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Elizabeth Brunk · SciRah

Researcher profile · Semantic Scholar

Elizabeth Brunk

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Elizabeth Brunk — researcher profile on SciRah

h-index: 22
Works: 53
Citations: 2,854

Most-cited papers

iML1515, a knowledgebase that computes Escherichia coli traits
Jonathan M. Monk, C. Lloyd, Elizabeth Brunk, Nathan Mih +8 more
2017Nature Biotechnology543 citations Open access
Semantic Scholar
Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism
Elizabeth Brunk, Swagatika Sahoo, D. Zielinski, Ali Altunkaya +17 more
2018Nature Biotechnology513 citations Open access
Semantic Scholar
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States.
Elizabeth Brunk, U. Rothlisberger
2015Chemical Reviews440 citations Open access
Semantic Scholar
NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodeling
S. Chowdhry, C. Zanca, Utkrisht Rajkumar, Tomoyuki Koga +11 more
2019Nature193 citations Open access
Semantic Scholar
Systems biology of the structural proteome
Elizabeth Brunk, Nathan Mih, Jonathan M. Monk, Zhen Zhang +6 more
2016BMC Systems Biology151 citations Open access
Semantic Scholar
Multi-omic data integration enables discovery of hidden biological regularities
A. Ebrahim, Elizabeth Brunk, Justin Tan, Edward J. O'Brien +8 more
2016Nature Communications149 citations Open access
Semantic Scholar
Characterizing strain variation in engineered E. coli using a multi-omics based workflow
Elizabeth Brunk, Kevin W. George, J. Alonso-Gutiérrez, M. Thompson +14 more
2016Cell Systems95 citations Open access
Semantic Scholar
Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability.
B. Mollwitz, Elizabeth Brunk, S. Schmitt, F. Pojer +4 more
2012Biochemistry86 citations Open access
Semantic Scholar
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
D. McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk +4 more
2018Nature Communications70 citations Open access
Semantic Scholar
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
Gwênlyn Glusman, Peter W. Rose, A. Prlić, J. Dougherty +33 more
2017Genome Medicine59 citations Open access
Semantic Scholar
Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.
D. McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk +4 more
2018Metabolic Engineering51 citations Open access
Semantic Scholar
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, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk +4 more
2018Metabolic Engineering50 citations Open access
Semantic Scholar
The Need for Integrated Approaches in Metabolic Engineering.
Anna Lechner, Elizabeth Brunk, J. Keasling
2016Cold Spring Harbor Perspectives in Biology49 citations Open access
Semantic Scholar
A streamlined ribosome profiling protocol for the characterization of microorganisms.
Haythem Latif, R. Szubin, Justin Tan, Elizabeth Brunk +3 more
2015BioTechniques49 citations Open access
Semantic Scholar
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +9 more
2018Proceedings of the National Academy of Sciences of the United States of America45 citations Open access
Semantic Scholar
ssbio: A Python Framework for Structural Systems Biology
Nathan Mih, Elizabeth Brunk, Ke Chen, E. Catoiu +6 more
2017bioRxiv40 citations Open access
Semantic Scholar
Integrating computational methods to retrofit enzymes to synthetic pathways
Elizabeth Brunk, M. Neri, I. Tavernelli, V. Hatzimanikatis +1 more
2012Biotechnology and Bioengineering36 citations Open access
Semantic Scholar
Role of environment for catalysis of the DNA repair enzyme MutY.
Elizabeth Brunk, J. S. Arey, U. Rothlisberger
2012Journal of the American Chemical Society34 citations Open access
Semantic Scholar
Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions
D. McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk +4 more
2018Applied and Environmental Microbiology29 citations Open access
Semantic Scholar
Model-driven discovery of underground metabolic functions in Escherichia coli
Gabriela I. Guzmán, J. Utrilla, S. Nurk, Elizabeth Brunk +4 more
2015Proceedings of the National Academy of Sciences of the United States of America28 citations Open access
Semantic Scholar
Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome
D. McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk +5 more
2018bioRxiv26 citations Open access
Semantic Scholar
Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.
Elizabeth Brunk, Negar Ashari, Prashanth Athri, P. Campomanes +13 more
2011Chimia (Basel)23 citations Open access
Semantic Scholar
Machine learning in computational biology to accelerate high‐throughput protein expression
Anand V. Sastry, Jonathan M. Monk, Hanna Tegel, Mathias Uhlen +3 more
2017Bioinform.18 citations Open access
Semantic Scholar
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
Nathan Mih, Elizabeth Brunk, A. Bordbar, B. Palsson
2016PLoS Comput. Biol.16 citations Open access
Semantic Scholar
Free-energy landscape and characteristic forces for the initiation of DNA unzipping.
A. Mentes, A. Florescu, Elizabeth Brunk, Jeff Wereszczynski +2 more
2015Biophysical Journal12 citations Open access
Semantic Scholar
A Mechanochemical Switch to Control Radical Intermediates
Elizabeth Brunk, W. Kellett, N. Richards, U. Rothlisberger
2014Biochemistry12 citations Open access
Semantic Scholar
Computational, Structural and Kinetic Evidence that Vibrio vulnificus FrsA is not a Cofactor-Independent Pyruvate Decarboxylase
W. Kellett, Elizabeth Brunk, B. Desai, A. Fedorov +4 more
2013Biochemistry10 citations Open access
Semantic Scholar
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC
R. Aziz, Valerie L. Khaw, Jonathan M. Monk, Elizabeth Brunk +11 more
2015Frontiers in Microbiology9 citations Open access
Semantic Scholar
Lessons from nature: computational design of biomimetic compounds and processes.
E. Bozkurt, Negar Ashari, N. Browning, Elizabeth Brunk +3 more
2014Chimia (Basel)8 citations Open access
Semantic Scholar
Mechanism to Trigger Unfolding in O6‐Alkylguanine‐DNA Alkyltransferase
Elizabeth Brunk, B. Mollwitz, U. Rothlisberger
2013ChemBioChem6 citations Open access
Semantic Scholar
Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
2017bioRxiv4 citations Open access
Semantic Scholar
Characterizing strain variation in engineered E . coli using a multi-omics 1 based workflow 2 3
Elizabeth Brunk, Kevin W. George, J. Alonso-Gutiérrez, M. Thompson +11 more
20173 citations
Semantic Scholar
Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2.
Elizabeth Brunk, M. A. S. Perez, Prashanth Athri, U. Rothlisberger
2016ChemPhysChem3 citations Open access
Semantic Scholar
A Standardized Protocol for Sample Preparation for Scanning Electron Microscopy (SEM) to Visualize Extrachromosomal DNA (ecDNA)
Jillann A. Madren, Jing-Ting Chen, W. Dennis, Christina G. Ford +2 more
2023bioRxiv0 citations Open access
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments Metabolic regulation can be predicted in genome-scale models modifications on metabolic regulation
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Systemic post-translational control of bacterial metabolism 1 regulates adaptation in dynamic environments
Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi +8 more
20170 citations
Semantic Scholar
Understanding Evolutionary Strategies of Enzymes and Exploiting them for Biomimetic Purposes
Elizabeth Brunk
20130 citations
Semantic Scholar
Computational evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase
W. Kellett, Elizabeth Brunk, B. Desai, A. Fedorov +4 more
20130 citations
Semantic Scholar
Role of environment in the catalysis of the MutY DNA repair enzyme
Elizabeth Brunk, J. S. Arey, U. Rothlisberger
20130 citations
Semantic Scholar
Computational design of biomimetic strategies for the production of chemical compounds
Elizabeth Brunk, U. Roethlisberger
20130 citations
Semantic Scholar
Mechanism to trigger unfolding in alkylguanine alkyltransferase
Elizabeth Brunk, B. Mollwitz, U. Rothlisberger
20130 citations
Semantic Scholar

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