User:Megen002 - Revision history

Megen002 at 12:42, 7 June 2017

2017-06-07T12:42:20Z

← Older revision		Revision as of 14:42, 7 June 2017
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	'''Main programming languages:'''		'''Main programming languages:'''
	* Python		* Python
			* R
	* Linux shell scripting		* Linux shell scripting
	* Perl		* Perl (once upon a time....)
	* R
	* SQL		* SQL

Megen002 at 19:40, 18 February 2015

2015-02-18T19:40:38Z

← Older revision		Revision as of 21:40, 18 February 2015
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	'''Scientific interests:'''		'''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:		Coming from a wet-lab background I discovered I had more talent for programming than for pipetting. I have moved into applied bioinformatics since 2004, 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)		* 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)		* population genetics (genetic consequences of population management, domestication, selection)
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	* Re-sequencing projects on various livestock species		* Re-sequencing projects on various livestock species
	* Functional aspects of genome variation		* Functional aspects of genome variation
			* De novo assembly and annotation of genomes

	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.		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.

Megen002 at 19:38, 18 February 2015

2015-02-18T19:38:37Z

← Older revision		Revision as of 21:38, 18 February 2015
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	* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]		* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]

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

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

	Favorite distros: Fedora/CentOS, ~~Ubuntu~~		Favorite distros: Ubuntu, Debian, Fedora, CentOS, Raspbian

	== See also ==		== See also ==
	[[List_of_users \| List of users of the HPC Agrogenomics]]		[[List_of_users \| List of users of the HPC Agrogenomics]]

Megen002 at 15:01, 20 December 2013

2013-12-20T15:01:03Z

← Older revision		Revision as of 17:01, 20 December 2013
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	[[File:HJM.jpg\|right]]		[[File:HJM.jpg\|right]]
	* Profile on [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=4846 We@~~wur~~]		* Profile on [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=4846 We@WUR]
	* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]		* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]
	* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]		* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]

Megen002 at 15:00, 20 December 2013

2013-12-20T15:00:40Z

← Older revision		Revision as of 17:00, 20 December 2013
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	[[File:HJM.jpg\|right]]		[[File:HJM.jpg\|right]]
			* Profile on [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=4846 We@wur]
	* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]		* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]
	* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]		* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]

Megen002: /* See also */

2013-12-20T14:20:37Z

Megen002 at 14:18, 20 December 2013

2013-12-20T14:18:45Z

← Older revision		Revision as of 16:18, 20 December 2013
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	Favorite distros: Fedora/CentOS, Ubuntu		Favorite distros: Fedora/CentOS, Ubuntu

			== See also ==

Megen002: /* Hendrik-Jan Megens */

2013-12-20T10:17:04Z

Hendrik-Jan Megens

← Older revision		Revision as of 12:17, 20 December 2013
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	== Hendrik-Jan Megens ==		== Hendrik-Jan Megens ==

	[[File:~~http://scholar~~.~~google.nl/citations?view_op=view_photo&user=kGUIXOYAAAAJ&citpid=1200px~~\|right]]		[[File:HJM.jpg\|right]]
	* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]		* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]
	* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]		* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]

Megen002: /* Hendrik-Jan Megens */

2013-12-20T10:11:44Z

Hendrik-Jan Megens

← Older revision		Revision as of 12:11, 20 December 2013
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	== Hendrik-Jan Megens ==		== Hendrik-Jan Megens ==

			[[File:http://scholar.google.nl/citations?view_op=view_photo&user=kGUIXOYAAAAJ&citpid=1200px\|right]]
	* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]		* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn]
	* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]		* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar]

Megen002 at 11:36, 11 December 2013

2013-12-11T11:36:07Z

← Older revision		Revision as of 13:36, 11 December 2013
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	'''Main current projects'''		'''Main current projects'''
	* Genome sequencing of pig and turkey ~~(genetic map construction, repetitive element evolution)~~		* Genome sequencing of pig and turkey.
	* Re-sequencing projects on various livestock species		* Re-sequencing projects on various livestock species
			* Functional aspects of genome variation

	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.		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.
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	* Main sequencing platform is Illumina (We started in 2008 on Solexa GA, to currently Illumina HiSeq).		* 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)		* 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).		* Variant calling (Samtools, GATK).
	* Functional analysis of variants (Annovar, customly scripted tools)		* 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)		* Various population- and phylogenomic approaches to tackle specific questions (RAxML, Beagle, coalhmm, etc., and customly scripted tools)

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

	Favorite distros: Fedora/CentOS		Favorite distros: Fedora/CentOS, Ubuntu

← Older revision		Revision as of 16:20, 20 December 2013
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	== See also ==		== See also ==
			[[List_of_users \| List of users of the HPC Agrogenomics]]