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1

A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects

Noor, Elad, Flamholz, Avi, Liebermeister, Wolfram, Bar-Even, Arren, Milo, Ron

Journal:

Year:

2013

Language:

english

File:

PDF, 530 KB

english, 2013

2

The formate bio-economy

Yishai, Oren, Lindner, Steffen N, Gonzalez de la Cruz, Jorge, Tenenboim, Hezi, Bar-Even, Arren

Journal:

Current Opinion in Chemical Biology

Year:

2016

Language:

english

File:

PDF, 712 KB

english, 2016

3

Engineering specialized metabolic pathways—is there a room for enzyme improvements?

Bar-Even, Arren, Salah Tawfik, Dan

Journal:

Current Opinion in Biotechnology

Year:

2013

Language:

english

File:

PDF, 419 KB

english, 2013

4

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

Bar-Even, Arren, Noor, Elad, Savir, Yonatan, Liebermeister, Wolfram, Davidi, Dan, Tawfik, Dan S., Milo, Ron

Journal:

Year:

2011

Language:

english

File:

PDF, 2.44 MB

english, 2011

5

The moderately efficient enzyme: futile encounters and enzyme floppiness

Bar-Even, Arren, Milo, Ron, Noor, Elad, Tawfik, Dan S.

Journal:

Year:

2015

Language:

english

File:

PDF, 966 KB

english, 2015

6

Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction

Poust, Sean, Piety, James, Bar-Even, Arren, Louw, Catherine, Baker, David, Keasling, Jay D., Siegel, Justin B.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

7

Reinforcing carbon fixation: CO 2 reduction replacing and supporting carboxylation

Cotton, Charles AR, Edlich-Muth, Christian, Bar-Even, Arren

Journal:

Current Opinion in Biotechnology

Year:

2018

Language:

english

File:

PDF, 543 KB

english, 2018

8

Towards sustainable feedstocks: A guide to electron donors for microbial carbon fixation

Claassens, Nico Joannes, Sánchez-Andrea, Irene, Sousa, Diana Zita, Bar-Even, Arren

Journal:

Current Opinion in Biotechnology

Year:

2018

Language:

english

File:

PDF, 1.37 MB

english, 2018

9

In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli

Yishai, Oren, Bouzon, Madeleine, Döring, Volker, Bar-Even, Arren

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 1.17 MB

english, 2018

10

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Ferrari, Camilla, Proost, Sebastian, Janowski, Marcin, Becker, Jörg, Nikoloski, Zoran, Bhattacharya, Debashish, Price, Dana, Tohge, Takayuki, Bar-Even, Arren, Fernie, Alisdair, Stitt, Mark, Mutwil, Ma

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 2.79 MB

english, 2019

11

Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

Barak Shenhav, Arren Bar-Even, Ran Kafri, Doron Lancet

Journal:

Origins of Life and Evolution of Biospheres

Year:

2005

Language:

english

File:

PDF, 3.44 MB

english, 2005

12

Transcription control reprogramming in genetic backup circuits

Kafri, Ran, Bar-Even, Arren, Pilpel, Yitzhak

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 416 KB

english, 2005

13

Noise in protein expression scales with natural protein abundance

Bar-Even, Arren, Paulsson, Johan, Maheshri, Narendra, Carmi, Miri, O'Shea, Erin, Pilpel, Yitzhak, Barkai, Naama

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

14

A survey of carbon fixation pathways through a quantitative lens

Bar-Even, A., Noor, E., Milo, R.

Journal:

Journal of Experimental Botany

Year:

2012

Language:

english

File:

PDF, 1.33 MB

english, 2012

15

Rethinking glycolysis: on the biochemical logic of metabolic pathways

Bar-Even, Arren, Flamholz, Avi, Noor, Elad, Milo, Ron

Journal:

Nature Chemical Biology

Year:

2012

Language:

english

File:

PDF, 876 KB

english, 2012

16

Does acetogenesis really require especially low reduction potential?

Bar-Even, Arren

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2013

Language:

english

File:

PDF, 392 KB

english, 2013

17

Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes

Bar-Even, Arren, Noor, Elad, Flamholz, Avi, Milo, Ron

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2013

Language:

english

File:

PDF, 890 KB

english, 2013

18

Thermodynamic constraints shape the structure of carbon fixation pathways

Bar-Even, Arren, Flamholz, Avi, Noor, Elad, Milo, Ron

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2012

Language:

english

File:

PDF, 2.33 MB

english, 2012

19

Design and analysis of synthetic carbon fixation pathways

Bar-Even, A., Noor, E., Lewis, N. E., Milo, R.

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 675 KB

english, 2010

20

Design and analysis of synthetic carbon fixation pathways

Arren Bar-Even, Elad Noor, Nathan E. Lewis, Ron Milo and Paul G. Falkowski

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.47 MB

english, 2010

21

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification

Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D., Shmueli, O.

Journal:

Year:

2005

Language:

english

File:

PDF, 960 KB

english, 2005

22

Glycolytic strategy as a tradeoff between energy yield and protein cost

Flamholz, A., Noor, E., Bar-Even, A., Liebermeister, W., Milo, R.

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 1.17 MB

english, 2013

23

Computational protein design enables a novel one-carbon assimilation pathway

Siegel, Justin B., Smith, Amanda Lee, Poust, Sean, Wargacki, Adam J., Bar-Even, Arren, Louw, Catherine, Shen, Betty W., Eiben, Christopher B., Tran, Huu M., Noor, Elad, Gallaher, Jasmine L., Bale, Jac

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 3.05 MB

english, 2015

24

eQuilibrator--the biochemical thermodynamics calculator

Flamholz, A., Noor, E., Bar-Even, A., Milo, R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 777 KB

english, 2012

25

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

Noor, E., Bar-Even, A., Flamholz, A., Lubling, Y., Davidi, D., Milo, R.

Journal:

Year:

2012

Language:

english

File:

PDF, 624 KB

english, 2012

26

Spanning high-dimensional expression space using ribosome-binding site combinatorics

Zelcbuch, L., Antonovsky, N., Bar-Even, A., Levin-Karp, A., Barenholz, U., Dayagi, M., Liebermeister, W., Flamholz, A., Noor, E., Amram, S., Brandis, A., Bareia, T., Yofe, I., Jubran, H., Milo, R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

27

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Noor, Elad, Bar-Even, Arren, Flamholz, Avi, Reznik, Ed, Liebermeister, Wolfram, Milo, Ron, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 611 KB

english, 2014

28

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro k cat measurements

Davidi, Dan, Noor, Elad, Liebermeister, Wolfram, Bar-Even, Arren, Flamholz, Avi, Tummler, Katja, Barenholz, Uri, Goldenfeld, Miki, Shlomi, Tomer, Milo, Ron

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 792 KB

english, 2016

29

Pyruvate formate-lyase enables efficient growth of Escherichia coli on acetate and formate

Zelcbuch, Lior, Lindner, Steffen N., Zegman, Yonatan, Vainberg Slutskin, Ilya, Antonovsky, Niv, Gleizer, Shmuel, Milo, Ron, Bar-Even, Arren

Journal:

Year:

2016

Language:

english

File:

PDF, 533 KB

english, 2016

30

Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways

Bar-Even, Arren

Journal:

Year:

2016

Language:

english

File:

PDF, 740 KB

english, 2016

31

Synthetic metabolism: metabolic engineering meets enzyme design

Erb, Tobias J, Jones, Patrik R, Bar-Even, Arren

Journal:

Current Opinion in Chemical Biology

Year:

2017

Language:

english

File:

PDF, 505 KB

english, 2017

32

Engineered assimilation of exogenous and endogenous formate in Escherichia coli

Yishai, Oren, Goldbach, Leander, Tenenboim, Hezi, Lindner, Steffen N., Bar-Even, Arren

Journal:

ACS Synthetic Biology

Year:

2017

Language:

english

File:

PDF, 2.70 MB

english, 2017

33

Holistic bioengineering: rewiring central metabolism for enhanced bioproduction

Aslan, Selçuk, Noor, Elad, Bar-Even, Arren

Journal:

Biochemical Journal

Year:

2017

Language:

english

File:

PDF, 3.72 MB

english, 2017

34

Daring metabolic designs for enhanced plant carbon fixation

Bar-Even, Arren

Journal:

Year:

2017

Language:

english

File:

PDF, 972 KB

english, 2017

35

Ribulose Monophosphate Shunt Provides Nearly All Biomass and Energy Required for Growth of E. coli

He, Hai, Edlich-Muth, Christian, Lindner, Steffen N., Bar-Even, Arren

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 5.05 MB

english, 2018

36

Implementation of a reductive route of one-carbon assimilation in Escherichia coli through directed evolution

Döring, Volker, Darii, Ekaterina, Yishai, Oren, Bar-Even, Arren, Bouzon, Madeleine

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 786 KB

english, 2018

37

Quantum chemistry reveals thermodynamic principles of redox biochemistry

Jinich, Adrian, Flamholz, Avi, Ren, Haniu, Kim, Sung-Jin, Sanchez-Lengeling, Benjamin, Cotton, Charles A. R., Noor, Elad, Aspuru-Guzik, Alán, Bar-Even, Arren, Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.40 MB

english, 2018

38

NADPH-auxotrophic E. coli: a sensor strain for testing in vivo regeneration of NADPH

Lindner, Steffen N., Calzad&iacute, az Ramirez, Liliana, Krüsemann, Jan, Yishai, Oren, Belkhelfa, Sophia, He, Hai, Bouzon, Madeleine, Döring, Volker, Bar-Even, Arren

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 4.44 MB

english, 2018

39

Engineering Strategies to Boost Crop Productivity by Cutting Respiratory Carbon Loss

Amthor, Jeffrey S, Bar-Even, Arren, Hanson, Andrew D, Millar, A. Harvey, Stitt, Mark, Sweetlove, Lee J., Tyerman, Stephen D

Journal:

Year:

2019

File:

PDF, 1.97 MB

2019

40

Improving the efficiency of photosynthetic carbon reactions

Weber, Andreas P.M., Bar-Even, Arren

Journal:

PLANT PHYSIOLOGY

Year:

2019

Language:

english

File:

PDF, 609 KB

english, 2019

41

A critical comparison of cellular and cell-free bioproduction systems

Claassens, Nico J, Burgener, Simon, Vögeli, Bastian, Erb, Tobias J, Bar-Even, Arren

Journal:

Current Opinion in Biotechnology

Year:

2019

Language:

english

File:

PDF, 656 KB

english, 2019

42

Design and engineering of E. coli metabolic sensor strains with a wide sensitivity range for glycerate

Aslan, Selçuk, Noor, Elad, Vaquerizo, Sara Benito, Lindner, Steffen N., Bar-Even, Arren

Journal:

Metabolic Engineering

Year:

2019

Language:

english

File:

PDF, 11.47 MB

english, 2019

43

Renewable methanol and formate as microbial feedstocks

Cotton, Charles AR, Claassens, Nico J, Benito-Vaquerizo, Sara, Bar-Even, Arren

Journal:

Current Opinion in Biotechnology

Year:

2020

Language:

english

File:

PDF, 836 KB

english, 2020

44

Developing a Carbon-Conserving Photorespiration Bypass Pathway through Ancestral Genome Mining and Engineering

Ross, Brian L., Trudeau, Devin, Bar-Even, Arren, Tawfik, Dan

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 39 KB

2020

45

Growth of E. coli on formate and methanol via the reductive glycine pathway

Kim, Seohyoung, Lindner, Steffen N., Aslan, SelÃ§uk, Yishai, Oren, Wenk, Sebastian, Schann, Karin, Bar-Even, Arren

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 3.60 MB

2020

46

In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate

He, Hai, Noor, Elad, Ramos-Parra, Perla A., GarcÃa-Valencia, Liliana E., Patterson, Jenelle A., DÃaz de la Garza, RocÃo I., Hanson, Andrew D., Bar-Even, Arren

Journal:

Year:

2020

File:

PDF, 2.47 MB

2020

47

An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli

He, Hai, HÃ¶per, Rune, DodenhÃ¶ft, Moritz, MarliÃ¨re, Philippe, Bar-Even, Arren

Journal:

Metabolic Engineering

Year:

2020

File:

PDF, 5.71 MB

2020

48

In vivo selection for formate dehydrogenases with high efficiency and specificity towards NADP + .

Calzad&iacute, az Ramirez, Liliana, Calvo Tusell, Carla, Stoffel, Gabriele M. M., Lindner, Steffen N., Osuna, SÃlvia, Erb, Tobias J., Garcia-BorrÃ s, Marc, Bar-Even, Arren, Acevedo-Rocha, Carlos G.

Journal:

Year:

2020

File:

PDF, 1.77 MB

2020

49

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle

Claassens, Nico J., Scarinci, Giovanni, Fischer, Axel, Flamholz, Avi I., Newell, William, Frielingsdorf, Stefan, Lenz, Oliver, Bar-Even, Arren

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 962 KB

2020

50

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

SÃ¡nchez-Andrea, Irene, Guedes, Iame Alves, Hornung, Bastian, Boeren, Sjef, Lawson, Christopher E., Sousa, Diana Z., Bar-Even, Arren, Claassens, Nico J., Stams, Alfons J. M.

Journal:

Nature Communications

Year:

2020

File:

PDF, 1.82 MB

2020