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NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. 2019 05; 569(7757):570-575.
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 PS. PMID: 31019297.
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PubMed Mentions:
36 Fields:
Translation:
HumansAnimalsCells
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Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101.
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. PMID: 30301795.
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PubMed Mentions:
12 Fields:
Translation:
Cells
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Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun. 2018 09 18; 9(1):3796.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30228271.
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PubMed Mentions:
12 Fields:
Translation:
Cells
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Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018 10 01; 84(19).
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30054360.
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PubMed Mentions:
7 Fields:
Translation:
Cells
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Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30131786.
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PubMed Mentions:
9
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ssbio: a Python framework for structural systems biology. Bioinformatics. 2018 06 15; 34(12):2155-2157.
Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. PMID: 29444205.
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PubMed Mentions:
13 Fields:
Translation:
Cells
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Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. . 2018 07; 48:233-242.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29906504.
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PubMed Mentions:
9 Translation:
Cells
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Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. . 2018 07; 48:82-93.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29842925.
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PubMed Mentions:
11 Translation:
Cells
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Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 03; 36(3):272-281.
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. PMID: 29457794.
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PubMed Mentions:
112 Fields:
Translation:
Humans
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Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 2017 Dec 18; 9(1):113.
Glusman G, Rose PW, Prlic 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. PMID: 29254494.
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PubMed Mentions:
17 Fields:
Translation:
HumansCells
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iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 10 11; 35(10):904-908.
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. PMID: 29020004.
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PubMed Mentions:
85 Fields:
Translation:
Cells
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Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics. 2017 Aug 15; 33(16):2487-2495.
Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E. PMID: 28398465.
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PubMed Mentions:
1 Fields:
Translation:
HumansCells
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The Need for Integrated Approaches in Metabolic Engineering. Cold Spring Harb Perspect Biol. 2016 Nov 01; 8(11).
Lechner A, Brunk E, Keasling JD, Lechner A, Brunk E, Keasling JD. PMID: 27527588; PMCID: PMC5088530.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 10 26; 7:13091.
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. PMID: 27782110.
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PubMed Mentions:
40 Fields:
Translation:
Cells
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Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2. Chemphyschem. 2016 Dec 05; 17(23):3831-3835.
Brunk E, Perez MA, Athri P, Rothlisberger U, Brunk E, Perez MA, Athri P, Rothlisberger U. PMID: 27706880.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016 07; 12(7):e1005039.
Mih N, Brunk E, Bordbar A, Palsson BO. PMID: 27467583.
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PubMed Mentions:
3 Fields:
Translation:
HumansCells
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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 05 25; 2(5):335-46.
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, 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. PMID: 27211860; PMCID: PMC4882250.
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PubMed Mentions:
22 Fields:
Translation:
Cells
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Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26.
Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO, Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. PMID: 26969117; PMCID: PMC4787049.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Front Microbiol. 2015; 6:958.
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, 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. PMID: 26441892; PMCID: PMC4585216.
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PubMed Mentions:
2
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A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32.
Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO, Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. PMID: 26054770.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev. 2015 Jun 24; 115(12):6217-63.
Brunk E, Rothlisberger U, Brunk E, Rothlisberger U. PMID: 25880693.
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PubMed Mentions:
58 Fields:
Translation:
Cells
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Free-energy landscape and characteristic forces for the initiation of DNA unzipping. Biophys J. 2015 Apr 07; 108(7):1727-1738.
Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I, Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I. PMID: 25863064; PMCID: PMC4390814.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):929-34.
Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM, Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. PMID: 25564669; PMCID: PMC4311852.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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Lessons from nature: computational design of biomimetic compounds and processes. Chimia (Aarau). 2014 Sep; 68(9):642-7.
Bozkurt E, Ashari N, Browning N, Brunk E, Campomanesa P, Perez MA, Rothlisberger U, Bozkurt E, Ashari N, Browning N, Brunk E, Campomanesa P, Perez MA, Rothlisberger U. PMID: 25437785.
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PubMed Mentions:
1 Fields:
Translation:
HumansCells
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A mechanochemical switch to control radical intermediates. Biochemistry. 2014 Jun 17; 53(23):3830-8.
Brunk E, Kellett WF, Richards NG, Rothlisberger U, Brunk E, Kellett WF, Richards NG, Rothlisberger U. PMID: 24846280; PMCID: PMC4067147.
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PubMed Mentions: Fields:
Translation:
Cells
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Mechanism to trigger unfolding in O(6) -alkylguanine-DNA alkyltransferase. Chembiochem. 2013 Apr 15; 14(6):703-10.
Brunk E, Mollwitz B, Rothlisberger U, Brunk E, Mollwitz B, Rothlisberger U. PMID: 23532906.
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PubMed Mentions:
3 Fields:
Translation:
HumansCells
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Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Biochemistry. 2013 Mar 19; 52(11):1842-4.
Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NG, Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NG. PMID: 23452154; PMCID: PMC3788570.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Role of environment for catalysis of the DNA repair enzyme MutY. J Am Chem Soc. 2012 May 23; 134(20):8608-16.
Brunk E, Arey JS, Rothlisberger U, Brunk E, Arey JS, Rothlisberger U. PMID: 22537339.
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PubMed Mentions:
4 Fields:
Translation:
Cells
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Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability. Biochemistry. 2012 Feb 07; 51(5):986-94.
Mollwitz B, Brunk E, Schmitt S, Pojer F, Bannwarth M, Schiltz M, Rothlisberger U, Johnsson K, Mollwitz B, Brunk E, Schmitt S, Pojer F, Bannwarth M, Schiltz M, Rothlisberger U, Johnsson K. PMID: 22280500.
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PubMed Mentions:
21 Fields:
Translation:
HumansCells
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Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng. 2012 Feb; 109(2):572-82.
Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U, Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U. PMID: 21928337.
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PubMed Mentions:
7 Fields:
Translation:
Cells
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Pushing the frontiers of first-principles based computer simulations of chemical and biological systems. Chimia (Aarau). 2011; 65(9):667-71.
Brunk E, Ashari N, Athri P, Campomanes P, de Carvalho FF, Curchod BF, Diamantis P, Doemer M, Garrec J, Laktionov A, Micciarelli M, Neri M, Palermo G, Penfold TJ, Vanni S, Tavernelli I, Rothlisberger U, Brunk E, Ashari N, Athri P, Campomanes P, de Carvalho FF, Curchod BF, Diamantis P, Doemer M, Garrec J, Laktionov A, Micciarelli M, Neri M, Palermo G, Penfold TJ, Vanni S, Tavernelli I, Rothlisberger U. PMID: 22026176.
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PubMed Mentions:
5 Fields:
Translation:
Cells