Feist, Adam M: search on Z-Library

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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

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

2

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

Feist, Adam M, Palsson, Bernhard Ø

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 736 KB

english, 2008

3

Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

Weiqi Fu, Olafur Gudmundsson, Adam M. Feist, Gisli Herjolfsson, Sigurdur Brynjolfsson, Bernhard Ø. Palsson

Journal:

Journal of Biotechnology

Year:

2012

Language:

english

File:

PDF, 750 KB

english, 2012

4

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

Utrilla, Jose, O’Brien, Edward J., Chen, Ke, McCloskey, Douglas, Cheung, Jacky, Wang, Harris, Armenta-Medina, Dagoberto, Feist, Adam M., Palsson, Bernhard O.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.42 MB

english, 2016

5

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

Geertz-Hansen, Henrik Marcus, Blom, Nikolaj, Feist, Adam M., Brunak, Søren, Petersen, Thomas Nordahl

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 306 KB

english, 2014

6

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.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.29 MB

english, 2017

7

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash, Lewis, Nathan E, Rahmanian, Sorena, Kang, Joseph, Hyduke, Dan

Journal:

Bioentrepreneur

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

8

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 O., Herrgård, Markus J., Feist, Adam M.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.54 MB

english, 2016

9

High‐quality genome‐scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities

Nogales, Juan, Mueller, Joshua, Gudmundsson, Steinn, Canalejo, Francisco J., Duque, Estrella, Monk, Jonathan, Feist, Adam M., Ramos, Juan Luis, Niu, Wei, Palsson, Bernhard O.

Journal:

Environmental Microbiology

Year:

2019

Language:

english

File:

PDF, 1.16 MB

english, 2019

10

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 999 KB

english, 2011

11

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.

Journal:

Metabolic Engineering

Year:

2017

Language:

english

File:

PDF, 1.65 MB

english, 2017

12

Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

Luo, Hao, Yang, Lei, Kim, Se Hyeuk, Wulff, Tune, Feist, Adam M., Herrgard, Markus, Palsson, Bernhard Ã.

Journal:

ACS Synthetic Biology

Year:

2020

File:

PDF, 1.41 MB

2020

13

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.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 969 KB

english, 2015

14

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.

Journal:

Year:

2015

Language:

english

File:

PDF, 679 KB

english, 2015

15

OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

Anand, Amitesh, Chen, Ke, Catoiu, Edward, Sastry, Anand V, Olson, Connor A, Sandberg, Troy E, Seif, Yara, Xu, Sibei, Szubin, Richard, Yang, Laurence, Feist, Adam M, Palsson, Bernhard O, Pond, Sergei K

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 5.01 MB

english, 2019

16

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 O., Feist, Adam M.

Journal:

Biotechnology and Bioengineering

Year:

2014

Language:

english

File:

PDF, 822 KB

english, 2014

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, Douglas, Young, Jamey D., Xu, Sibei, Palsson, Bernhard O., Feist, Adam M.

Journal:

Analytical Chemistry

Year:

2015

Language:

english

File:

PDF, 2.62 MB

english, 2015

18

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

Campodonico, Miguel A., Vaisman, Daniela, Castro, Jean F., Razmilic, Valeria, Mercado, Francesca, Andrews, Barbara A., Feist, Adam M., Asenjo, Juan A.

Journal:

Metabolic Engineering Communications

Year:

2016

Language:

english

File:

PDF, 2.59 MB

english, 2016

19

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

Pekar, Jonathan E., Phaneuf, Patrick, Szubin, Richard, Palsson, Bernhard, Feist, Adam, Monk, Jonathan M., Putonti, Catherine

Journal:

Microbiology Resource Announcements

Year:

2018

Language:

english

File:

PDF, 108 KB

english, 2018

20

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, Chuankai, O’Brien, Edward J., McCloskey, Douglas, Utrilla, Jose, Olson, Connor, LaCroix, Ryan A., Sandberg, Troy E., Feist, Adam M., Palsson, Bernhard O., King, Zachary A., Hatzimanikatis, Vass

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 1.82 MB

2019

21

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Feist, Adam M, Scholten, Johannes C M, Palsson, Bernhard Ø, Brockman, Fred J, Ideker, Trey

Journal:

Molecular Systems Biology

Year:

2006

Language:

english

File:

PDF, 5.53 MB

english, 2006

22

What do cells actually want?

Feist, Adam M., Palsson, Bernhard O.

Journal:

Year:

2016

Language:

english

File:

PDF, 335 KB

english, 2016

23

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.

Journal:

Metabolic Engineering

Year:

2018

Language:

english

File:

PDF, 1.17 MB

english, 2018

24

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 M., Palsson, Bernhard Ø, Lovley, Derek R., Zengler, Karsten

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 1.36 MB

english, 2013

25

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

Mundhada, Hemanshu, Miguel, Jose S., Schneider, Konstantin, Koza, Anna, Christensen, Hanne B., Klein, Tobias, Phaneuf, Patrick V., Herrgard, Markus, Feist, Adam M., Nielsen, Alex T.

Journal:

Metabolic Engineering

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

26

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 M., Antoniewicz, Maciek R., Palsson, Bernhard O., Cirino, Patrick C.

Journal:

Year:

2016

Language:

english

File:

PDF, 748 KB

english, 2016

27

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

Gonnerman, Matthew C., Benedict, Matthew N., Feist, Adam M., Metcalf, William W., Price, Nathan D.

Journal:

Biotechnology Journal

Year:

2013

Language:

english

File:

PDF, 625 KB

english, 2013

28

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

Lee, Dae-Hee, Feist, Adam M., Barrett, Christian L., Palsson, Bernhard Ø., Kao, Katy C.

Journal:

Year:

2011

Language:

english

File:

PDF, 824 KB

english, 2011

29

A Model for Designing Adaptive Laboratory Evolution Experiments

LaCroix, Ryan A., Palsson, Bernhard O., Feist, Adam M., Kivisaar, Maia

Journal:

Applied and Environmental Microbiology

Year:

2017

Language:

english

File:

PDF, 1.71 MB

english, 2017

30

Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution

Pereira, Rui, Mohamed, Elsayed T., Radi, Mohammad S., HerrgÃ¥rd, Markus J., Feist, Adam M., Nielsen, Jens, Chen, Yun

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.29 MB

2020

31

Diffusion von Cefamandol in das Herzmuskelgewebe

D. Adam, B. Reichart, W. Feist

Journal:

Year:

1978

Language:

german

File:

PDF, 226 KB

german, 1978

32

Stress does not inhibit induced vitellogenesis in juvenile rainbow trout

Adam R. Schwindt, Grant W. Feist, Carl B. Schreck

Journal:

Environmental Biology of Fishes

Year:

2007

Language:

english

File:

PDF, 305 KB

english, 2007

33

Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells

Lewis, Caroline A., Parker, Seth J., Fiske, Brian P., McCloskey, Douglas, Gui, Dan Y., Green, Courtney R., Vokes, Natalie I., Feist, Adam M., Vander Heiden, Matthew G., Metallo, Christian M.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.28 MB

english, 2014

34

Lipid and carotenoid production from wheat straw hydrolysates by different oleaginous yeasts

Liu, Zhijia, Feist, Adam M., Dragone, Giuliano, Mussatto, Solange I.

Journal:

Journal of Cleaner Production

Year:

2019

Language:

english

File:

PDF, 1.96 MB

english, 2019

35

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Anand, Amitesh, Chen, Ke, Yang, Laurence, Sastry, Anand V., Olson, Connor A., Poudel, Saugat, Seif, Yara, Hefner, Ying, Phaneuf, Patrick V., Xu, Sibei, Szubin, Richard, Feist, Adam M., Palsson, Bernha

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

File:

PDF, 741 KB

2019

36

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

Becker, Scott A, Feist, Adam M, Mo, Monica L, Hannum, Gregory, Palsson, Bernhard Ø, Herrgard, Markus J

Journal:

Nature Protocols

Year:

2007

Language:

english

File:

PDF, 359 KB

english, 2007

37

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Feist, Adam M, Henry, Christopher S, Reed, Jennifer L, Krummenacker, Markus, Joyce, Andrew R, Karp, Peter D, Broadbelt, Linda J, Hatzimanikatis, Vassily, Palsson, Bernhard Ø

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 953 KB

english, 2007

38

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Anand, Amitesh, Chen, Ke, Yang, Laurence, Sastry, Anand V., Olson, Connor A., Poudel, Saugat, Seif, Yara, Hefner, Ying, Phaneuf, Patrick V., Xu, Sibei, Szubin, Richard, Feist, Adam M., Palsson, Bernha

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 741 KB

english, 2019

39

Investigating the involvement of a Midichloria -like organism (MLO) in red mark syndrome in rainbow trout Oncorhynchus mykiss

Metselaar, Matthijs, Thompson, Kim D., Paley, Richard, Green, Darren M., Verner-Jeffreys, David, Feist, Stephen, Adams, Alexandra

Journal:

Year:

2020

File:

PDF, 2.14 MB

2020

40

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 O., Feist, Adam M.

Journal:

Metabolic Engineering

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

41

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 M.

Journal:

Year:

2015

Language:

english

File:

PDF, 924 KB

english, 2015

42

Forty years of seagrass population stability and resilience in an urbanizing estuary

Shelton, Andrew Olaf, Francis, Tessa B., Feist, Blake E., Williams, Gregory D., Lindquist, Adam, Levin, Philip S.

Journal:

Journal of Ecology

Year:

2016

Language:

english

File:

PDF, 791 KB

english, 2016

43

Underground metabolism: network-level perspective and biotechnological potential

Notebaart, Richard A, Kintses, Bálint, Feist, Adam M, Papp, Balázs

Journal:

Current Opinion in Biotechnology

Year:

2018

Language:

english

File:

PDF, 1.13 MB

english, 2018

44

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

Dinh, Hoang V., King, Zachary A., Palsson, Bernhard O., Feist, Adam M.

Journal:

Metabolic Engineering Communications

Year:

2018

Language:

english

File:

PDF, 1.52 MB

english, 2018

45

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.

Journal:

Metabolic Engineering

Year:

2017

Language:

english

File:

PDF, 3.10 MB

english, 2017

46

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.

Journal:

Applied and Environmental Microbiology

Year:

2018

Language:

english

File:

PDF, 3.52 MB

english, 2018

47

High‐quality genome‐scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities

Nogales, Juan, Mueller, Joshua, Gudmundsson, Steinn, Canalejo, Francisco J., Duque, Estrella, Monk, Jonathan, Feist, Adam M., Ramos, Juan Luis, Niu, Wei, Palsson, Bernhard O.

Journal:

Environmental Microbiology

Year:

2019

File:

PDF, 1.16 MB

2019

48

An oxytocin-dependent social interaction between larvae and adult C. elegans

Scott, Euan, Hudson, Adam, Feist, Emily, Calahorro, Fernando, Dillon, James, de Freitas, Raissa, Wand, Matthew, Schoofs, Liliane, O’Connor, Vincent, Holden-Dye, Lindy

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 4.85 MB

english, 2017

49

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, Pier

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 4.48 MB

english, 2019

50

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.48 MB

2020

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