174 citations · 209 across the 3 of their papers we have counts for
4 papers
Modeling DNA methylation dynamics with approaches from phylogenetics
John A. Capra, Dennis Kostka
Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates, and changes in CpG methylation are essential to cell…
motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences
Dennis Kostka, Tara Friedrich, Alisha K. Holloway +1
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if t…
Integrating diverse datasets improves developmental enhancer prediction
Genevieve D. Erwin, Rebecca M. Truty, Dennis Kostka +2
Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence…
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
John A. Capra, Melissa J. Hubisz, Dennis Kostka +2
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to v…