Brunk, Elizabeth: 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

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

Brunk, Elizabeth, Rothlisberger, Ursula

Journal:

Chemical Reviews

Year:

2015

Language:

english

File:

PDF, 10.49 MB

english, 2015

3

Systems biology of the structural proteome

Brunk, Elizabeth, Mih, Nathan, Monk, Jonathan, Zhang, Zhen, O’Brien, Edward J., Bliven, Spencer E., Chen, Ke, Chang, Roger L., Bourne, Philip E., Palsson, Bernhard O.

Journal:

BMC Systems Biology

Year:

2016

Language:

english

File:

PDF, 3.27 MB

english, 2016

4

Recon3D enables a three-dimensional view of gene variation in human metabolism

Brunk, Elizabeth, Sahoo, Swagatika, Zielinski, Daniel C, Altunkaya, Ali, Dräger, Andreas, Mih, Nathan, Gatto, Francesco, Nilsson, Avlant, Preciat Gonzalez, German Andres, Aurich, Maike Kathrin, Prlić,

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 6.22 MB

english, 2018

5

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

6

ssbio: A Python Framework for Structural Systems Biology

Mih, Nathan, Brunk, Elizabeth, Chen, Ke, Catoiu, Edward, Sastry, Anand, Kavvas, Erol, Monk, Jonathan M, Zhang, Zhen, Palsson, Bernhard O, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 585 KB

english, 2018

7

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

8

Mechanism to Trigger Unfolding in O 6 -Alkylguanine-DNA Alkyltransferase

Brunk, Elizabeth, Mollwitz, Birgit, Rothlisberger, Ursula

Journal:

Year:

2013

Language:

english

File:

PDF, 2.11 MB

english, 2013

9

Genetic Algorithm Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2

Brunk, Elizabeth, Da Silva Perez Gomes, Marta, Athri, Prashanth, Rothlisberger, Ursula

Journal:

Year:

2016

Language:

english

File:

PDF, 2.00 MB

english, 2016

10

NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling

Chowdhry, Sudhir, Zanca, Ciro, Rajkumar, Utkrisht, Koga, Tomoyuki, Diao, Yarui, Raviram, Ramya, Liu, Feng, Turner, Kristen, Yang, Huijun, Brunk, Elizabeth, Bi, Junfeng, Furnari, Frank, Bafna, Vineet,

Journal:

Year:

2019

File:

PDF, 23.33 MB

2019

11

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism

Mih, Nathan, Brunk, Elizabeth, Bordbar, Aarash, Palsson, Bernhard O., Punta, Marco

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 5.53 MB

english, 2016

12

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

13

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.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.39 MB

english, 2018

14

Role of Environment for Catalysis of the DNA Repair Enzyme MutY

Brunk, Elizabeth, Arey, J. Samuel, Rothlisberger, Ursula

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 3.46 MB

english, 2012

15

A Mechanochemical Switch to Control Radical Intermediates

Brunk, Elizabeth, Kellett, Whitney F., Richards, Nigel G. J., Rothlisberger, Ursula

Journal:

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014

16

Free-Energy Landscape and Characteristic Forces for the Initiation of DNA Unzipping

Mentes, Ahmet, Florescu, Ana Maria, Brunk, Elizabeth, Wereszczynski, Jeff, Joyeux, Marc, Andricioaei, Ioan

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 1.53 MB

english, 2015

17

NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling

Chowdhry, Sudhir, Zanca, Ciro, Rajkumar, Utkrisht, Koga, Tomoyuki, Diao, Yarui, Raviram, Ramya, Liu, Feng, Turner, Kristen, Yang, Huijun, Brunk, Elizabeth, Bi, Junfeng, Furnari, Frank, Bafna, Vineet,

Journal:

Year:

2019

Language:

english

File:

PDF, 23.33 MB

english, 2019

18

Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase

Kellett, Whitney F., Brunk, Elizabeth, Desai, Bijoy J., Fedorov, Alexander A., Almo, Steven C., Gerlt, John A., Rothlisberger, Ursula, Richards, Nigel G. J.

Journal:

Year:

2013

Language:

english

File:

PDF, 886 KB

english, 2013

19

Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Brunk, Elizabeth, Ashari, Negar, Athri, Prashanth, Campomanes, Pablo, de Carvalho, F. Franco, Curchod, Basile F. E., Diamantis, Polydefkis, Doemer, Manuel, Garrec, Julian, Laktionov, Andrey, Micciarel

Journal:

CHIMIA International Journal for Chemistry

Year:

2011

Language:

english

File:

PDF, 657 KB

english, 2011

20

Directed Evolution of the Suicide Protein O 6 -Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability

Mollwitz, Birgit, Brunk, Elizabeth, Schmitt, Simone, Pojer, Florence, Bannwarth, Michael, Schiltz, Marc, Rothlisberger, Ursula, Johnsson, Kai

Journal:

Year:

2012

Language:

english

File:

PDF, 3.22 MB

english, 2012

21

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Bozkurt, Esra, Ashari, Negar, Browning, Nicholas, Brunk, Elizabeth, Campomanesa, Pablo, Perez, Marta A. S., Rothlisberger, Ursula

Journal:

CHIMIA International Journal for Chemistry

Year:

2014

Language:

english

File:

PDF, 436 KB

english, 2014

22

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.

Journal:

Metabolic Engineering

Year:

2018

Language:

english

File:

PDF, 1018 KB

english, 2018

23

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

Aziz, Ramy K., Khaw, Valerie L., Monk, Jonathan M., Brunk, Elizabeth, Lewis, Robert, Loh, Suh I., Mishra, Arti, Nagle, Amrita A., Satyanarayana, Chitkala, Dhakshinamoorthy, Saravanakumar, Luche, Miche

Journal:

Frontiers in Microbiology

Year:

2015

Language:

english

File:

PDF, 4.05 MB

english, 2015

24

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 M., Palsson, Bernhard O.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 2.94 MB

english, 2016

25

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.

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 6.41 MB

english, 2018

26

Integrating computational methods to retrofit enzymes to synthetic pathways

Elizabeth Brunk, Marilisa Neri, Ivano Tavernelli, Vassily Hatzimanikatis, Ursula Rothlisberger

Journal:

Biotechnology and Bioengineering

Year:

2012

Language:

english

File:

PDF, 671 KB

english, 2012

27

A Molecular Breadboard: Removal and Replacement of Subunits in an Hepatitis B Virus Capsid

Lee, Lye Siang, Brunk, Nicholas, Haywood, Daniel G, Keifer, David, Pierson, Elizabeth, Kondylis, Panagiotis, Wang, Joseph Che-Yen, Jacobson, Stephen C, Jarrold, Martin F, Zlotnick, Adam

Journal:

Protein Science

Year:

2017

Language:

english

File:

PDF, 2.43 MB

english, 2017

28

Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression

Sastry, Anand, Monk, Jonathan, Tegel, Hanna, Uhlén, Mathias, Palsson, Bernhard O., Rockberg, Johan, Brunk, Elizabeth

Journal:

Year:

2017

Language:

english

File:

PDF, 1.66 MB

english, 2017

29

The Need for Integrated Approaches in Metabolic Engineering

Lechner, Anna, Brunk, Elizabeth, Keasling, Jay D.

Journal:

Cold Spring Harbor Perspectives in Biology

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

30

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

Brunk, Elizabeth, George, Kevin W., Alonso-Gutierrez, Jorge, Thompson, Mitchell, Baidoo, Edward, Wang, George, Petzold, Christopher J., McCloskey, Douglas, Monk, Jonathan, Yang, Laurence, O’Brien, Edw

Journal:

Year:

2016

Language:

english

File:

PDF, 4.14 MB

english, 2016

31

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Glusman, Gustavo, Rose, Peter W., Prlić, Andreas, Dougherty, Jennifer, Duarte, José M., Hoffman, Andrew S., Barton, Geoffrey J., Bendixen, Emøke, Bergquist, Timothy, Bock, Christian, Brunk, Elizabeth,

Journal:

Genome Medicine

Year:

2017

Language:

english

File:

PDF, 456 KB

english, 2017

32

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Brunk, Elizabeth, Chang, Roger L., Xia, Jing, Hefzi, Hooman, Yurkovich, James T., Kim, Donghyuk, Buckmiller, Evan, Wang, Harris H., Cho, Byung-Kwan, Yang, Chen, Palsson, Bernhard O., Church, George M.

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 2.62 MB

english, 2018

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