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High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing.

Deatherage DE, Barrick JE. Deatherage DE, et al. Cell Syst. 2021 Dec 15;12(12):1187-1200.e4. doi: 10.1016/j.cels.2021.08.011. Epub 2021 Sep 17. Cell Syst. 2021. PMID: 34536379

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Methylation analysis by microarray.

Deatherage DE, Potter D, Yan PS, Huang TH, Lin S. Deatherage DE, et al. Methods Mol Biol. 2009;556:117-39. doi: 10.1007/978-1-60327-192-9_9. Methods Mol Biol. 2009. PMID: 19488875 Free PMC article.

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Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates.

Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE. Deatherage DE, et al. Nucleic Acids Res. 2018 Sep 28;46(17):9236-9250. doi: 10.1093/nar/gky751. Nucleic Acids Res. 2018. PMID: 30137492 Free PMC article.

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Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition.

Bazurto JV, Riazi S, D'Alton S, Deatherage DE, Bruger EL, Barrick JE, Marx CJ. Bazurto JV, et al. Among authors: deatherage de. Microorganisms. 2021 Feb 10;9(2):347. doi: 10.3390/microorganisms9020347. Microorganisms. 2021. PMID: 33578755 Free PMC article.

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Tempo and mode of genome evolution in a 50,000-generation experiment.

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE. Tenaillon O, et al. Among authors: deatherage de. Nature. 2016 Aug 11;536(7615):165-70. doi: 10.1038/nature18959. Epub 2016 Aug 1. Nature. 2016. PMID: 27479321 Free PMC article.

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Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria.

Zhang X, Deatherage DE, Zheng H, Georgoulis SJ, Barrick JE. Zhang X, et al. Among authors: deatherage de. Nat Commun. 2019 Dec 20;10(1):5809. doi: 10.1038/s41467-019-13709-x. Nat Commun. 2019. PMID: 31863068 Free PMC article.

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Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures.

Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE. Deatherage DE, et al. Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1904-E1912. doi: 10.1073/pnas.1616132114. Epub 2017 Feb 15. Proc Natl Acad Sci U S A. 2017. PMID: 28202733 Free PMC article.

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Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.

Deatherage DE, Barrick JE. Deatherage DE, et al. Methods Mol Biol. 2014;1151:165-88. doi: 10.1007/978-1-4939-0554-6_12. Methods Mol Biol. 2014. PMID: 24838886 Free PMC article.

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Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer.

Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH. Zuo T, et al. Among authors: deatherage de. Cancer Res. 2011 Mar 1;71(5):1752-62. doi: 10.1158/0008-5472.CAN-10-3573. Epub 2011 Jan 7. Cancer Res. 2011. PMID: 21216892 Free PMC article.

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Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D. Raeside C, et al. Among authors: deatherage de. mBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14. mBio. 2014. PMID: 25205090 Free PMC article.

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