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Selected Papers


Chowdhry, S; Zanca, C; Rajkumar, U.; Koga, T.; Diao, Y.; Raviram, R.; Liu, F.; Turner, K.; Yang, H.; Brunk, E.; Bi, J.;  Furnari, F.; Bafna, V.; Ren, B.; Mischel, P. NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. 569, 570


Brunk, E; Chang, RL; Xia, J; Hefzi, H; et al. Characterizing post-translational modifications in prokaryote metabolism using a multi-scale workflow. PNAS. 115

Brunk, E; Sahoo, S; et. al. Recon 3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. 36, 272–281

Mih, N; Brunk, E; Chen, K; Catoiu, E; Sastry, A; Kavvas, E; Monk, JMM; Zhang, Z; Palsson, BO. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics. 34(12), 2155-21572018 McCloskey D; Xu S; Sandberg TE; Brunk E; Hefner Y; Szubin R; Feist AM; Palsson BO. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metabolic Engineering. 48, 233-242

McCloskey D; Xu S; Sandberg TE; Brunk E; Hefner Y; Szubin R; Feist AM; Palsson BO. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metabolic Engineering. 48, 82-93

McCloskey D; Xu S; Sandberg TE; Brunk E; Hefner Y; Szubin R; Feist AM; Palsson BO. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nature Communications. 9, 3796


Monk, J.*; Llyod, C*; Brunk, E*; Mih, N., Sastry, A; King, Z; Takeuchi, R; Nomura, W; Mori, H; Feist, AM; Palsson, BO. iML1515; a computable knowledgebase for E coli. Nature Biotechnology. 5(10), 904-908

Glusman G.; Rose PW.; Prlić A.; Dougherty J.; Duarte JM.; Hoffman AS.; Barton GJ.; Bendixen E.; Bergquist T.; Bock C.; Brunk E.; et al.. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation. Genome Medicine. (2017) 9:113

Sastry, A; Monk, J; Tegel, H; Uhlen, M; Rockberg, J†; Palsson, BO, Brunk, E†. Machine Learning in Computational Biology to Accelerate High-throughput protein expression. Bioinformatics. 33(16), 2487-2495


Brunk, E; Perez, M; Athri, P; Rothlisberger, U. Genetic Algorithm Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2 chemphyschem. 17, 23, 3831-3835

Mih, N*; Brunk, E*†; Bordbar, A; Palsson, BO†. The Effect of Single Nucleotide Polymorphisms on Native Metabolite and Drug Responses in Human Erythrocyte Metabolism. Plos. Comp. Bio.  12(7), e1005039

Ebrahim, A*; Brunk, E*; Tan, J*; O’Brien, EJ; Donghyuk, K; Lerman, J; Lechner, A; Sastry, A; Bordbar, A; Feist, A; Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7, 13091

Brunk, E*; George, KJ*; Alonso-Gutierrez, J; Thompson, M; Baidoo, E; … Adams, P; Keasling, JD; Palsson, BO; Lee, TS. Characterizing Strain Variation in Engineered E. coli Using a Multi-omics Based Workflow. Cell Systems. 2 (5), 335

Brunk, E*; Mih, N*, Monk, J; Chen, K; Zhang, Z; Bliven, S; O’Brien, E; Chang, RL; Bourne, PE; Palsson, BO. Systems Biology of the Structural Proteome. BMC systems biology. 10, 1, 26


Guzman, G*; Utrilla, J*; Nurk, S; Brunk, E; Monk, JM; Ebrahim, A; Palsson, B; Feist, AM.  Model-driven discovery of underground metabolic functions in Escherichia coli. PNAS. 112,3, 929-934

Aziz, RK; Khaw, V; Monk, JM; Brunk, E; et al. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.  Frontiers in Microbiology. 6, 9582015 Latif, H; Szubin, R; Tan, J; Brunk, E; Lechner, A; Zengler, K; Palsson, BO. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 58, 329.

Mentes, A; Florescu, AM; Brunk, E; Wereszczynski, J; Joyeux, M; Andricioaei I. Free energy landscape and characteristic forces for the initiation of DNA unzipping.  Biophysical Journal. 108

Peer Reviewed Review Articles 


Lechner, A.; Brunk, E.; Keasling, JD. The Need For Integrated Approaches in Metabolic Engineering. Cold Springs Harbor Perspectives. 8 (11) 


Brunk, E; Rothlisberger, U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chemical Reviews. 115 (12): 6217–6263