essentiality in terms of adaptive flexibility

Guzmán, Gabriela I. ; Olson, Connor A. ; Hefner, Ying ; Phaneuf, Patrick V. ; Catoiu, Edward ; Crepaldi, Lais B. ; Micas, Lucas Goldschmidt ; Palsson, Bernhard O. ; Feist, Adam M.
in: BMC Systems Biology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12918-018-0653-z

 

Underground metabolism: network-level perspective and biotechnological potential

Notebaart, Richard A ; Kintses, Bálint ; Feist, Adam ; Papp, Balázs
in: Current Opinion in Biotechnology, vol: 49, pages: 108-114

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.copbio.2017.07.015

2017
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Bacterial cells with improved tolerance to polyols

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2017211883, Date: 2017-12-14

Type: Patent

Status: Published     |    Year: 2017

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A Model for Designing Adaptive Laboratory Evolution Experiments

LaCroix, Ryan A. ; Palsson, Bernhard O. ; Feist, Adam M. ; Kivisaar, Maia (Editor)
in: Applied and Environmental Microbiology, vol: 83, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1128/AEM.03115-16

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

Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam M. ; Palsson, Bernhard O ; Antoniewicz, Maciek R.
in: Metabolic Engineering, vol: 44, pages: 100-107

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.ymben.2017.09.012

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

Mohamed, Elsayed T. ; Wang, Shizeng ; Lennen, Rebecca M. ; Herrgård, Markus J. ; Simmons, Blake A. ; Singer, Steven W. ; Feist, Adam M.
in: Microbial Cell Factories, vol: 16, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1186/s12934-017-0819-1

 

iML1515, a knowledgebase that computes Escherichia coli traits

Monk, Jonathan M. ; Lloyd, Colton J. ; Brunk, Elizabeth ; Mih, Nathan ; Sastry, Anand ; King, Zachary ; Takeuchi, Rikiya ; Nomura, Wataru ; Zhang, Zhen ; Mori, Hirotada ; Feist, Adam M. ; Palsson, Bernhard O.
in: Nature Biotechnology, vol: 35, issue: 10, pages: 904-908

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/nbt.3956

 

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

Sandberg, Troy E. ; Lloyd, Colton J. ; Palsson, Bernhard O. ; Feist, Adam M. ; Kivisaar, Maia (Editor)
in: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol: 83, issue: 13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1128/AEM.00410-17

 

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

King, Zachary A. ; O'Brien, Edward J. ; Feist, Adam M. ; Palsson, Bernhard O.
in: Metabolic Engineering, vol: 39, pages: 220–227

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.ymben.2016.12.004

2016
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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Brunk, Elizabeth ; George, Kevin W. ; Alonso-Gutierrez, Jorge ; Tjompson, Mitchell ; Baidoo, Edward ; Wang, George ; Petzold, Christopher J. ; McCloskey , Douglas ; Monk, Jonathan ; Yang, Laurence ; O’Brien, Edward J. ; Batth , Tanveer S. ; Garcia Martin, Hector ; Feist, Adam ; Adams, Paul D. ; Keasling , Jay D. ; Palsson, Bernhard ; Soon Lee, Taek
in: Cell Systems, vol: 2, issue: 5, pages: 335-346

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.04.004

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

Sandberg, Troy E. ; Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam ; Antoniewicz, Maciek R. ; Palsson, Bernhard
in: P L o S One, vol: 11, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1371/journal.pone.0151130

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

Utrilla, José ; O'Brien, Edward J. ; Chen, Ke ; McCloskey, Douglas ; Cheung , Jacky ; Wang , Harris ; Armenta-Medina , Dagoberto ; Feist, Adam ; Palsson, Bernhard
in: Cell, vol: 2, pages: 260-271

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.04.003

 

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, Douglas ; Young, Jamey D. ; Xu, Sibei ; Palsson, Bernhard ; Feist, Adam
in: Analytical Chemistry, vol: 88, issue: 2, pages: 1362–1370

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1021/acs.analchem.5b03887

 

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

McCloskey, Douglas ; Young, Jamey D. ; Xu, Sibei ; Palsson, Bernhard ; Feist, Adam
in: Analytical chemistry, vol: 88, issue: 7, pages: 3844-3852

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1021/acs.analchem.5b04914

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Multi-omic data integration enables discovery of hidden biological regularities

Ebrahim, Ali ; Brunk, Elizabeth ; Tan, Justin ; O'Brien, Edward J. ; Kim, Donghyuk ; Szubin, Richard ; Lerman, Joshua A. ; Lechner, Anna ; Sastry, Anand ; Bordbar, Aarash ; Feist, Adam ; Palsson, Bernhard
in: Nature Communications, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/ncomms13091

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

Monk, Jonathan M ; Koza, Anna ; Campodonico, Miguel A ; Machado, Daniel ; Seoane, Jose Miguel ; Palsson, Bernhard ; Herrgard, Markus ; Feist, Adam
in: Cell Systems, vol: 3, issue: 3, pages: 238-251

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.08.013

2015
 

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites

McCloskey, Douglas ; Gangoiti, Jon A. ; Palsson, Bernhard O. ; Feist, Adam M.
in: Metabolomics, vol: 11, issue: 5, pages: 1338-1350

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1007/s11306-015-0790-y

 

Development Of An Efficient Glycerol Utilizing Saccharomyces Cerevisiae Strain Via Adaptive Laboratory Evolution

Strucko, Tomas ; Zirngibl, Katharina ; Tharwat Tolba Mohamed, Elsayed ; Feist, Adam ; Patil, Kiran R. ; Förster, Jochen
part of: The Danish Microbiological Society Annual Congress 2015, pages: 22-22, 2015, Copenhagen
Presented at:
The Danish Microbiological Society Annual Congress 2015

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2015

 

Development of an efficient glycerol utilizing Saccharomyces cerevisiae platform strain via adaptive laboratory evolution

Strucko, Tomas ; Tharwat Tolba Mohamed, Elsayed ; Feist, Adam ; Förster, Jochen
in: Yeast, vol: 32, issue: S1, pages: S242-S242

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1002/yea.3092

 

Fast Swinnex Filtration (FSF): A fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media

McCloskey, Douglas ; Utrilla, Jose ; Naviaux, Robert K. ; Palsson, Bernhard O. ; Feist, Adam
in: Metabolomics, vol: 11, issue: 1, pages: 198-209

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1007/s11306-014-0686-2

 

Model-driven discovery of underground metabolic functions in Escherichia coli

Guzmán, Gabriela I. ; Utrilla, José ; Nurk, Sergey ; Brunk, Elizabeth ; Monk, Jonathan M. ; Ebrahim, Ali ; Palsson, Bernhard O. ; Feist, Adam M.
in: Proceedings of the National Academy of Sciences, vol: 112, issue: 3, pages: 929-934

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1073/pnas.1414218112

 

Next-generation genome-scale models for metabolic engineering

King, Zachary A. ; Lloyd, Colton J. ; Feist, Adam M. ; Palsson, Bernhard O.
in: Current Opinion in Biotechnology, vol: 35, pages: 23-29

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.copbio.2014.12.016

 

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

LaCroix, Ryan A. ; Sandberg, Troy E. ; O'Brien, Edward J. ; Utrilla, Jose ; Ebrahim, Ali ; Guzman, Gabriela I. ; Szubin, Richard ; Palsson, Bernhard ; Feist, Adam
in: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol: 81, issue: 1, pages: 17-30

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1128/AEM.02246-14

2014
 

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

McCloskey, Douglas ; Gangoiti, Jon A. ; King, Zachary A. ; Naviaux, Robert K. ; Barshop, Bruce A. ; Palsson, Bernhard ; Feist, Adam
in: Biotechnology and Bioengineering, vol: 111, issue: 4, pages: 803-815

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1002/bit.25133

 

Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds

Geertz-Hansen, Henrik Marcus ; Blom, Nikolaj ; Feist, Adam ; Brunak, Søren ; Petersen, Thomas Nordahl
in: Proteins: Structure, Function, and Bioinformatics, vol: 82, issue: 9, pages: 1819-1828

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1002/prot.24536

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Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.

Sandberg, Troy E. ; Pedersen, Margit ; LaCroix, Ryan A. ; Ebrahim, Ali ; Bonde, Mads ; Herrgard, Markus ; Palsson, Bernhard ; Sommer, Morten ; Feist, Adam
in: Molecular Biology and Evolution, vol: 31, issue: 10, pages: 2647-2662

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1093/molbev/msu209

 

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

Campodonico, Miguel A. ; Andrews, Barbara A. ; Asenjo, Juan A. ; Palsson, Bernhard ; Feist, Adam
in: Metabolic Engineering, vol: 25, pages: 140-158

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.ymben.2014.07.009

 

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

Olavarria, K. ; De Ingeniis, J. ; Zielinski, D. C. ; Fuentealba, M. ; Muñoz, R. ; McCloskey, D. ; Feist, Adam ; Cabrera, R.
in: Microbiology, vol: 160, issue: Pt 12, pages: 2780-2793

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1099/mic.0.082180-0

 

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

King, Zachary A. ; Feist, Adam
in: Metabolic Engineering, vol: 24, pages: 117-128

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.ymben.2014.05.009

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

Liu, Joanne K. ; O’Brien, Edward J. ; Lerman, Joshua A. ; Zengler, Karsten ; Palsson, Bernhard ; Feist, Adam
in: BMC Systems Biology, vol: 8, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1186/s12918-014-0110-6

2013
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Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

McCloskey, Douglas ; Palsson, Bernhard ; Feist, Adam
in: Molecular Systems Biology, vol: 9, pages: 661

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1038/msb.2013.18

 

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

Nagarajan, Harish ; Embree, Mallory ; Rotaru, Amelia-Elena ; Shrestha, Pravin M. ; Feist, Adam ; Palsson, Bernhard Ø. ; Lovley, Derek R. ; Zengler, Karsten
in: Nature Communications, vol: 4, pages: 2809

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1038/ncomms3809

 

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

Gonnerman, Matthew C. ; Benedict, Matthew N. ; Feist, Adam ; Metcalf, William W. ; Price, Nathan D.
in: Biotechnology Journal, vol: 8, issue: 9, pages: 1070-1079

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1002/biot.201200266

 

Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap

King, Zachary A. ; Feist, Adam
in: Industrial Biotechnology, vol: 9, issue: 4, pages: 236

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1089/ind.2013.0005

 

Sulfide-Driven Microbial Electrosynthesis

Gong, Yanming ; Ebrahim, Ali ; Feist, Adam ; Embree, Mallory ; Zhang, Tian ; Lovley, Derek ; Zengler, Karsten
in: Environmental Science & Technology (Washington), vol: 47, issue: 1, pages: 568-573

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1021/es303837j

2010
 

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

Feist, Adam ; Zielinski, Daniel C. ; Orth, Jeffrey D. ; Schellenberger, Jan ; Herrgard, Markus ; Palsson, Bernhard
in: Metabolic Engineering, vol: 12, issue: 3, pages: 173-186

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2010     |    DOI: https://doi.org/10.1016/j.ymben.2009.10.003

2009
 

Reconstruction of biochemical networks in microorganisms.

Feist, Adam ; Herrgard, Markus ; Thiele, Ines ; Reed, Jennie L ; Palsson, Bernhard Ø
in: Nature Reviews. Microbiology, vol: 7, issue: 2, pages: 129-143

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2009     |    DOI: https://doi.org/10.1038/nrmicro1949

2007
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

Beck, Scott A. ; Feist, Adam ; Mo, M. L. ; Hannum, G. ; Palsson, B. O. ; Herrgard, Markus
in: Nature Protocols (Online), vol: 2, issue: 3, pages: 727-738

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2007     |    DOI: https://doi.org/10.1038/nprot.2007.99