Milí kolegové a kolegyně,
chtěli bychom vás srdečně pozvat na další přednášku semináře, která se
koná již zítra, tj. ve středu 20.12.2017, od 17:20 v posluchárně S4.
Hostem na semináři bude Tomáš Gavenčiak z MFF UK a téma přednášky bude
Genotype refinement with PBWT
Těšíme se srdečně na vaši účast!
Za všechny organizátory semináře s pozdravem,
Petr Daněček
Stránky semináře
http://bioinformatika.mff.cuni.cz/seminar/
--------------------------------------
Tomáš Gavenčiak
Genotype refinement with PBWT
Genotype refinement is one of the latest phases of the genome
sequencing process. It is used to infer the most likely genotype from
the observed genotype likelihoods and is usually followed by variant
phasing. Most of the state-of-the-art approaches for these steps
use population data as a reference, modeling recombinations
and population inheritance using the Li-Stephens model. The
problems are usually stated as Hidden Markov Models.
However, direct computation of these HMMs is very costly and
faster methods are needed.
After a brief introduction to the field and the Li-Stephens model,
I will introduce some algorithms based on PBWT used to
accelerate the computation. I will described the Hap-hedge
structure which was developed by the Eagle2 phasing software
and show a modified approach which can be extended to the
problem of genotype refinement, which is the main subject of
my current work.
Milí kolegové a kolegyně,
chtěli bychom vás srdečně pozvat na další přednášku semináře, která se
koná tuto středu 6.12.2017, od 17:20 v posluchárně S4.
Hostem na semináři bude Audrey Lin z University of Oxford, UK,
a téma přednášky bude
Rates of evolutionary change in ancient domesticated animals
Těšíme se srdečně na vaši účast!
Za všechny organizátory semináře s pozdravem,
Petr Daněček
Stránky semináře
http://bioinformatika.mff.cuni.cz/seminar/
--------------------------------------
Speaker: Audrey Lin
Title: Rates of evolutionary change in ancient domesticated animals
Abstract: The molecular clock hypothesis is described as the
accumulation of nucleotide substitutions at a constant rate over time.
This rate can then be used to estimate divergence times between
sequences. However, in reality, molecular clocks do not “tick”
consistently over time and instead, there is a measurable continuous
transition from an increased, short-term mutation rate to a slow, long-
term substitution rate.
The hypothesis of time-dependency in molecular evolution states that
the rate of observable evolution varies depending on the timeframe over
which the rate is measured. To test this hypothesis, I use high-quality
mitochondrial genomes of direct-dated domesticated and wild animals.
This study may yield interesting observations on the evolutionary
dynamics regarding the genetic processes of domestication
within and between the different animal populations of study, as well
as improve fossil calibration of current molecular clock models.