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The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
Related publications (42)
Inferring the age and strength of mutations evolving under positive selection
A fundamental goal of population genetics is to determine and quantify the interplay of mutation, natural selection, genetic drift and migration in shaping allelic frequency changes that underpin evolution-ary change. In this dissertation, I present comput ...
EPFL2017The evolution of gene expression and binding specificity of the largest transcription factor family in primates
Didier Trono, Jeffrey David Jensen, Adamantia Kapopoulou, Lisha Mathew
The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for the great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fractio ...
Wiley-Blackwell2016An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data
Jeffrey David Jensen, Anna Ferrer Admetlla
The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional informat ...
Genetics Society America2016The Impact of Linked Selection in Chimpanzees: A Comparative Study
Jeffrey David Jensen, Susanne Petra Pfeifer
Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the ...
Oxford University Press (OUP)2016Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856
Tobias Johannes Schmid, Roel Paulus Josephus Bevers
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have gener ...
2015Models and Algorithms for Comparative Genomics
The deluge of sequenced whole-genome data has motivated the study of comparative genomics, which provides global views on genome evolution, and also offers practical solutions in deciphering the functional roles of components of genomes. A fundamental comp ...
EPFL2015Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces
Ricardo Cesar Guerrero Ferreira, Nikolai Prokhorov
We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96 % nucleotide sequence identity and can thus be considered representat ...
Springer Wien2015Genome-wide patterns of adaptation to climate-mediated selective pressures in sheep
Sheep (Ovis aries) have been well adapted to thrive in a diverse range of climates during the domestication and breed development process. These climate-mediated selective pressures have shown to influence phenotypic variation within and among breeds and, ...
2014Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families
In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...
Public Library of Science2014Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
Bart Deplancke, Andreas Massouras, Sandy Lee, Yi Han, Yiming Zhu
The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used a ...
Cold Spring Harbor Laboratory Press2014