Search Results - "Deatherage, Daniel E"

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq by Deatherage, Daniel E, Barrick, Jeffrey E

“…Next-generation DNA sequencing (NGS) can be used to reconstruct eco-evolutionary population dynamics and to identify the genetic basis of adaptation in…”
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Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq by Barrick, Jeffrey E, Colburn, Geoffrey, Deatherage, Daniel E, Traverse, Charles C, Strand, Matthew D, Borges, Jordan J, Knoester, David B, Reba, Aaron, Meyer, Austin G

“…Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in…”
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Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria by Zhang, Xue, Deatherage, Daniel E., Zheng, Hao, Georgoulis, Stratton J., Barrick, Jeffrey E.

“…Transmissible plasmids spread genes encoding antibiotic resistance and other traits to new bacterial species. Here we report that laboratory populations of…”
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Epigenetic Repression of microRNA-129-2 Leads to Overexpression of SOX4 Oncogene in Endometrial Cancer by HUANG, Yi-Wen, LIU, Joseph C, DEATHERAGE, Daniel E, JINGQIN LUO, MUTCH, David G, GOODFELLOW, Paul J, MILLER, David S, HUANG, Tim H-M

“…Genetic amplification, mutation, and translocation are known to play a causal role in the upregulation of an oncogene in cancer cells. Here, we report an…”
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Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli by Quandt, Erik M., Deatherage, Daniel E., Ellington, Andrew D., Georgiou, George, Barrick, Jeffrey E.

“…Evolutionary innovations often arise from complex genetic and ecological interactions, which can make it challenging to understand retrospectively how a novel…”
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Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli by Raeside, Colin, Gaffé, Joël, Deatherage, Daniel E, Tenaillon, Olivier, Briska, Adam M, Ptashkin, Ryan N, Cruveiller, Stéphane, Médigue, Claudine, Lenski, Richard E, Barrick, Jeffrey E, Schneider, Dominique

“…Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point…”
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Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq by Deatherage, Daniel E, Traverse, Charles C, Wolf, Lindsey N, Barrick, Jeffrey E

“…New mutations leading to structural variation (SV) in genomes-in the form of mobile element insertions, large deletions, gene duplications, and other…”
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Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells by Weng, Yu-I, Hsu, Pei-Yin, Liyanarachchi, Sandya, Liu, Joseph, Deatherage, Daniel E., Huang, Yi-Wen, Zuo, Tao, Rodriguez, Benjamin, Lin, Ching-Hung, Cheng, Ann-Lii, Huang, Tim H.-M.

“…Substantial evidence indicates that exposure to bisphenol A (BPA) during early development may increase breast cancer risk later in life. The changes may…”
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Xenoestrogen-Induced Epigenetic Repression of microRNA-9-3 in Breast Epithelial Cells by HSU, Pei-Yin, DEATHERAGE, Daniel E, RODRIGUEZ, Benjamin A. T, LIYANARACHCHI, Sandya, WENG, Yu-I, TAO ZUO, LIU, Joseph, CHENG, Alfred S. L, HUANG, Tim H-M

“…Early exposure to xenoestrogens may predispose to breast cancer risk later in adult life. It is likely that long-lived, self-regenerating epithelial progenitor…”
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Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping by Hsu, Pei-Yin, Hsu, Hang-Kai, Singer, Gregory A C, Yan, Pearlly S, Rodriguez, Benjamin A T, Liu, Joseph C, Weng, Yu-I, Deatherage, Daniel E, Chen, Zhong, Pereira, Julia S, Lopez, Ricardo, Russo, Jose, Wang, Qianben, Lamartiniere, Coral A, Nephew, Kenneth P, Huang, Tim H-M

“…The current concept of epigenetic repression is based on one repressor unit corresponding to one silent gene. This notion, however, cannot adequately explain…”
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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 by Bazurto, Jannell V, Riazi, Siavash, D'Alton, Simon, Deatherage, Daniel E, Bruger, Eric L, Barrick, Jeffrey E, Marx, Christopher J

“…The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as…”
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Tempo and mode of genome evolution in a 50,000-generation experiment by Tenaillon, Olivier, Barrick, Jeffrey E., Ribeck, Noah, Deatherage, Daniel E., Blanchard, Jeffrey L., Dasgupta, Aurko, Wu, Gabriel C., Wielgoss, Sébastien, Cruveiller, Stéphane, Médigue, Claudine, Schneider, Dominique, Lenski, Richard E.

“…Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations…”
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ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer by Kennedy, Brian A, Deatherage, Daniel E, Gu, Fei, Tang, Binhua, Chan, Michael W Y, Nephew, Kenneth P, Huang, Tim H-M, Jin, Victor X

“…Deregulation of the transforming growth factor-β (TGFβ) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying…”
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Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures by Deatherage, Daniel E., Kepner, Jamie L., Bennett, Albert F., Lenski, Richard E., Barrick, Jeffrey E.

“…Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To…”
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Aberrant TGFβ/SMAD4 signaling contributes to epigenetic silencing of a putative tumor suppressor, RunX1T1 in ovarian cancer by Yeh, Kun-Tu, Chen, Tze-Ho, Yang, Hui-Wen, Chou, Jian-Liang, Chen, Lin-Yu, Yeh, Chia-Ming, Chen, Yu-Hsin, Lin, Ru-Inn, Su, Her-Young, Chen, Gary C.-W., Deatherage, Daniel E., Huang, Yi-Wen, Yan, Pearlly S., Lin, Huey-Jen, Nephew, Kenneth P., Huang, Tim H.-M., Lai, Hung-Cheng, Chan, Michael W.Y.

“…Aberrant TGFβ signaling pathway may alter the expression of down-stream targets and promotes ovarian carcinogenesis. However, the mechanism of this impairment…”
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Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates by Deatherage, Daniel E, Leon, Dacia, Rodriguez, Álvaro E, Omar, Salma K, Barrick, Jeffrey E

“…Abstract Unwanted evolution of designed DNA sequences limits metabolic and genome engineering efforts. Engineered functions that are burdensome to host cells…”
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Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host by Rodríguez-Pastor, Ruth, Knossow, Nadav, Shahar, Naama, Hasik, Adam Z, Deatherage, Daniel E, Gutiérrez, Ricardo, Harrus, Shimon, Zaman, Luis, Lenski, Richard E, Barrick, Jeffrey E, Hawlena, Hadas

“…Parasites, including pathogens, can adapt to better exploit their hosts on many scales, ranging from within an infection of a single individual to series of…”
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High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing by Deatherage, Daniel E, Barrick, Jeffrey E

“…Understanding how cells are likely to evolve can guide medical interventions and bioengineering efforts that must contend with unwanted mutations. The adaptome…”
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Promoter hypermethylation of FBXO32, a novel TGF-β/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer by Chou, Jian-Liang, Su, Her-Young, Chen, Lin-Yu, Liao, Yu-Ping, Hartman-Frey, Corinna, Lai, Yi-Hui, Yang, Hui-Wen, Deatherage, Daniel E, Kuo, Chieh-Ti, Huang, Yi-Wen, Yan, Pearlly S, Hsiao, Shu-Huei, Tai, Chien-Kuo, Lin, Huey-Jen L, Davuluri, Ramana V, Chao, Tai-Kuang, Nephew, Kenneth P, Huang, Tim H-M, Lai, Hung-Cheng, Chan, Michael W-Y

“…Resistance to TGF-β is frequently observed in ovarian cancer, and disrupted TGF-β/SMAD4 signaling results in the aberrant expression of downstream target genes…”
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Epigenetic Silencing Mediated through Activated PI3K/AKT Signaling in Breast Cancer by TAO ZUO, LIU, Ta-Ming, TASLIM, Cenny, RAMASWAMY, Bhuvaneswari, SHAPIRO, Charles L, LIN, Huey-Jen L, CHENG, Alfred S. L, JIN, Victor X, HUANG, Tim H.-M, XUN LAN, WENG, Yu-I, SHEN, Rulong, FEI GU, HUANG, Yi-Wen, LIYANARACHCHI, Sandya, DEATHERAGE, Daniel E, HSU, Pei-Yin

“…Trimethylation of histone 3 lysine 27 (H3K27me3) is a critical epigenetic mark for the maintenance of gene silencing. Additional accumulation of DNA…”
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