Elizabeth Brunk
Elizabeth Brunk
Moores Cancer Research Center
Verified email at ucsd.edu - Homepage
Cited by
Cited by
Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
E Brunk, U Rothlisberger
Chemical reviews 115 (12), 6217-6263, 2015
Recon 3D enables a three-dimensional view of gene variation in human metabolism
E Brunk, S Sahoo, DC Zielinski, A Altunkaya, N Mih, A Prlić, A Sastry, ...
Nature Biotechnology 36 (3), 272-281, 2018
iML1515, a knowledgebase that computes Escherichia coli traits
J Monk*, C Llyod*, E Brunk*, A Mih, N., Sastry, Z King, R Takeuchi, ...
Nature Biotechnology, 2017
Multi-omic data integration enables discovery of hidden biological regularities
A Ebrahim*, E Brunk*, J Tan*, EJ O’Brien, K Donghyuk, J Lerman, ...
Nature Communications 7 (doi:10.1038/ncomms13091), 2016
Model-driven discovery of underground metabolic functions in Escherichia coli
GI Guzmán*, J Utrilla*, S Nurk, E Brunk, JM Monk, A Ebrahim, BO Palsson, ...
Proceedings of the National Academy of Sciences 112 (3), 929-934, 2015
Directed Evolution of the Suicide Protein O6-Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability
B Mollwitz, E Brunk, S Schmitt, F Pojer, M Bannwarth, M Schiltz, ...
Biochemistry 51 (5), 986-994, 2012
Characterizing Strain Variation in Engineered E. coli Using a Multi-omics Based Workflow
E Brunk*, KJ George*, J Alonso-Gutierrez, M Thompson, E Baidoo, ...
Cell Systems, 2016
NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling
S Chowdhry, C Zanca, U Rajkumar, T Koga, Y Diao, R Raviram, F Liu, ...
Nature 569 (7757), 570-575, 2019
Systems Biology of the Structural Proteome
E Brunk*, J Mih*, N, Monk, K Chen, Z Zhang, S Bliven, E O’Brien, ...
BMC Systems Biology, 2016
Integrating computational methods to retrofit enzymes to synthetic pathways
E Brunk, M Neri, I Tavernelli, V Hatzimanikatis, U Rothlisberger
Biotechnology and Bioengineering 109 (2), 572-582, 2012
A streamlined ribosome profiling protocol for the characterization of microorganisms
H Latif, R Szubin, J Tan, E Brunk, A Lechner, K Zengler, BO Palsson
BioTechniques 58 (6), 329–332, 2015
The Need for Integrated Approaches in Metabolic Engineering
A Lechner, E Brunk, JD Keasling
Cold Spring Harbor Perspectives, 2016
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ...
Nature communications 9 (1), 1-15, 2018
Role of environment for catalysis of the DNA repair enzyme MutY
E Brunk, JS Arey, U Rothlisberger
Journal of the American Chemical Society 134 (20), 8608-8616, 2012
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
G Glusman, PW Rose, A Prlić, J Dougherty, JM Duarte, AS Hoffman, ...
Genome medicine 9 (1), 1-10, 2017
Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the phosphotransferase system
D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ...
Metabolic engineering 48, 233-242, 2018
Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes
D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ...
Metabolic engineering 48, 82-93, 2018
Pushing the frontiers of first-principles based computer simulations of chemical and biological systems
E Brunk, N Ashari, P Athri, P Campomanes, FF de Carvalho, ...
CHIMIA International Journal for Chemistry 65 (9), 667-671, 2011
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
N Mih*, E Brunk*, A Bordbar, BO Palsson
PLOS Comput Biol 12 (7), e1005039, 2016
Growth adaptation of gnd and sdhCB Escherichia coli deletion strains diverges from a similar initial perturbation of the transcriptome
D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ...
Frontiers in microbiology 9, 1793, 2018
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