NCBI Library
google scholar citations

Peer Reviewed

* Equal contribution;  †Corresponding author


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 remodellingNature (2019) 569. 570


30. Brunk, E*; Chang, RL; Xia, J; Hefzi, H; Yurkovich, JT; Kim, D; Buckmiller, E; Wang, H; Yang, C; Palsson, B; Church, GM; Lewis, NE*. Characterizing post-translational modifications in prokaryote metabolism using a multi-scale workflow PNAS (2018) 115

29. Brunk, E; Sahoo, S; Zielinski, DC; Altunkaya, A; Mih, N; Prlić, … ; Burley, SK; Dräger, A; Fleming, RMT; Nielsen, J; Thiele, I; Palsson, BO. Recon 3D enables a three-dimensional view of gene variation in human metabolism Nature Biotechnology (2018) 36, 272–281

28. 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 (2018)

27. 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 (2018)

26. 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 (2018)

25. 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 (2018)   biorxiv


24. Glusman et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation Genome Medicine (2017) 9:113     original conference website

23.  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 coliNature Biotechnology. (2017)    link

22.  Sastry, A and Brunk, E. Principles of Systems Biology N. 18  Cell Systems  (2017)    link        PDF

21.  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 (2017).


20.  Brunk, E; Perez, M; Athri, P; Rothlisberger, U. Genetic Algorithm Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2 chemphyschem (2016) 17(23):3831-3835

19.  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 (2016) link

18.  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 (2016)  doi:10.1038/ncomms13091

17.  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 (2016) 2 (5): 335     article link     preview commentary

16.  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 (2016) 10(1):26

15. Lechner, A; Brunk, E; Keasling, JD. The Need for Integrated Approaches in Metabolic Engineering Cold Spring Harbor Perspectives (2016)    article link    doi: 10.1101/cshperspect.a023903


14.   Brunk, E; Rothlisberger, U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chemical Reviews (2015) DOI: 10.1021/cr500628b

13.  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 (2015) 112 (3) 929-934

12.  Aziz, RK; Khaw, V; Monk, JM; Brunk, E; Lewis, R; Loh, SI; Mishra, A; Nagle, AA; Satyanarayana,  C; Dhakshinamoorthy, S; Luche, M; Kitchen, DB; Andrews, KA; Palsson, BO; Charusanti, P. 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 (2015)

11.  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 (2015) 58, 329.

10.  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 (2015) 108


9.  Brunk, E; Kellett, WF; Richards, NGJ; Rothlisberger, U. A Mechano-Chemical Switch to Control Reactive Intermediates. Biochemistry (2014) 53 (23), 3830-3838

8.  Bozkurt, E; Ashari, N; Browning, N; Brunk, E; Campomanesa, P; Perez, MAS; Rothlisberger, U. Lessons from Nature: Computational Design of Biomimetic Compounds and Processes (2014) CHIMIA 68 (9) 642.


7.  Brunk, E; Rothlisberger, U. Understanding Evolutionary Strategies of Enzymes and Exploiting them for Biomimetic Purposes. (2013) EPFL Thesis.   EPFL    PDF link

6.  Brunk, E; Mollwitz, B; Rothlisberger, U. Mechanism for Triggering Unfolding in O6-Alkylguanine DNA Alkyltransferase. ChemBioChem (2013) doi: 10.1002/cbic.201200566

5.  Kellett, WF; Brunk, E; Desai, BJ; Fedorov, AA; Almo, SC; Gerlt, JA; Rothlisberger, U; Richards, NGJ. Computational, Structural and Kinetic Evidence that Vibrio vulnicus FrsA is not a Cofactor-Independent Pyruvate Decarboxylase. Biochemistry (2013) 2 (11), 1842-1844.


4.  Brunk, E; Arey, JS; Rothlisberger, U. The Role of Environment in the Catalysis of the MutY DNA Repair Enzyme Journal of American Chemical Society (2012) 134, 8608.

3.  Mollwitz, B; Brunk, E; Schmitt, S; Pojer, F; Bannwarth, M; Schiltz, M; Rothlisberger U; Johnsson, K. Directed Evolution of the Suicide Protein O-6-Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability. Biochemistry (2012) 51, 986.


2.  Brunk, E; Neri, M; Tavernelli, I; Hatzimanikatis, V; Rothlisberger, U. Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnology and Bioengineering (2011) 109, 572.

1.  Brunk, E; Ashari, N; Athri, P; Campomanes, P; de Carvalho, FF; Curchod, BFE; Diamantis, P; Doemer, M; Garrec, J; Laktionov, A; Micciarelli, M; Neri, M; Palermo, G; Penfold, TJ; Vanni, S; Tavernelli, I; Rothlisberger, U. Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems CHIMIA (2011) 65, 667.