Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq

DE Deatherage, JE Barrick - Engineering and analyzing multicellular …, 2014 - Springer
… NGS technologies can be used for RNA-seq transcriptomics, the de novo assembly of
non-model organism genomes, and characterizing epigenetic DNA modifications, among many …

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

O Tenaillon, JE Barrick, N Ribeck, DE Deatherage… - Nature, 2016 - nature.com
Adaptation by natural selection depends on the rates, effects and interactions of many
mutations, making it difficult to determine what proportion of mutations in an evolving lineage are …

Epigenetic Repression of microRNA-129-2 Leads to Overexpression of SOX4 Oncogene in Endometrial Cancer

YW Huang, JC Liu, DE Deatherage, J Luo, DG Mutch… - Cancer research, 2009 - AACR
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 emerging role of microRNA, the …

[HTML][HTML] Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

JE Barrick, G Colburn, DE Deatherage, CC Traverse… - BMC genomics, 2014 - Springer
… A final strategy for predicting SV is to perform de novo assembly of the sequencing reads
and then map the resulting contigs back to the reference genome to find discrepancies …

Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells

…, PY Hsu, S Liyanarachchi, J Liu, DE Deatherage… - Toxicology and applied …, 2010 - Elsevier
Substantial evidence indicates that exposure to bisphenol A (BPA) during early development
may increase breast cancer risk later in life. The changes may persist into puberty and …

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

C Raeside, J Gaffé, DE Deatherage, O Tenaillon… - MBio, 2014 - Am Soc Microbiol
Large-scale rearrangements may be important in evolution because they can alter chromosome
organization and gene expression in ways not possible through point mutations. In a …

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

DE Deatherage, JL Kepner… - Proceedings of the …, 2017 - National Acad Sciences
Isolated populations derived from a common ancestor are expected to diverge genetically
and phenotypically as they adapt to different local environments. To examine this process, 30 …

[HTML][HTML] Promoter hypermethylation of FBXO32, a novel TGF-β/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer

…, YH Lai, HW Yang, DE Deatherage… - Laboratory …, 2010 - Elsevier
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 in the disease. Our …

Xenoestrogen-Induced Epigenetic Repression of microRNA-9-3 in Breast Epithelial Cells

PY Hsu, DE Deatherage, BAT Rodriguez… - Cancer research, 2009 - AACR
… This programmed repression during epithelial differentiation leads to an increased
susceptibility to stochastic de novo methylation, which in turn may act as “seeds” to trigger more …

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

EM Quandt, DE Deatherage… - Proceedings of the …, 2014 - National Acad Sciences
Evolutionary innovations often arise from complex genetic and ecological interactions, which
can make it challenging to understand retrospectively how a novel trait arose. In a long-…