For a full list of publications:
Google Scholar – MyNCBI
Selected Papers
2024
Shukla K, Idanwekhai K, Naradikian M, Ting S, Schoenberger SP, Brunk E
Machine learning of three-dimensional protein structures to predict the functional impacts of genome variation.
ACS J. Chem. Inf and Mod.
Available from https://doi.org/10.1021/acs.jcim.3c01967
Madren JA*, Chen J*, Dennis WC, Gutierrez Ford C, White K, Brunk E.
A Standardized Protocol for Sample Preparation for Scanning Electron Microscopy (SEM) to Visualize Extrachromosomal DNA (ecDNA).
Biotechniques
Available from https://doi.org/10.1101/2023.08.24.554665
Fessler J*, Ting S*, Yi H, Haase S, Chen J, Gulec S, Wang Y, Smyers N, Goble K, Cannon D, Mehta A, Ford C, Brunk E
CytoCellDB: A Resource Database For Classification and Analysis of Extrachromosomal DNA in Cancer NAR Cancer
Available from https://doi.org/10.1093/narcan/zcae035
Brunk R, Shukla K, Hutson B, Wang Y, Verber M, Gutierrez Ford C, Dennis W, Mehta A, Hogan B, Swetnam T, Brunk E.
Data science for Biochemists: Integrating and evaluating the use of interactive digital python notebooks in a large enrollment undergraduate biochemistry course
ACS Chem Education
Available from https://doi.org/10.1021/acs.jchemed.4c0016738
Goble K*, Mehta A*, Guilbaud D, Fessler J, Chen J, Nenad W, Cope O, Cheng D, Dennis W, Gurumurthy N, Wang Y, Shukla K, Brunk E
AI for Drug Treatment Analytics: Automated Detection and Quantification of Extrachromosomal DNA in Fluorescent Images Using Microscopy Image Analyzer
In Review
Available from https://doi.org/10.1101/2024.10.23.619848
2023
Bhardwaj PV, Wang Y, Brunk E, Spanheimer PM, Abdou YG
Advances in the Management of Early-Stage Triple-Negative Breast Cancer
International Journal of Molecular Sciences. 24 (15), 12478
Browning NJ, Perez MAS, Brunk E, Rothlisberger, U
EVOLVE: An Evolutionary Toolbox for the Design of Peptides and Proteins.
Chemrxiv 2023
Available from https://10.26434/chemrxiv-2023-gb366
2019
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
2018
Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE
Characterizing post-translational modifications in prokaryote metabolism using a multi-scale workflow.
PNAS. 115
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.
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
2017
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. Oct 11;35(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, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation. Genome Medicine. 2017 Dec 18;9(1):113.
Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E.
Machine Learning in Computational Biology to Accelerate High-throughput protein expression. Bioinformatics. 2017 Aug 15;33(16):2487-2495.
2016
Brunk E, Perez MA, Athri P, Rothlisberger U.
Genetic Algorithm Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2 chemphyschem. 2016 Dec 5;17(23):3831-3835.
Mih N*, Brunk E*†, Bordbar A, Palsson BO†.
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.
PLoS Comput Biol. 2016 Jul;12(7):e1005039.
Ebrahim A*, Brunk E*, Tan J*, O’Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO.
Multi-omic data integration enables discovery of hidden biological regularities.
Nature Communications. 2016 Oct 26;7:13091.
Brunk E*, George KW*, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O’Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS.
Characterizing Strain Variation in Engineered E. coli Using a Multi-omics Based Workflow.
Cell Syst. 2016 May 25;2(5):335-46.
Brunk E, Mih N, Monk J, Zhang Z, O’Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO.
Systems Biology of the Structural Proteome.
BMC systems biology. 2016 Mar 11;10:26.
Lechner A, Brunk E, Keasling JD.
The Need For Integrated Approaches in Metabolic Engineering.
Cold Spring Harb Perspect Biol. 2016 Nov 1;8(11).
2015
Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM.
Model-driven discovery of underground metabolic functions in Escherichia coli.
Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):929-34.
Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, 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;6:958.
Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I.
Free energy landscape and characteristic forces for the initiation of DNA unzipping.
Biophys J. 2015 Apr 7;108(7):1727-1738.
Brunk E, Rothlisberger U.
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States.
Chemical Reviews. 2015 Jun 24;115(12):6217-63.
Brunk Lab 