Hjmegens: Created page with "Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn] Senior Researcher and lecturer at Wageningen University, Animal Breeding and Genomics Centre. '..."

2012-03-21T13:41:38Z

Created page with "Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn] Senior Researcher and lecturer at Wageningen University, Animal Breeding and Genomics Centre. '..."

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Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]

Senior Researcher and lecturer at Wageningen University, Animal Breeding and Genomics Centre.

'''Scientific interests:'''

Coming from a wet-lab background I discovered I had more talent for programming than for pipetting. I have moved into applied bioinformatics in the past 7 years, while retaining focus on my research interests:
* evolutionary genomics (generation and maintenance of, and selection on, structural and single nucleotide variation; speciation and outbreeding depression; inbreeding depression and heterosis)
* population genetics (genetic consequences of population management, domestication, selection)

'''Main current projects'''
* Genome sequencing of pig and turkey (genetic map construction, repetitive element evolution)
* Re-sequencing projects on various livestock species

We are currently sequencing >300 pigs, wild boar, and outgroup species. The project aims to elucidate major patterns in biogeography and domestication of the pig, resulting from selection and demography.

'''Procedures'''
* Main sequencing platform is Illumina (We started in 2008 on Solexa GA, to currently Illumina HiSeq).
* Depending on research questions various short-read mapping programs are used (Mosaik, BWA, BWA/Stampy, MrsFAST)
* Variant calling is done mostly by SamTools, but we are currently investigating other software (GATK).
* Functional analysis of variants (Annovar, customly scripted tools)
* Various population- and phylogenomic approaches to tackle specific questions (RAxML, Beagle, coalhmm, etc., and customly scripted tools)

'''Main programming languages:'''
* shell scripting
* Perl
* Python
* R
* SQL

Favorite distros: Fedora/CentOS

User:Hjmegens - Revision history

Hjmegens: Created page with "Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn] Senior Researcher and lecturer at Wageningen University, Animal Breeding and Genomics Centre. '..."