Elizabeth Brunk

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Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation. J Chem Inf Model. 2024 Apr 18. Shukla K, Idanwekhai K, Naradikian M, Ting S, Schoenberger SP, Brunk E. PMID: 38635316.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Advances in the Management of Early-Stage Triple-Negative Breast Cancer. Int J Mol Sci. 2023 Aug 05; 24(15). Bhardwaj PV, Wang Y, Brunk E, Spanheimer PM, Abdou YG. PMID: 37569851; PMCID: PMC10419523.
      View in: PubMed   Mentions: 1     Fields:    
    3. 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; PMCID: PMC7138021.
      View in: PubMed   Mentions: 95     Fields:    Translation:HumansAnimalsCells
    4. 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; PMCID: PMC6205427.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    5. 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; PMCID: PMC6143558.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    6. 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; PMCID: PMC6146989.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    7. 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; PMCID: PMC6090065.
      View in: PubMed   Mentions: 15  
    8. 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; PMCID: PMC6658713.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    9. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018 07; 48:233-242. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29906504.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    10. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng. 2018 07; 48:82-93. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29842925.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    11. 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; PMCID: PMC5840010.
      View in: PubMed   Mentions: 269     Fields:    Translation:Humans
    12. 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; PMCID: PMC5735928.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    13. 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; PMCID: PMC6521705.
      View in: PubMed   Mentions: 200     Fields:    Translation:Cells
    14. 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; PMCID: PMC5870730.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    15. The Need for Integrated Approaches in Metabolic Engineering. Cold Spring Harb Perspect Biol. 2016 Nov 01; 8(11). Lechner A, Brunk E, Keasling JD. PMID: 27527588; PMCID: PMC5088530.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    16. 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; PMCID: PMC5095171.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    17. 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. PMID: 27706880.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    18. 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; PMCID: PMC4965186.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    19. 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. PMID: 27211860; PMCID: PMC4882250.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    20. 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. PMID: 26969117; PMCID: PMC4787049.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    21. 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. PMID: 26441892; PMCID: PMC4585216.
      View in: PubMed   Mentions: 3  
    22. 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. PMID: 26054770.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    23. 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. PMID: 25880693.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    24. 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. PMID: 25863064; PMCID: PMC4390814.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    25. 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. PMID: 25564669; PMCID: PMC4311852.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    26. 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. PMID: 25437785.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    27. A mechanochemical switch to control radical intermediates. Biochemistry. 2014 Jun 17; 53(23):3830-8. Brunk E, Kellett WF, Richards NG, Rothlisberger U. PMID: 24846280; PMCID: PMC4067147.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    28. Mechanism to trigger unfolding in O(6) -alkylguanine-DNA alkyltransferase. Chembiochem. 2013 Apr 15; 14(6):703-10. Brunk E, Mollwitz B, Rothlisberger U. PMID: 23532906.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    29. 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. PMID: 23452154; PMCID: PMC3788570.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    30. 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. PMID: 22537339.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    31. 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. PMID: 22280500.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    32. 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. PMID: 21928337.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    33. 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. PMID: 22026176.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
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