Nice introductory videos on DNA, Y chromosome, mitochondrial DNA and phylogeography

• The genetic code
• YChr
• mtDNA
• PhyloGeography
• Autosomal DNA

Integrating quantitative genetics and genomic in animal breeding graduate learning

Follow link bellow for a set of graduate courses funded by USDA:

• Integrating quantitative genetics and genomic in animal breeding graduate learning

“Livestock Conservation Genomics: Data, Tools and Trends“ Summer School, Croatia, Oct 1-7, 2012

There will be an ESF GENOMIC-RESOURCES (link1, link2) summer school “Livestock Conservation Genomics: Data, Tools and Trends“ Summer School, Croatia, Oct 1-7, 2012. You can find more details here.

Recently discovered study resources

• Khan Academy - a set of 2600 free videos from basic to more advances quantitative skills
• Introduction to Artifical Inteligence - Stanford on-line course for masses
• Machine Learning - Stanford on-line course for masses

ABG-HUB - Animal Breeding and Genetics Hub

Gabor Meszaros sent out today this message

Dear colleagues,

I would like to officially announce the website “Animal Breeding and Genetics Hub” we created with Gregor Gorjanc (Slovenia). The site supposed to serve as a place holding links to free animal breeding relatedsites throughout the Web.

At this point we have links to some online course materials,conference proceedings, links to ABG software sites, mailing lists, biodiversity and agricultural development resources. We also make use of the Web 2.0features such as RSS feeds, which show you the links to papers from various scientific journals in real time on one page meaning that if anew paper comesout it shows up in the RSS feed). Also there are some pictures and videos fromsome organizations, and more…

The link to the website is: http://www.netvibes.com/ABG-Hub#General

We tried to include most of our links to have some contentright at the start. But it is likely that we missed some good resources/journals out there. We would like to ask you that if you know about something that is not yet on the site, please let us know via the email: ABGHub@gmail.com

Also we would be happy to get any kind of feedback on ourwork.

onlinecourses.net

The website http://www.onlinecourses.net/ offers a nice index to online courses. The section with free courses is particularly rich.

Claim: I was asked to spread the word about this website and I believe it is worth doing it;)

"Survival Analysis - Theory and Application" course

See here.

Free copy of book by Hastie, Tibshirani, and Friedman

Hastie and Tibshirani mentioned in their course in Krems am Donau (Austria) that the last edition of their book "The Elements of Statistical Learning: Data Mining, Inference, and Prediction" will be freely available. It is true! You can fetch a free copy from Hastie's webpage (8.2 MB).

European Summer Institute in Statistical Genetics 2009

... will take place at Univeristy of Liege from Aug. 31 to Sep. 9. The Graphical model for genetics module looks particularly interesting to me, but there are also other very fine modules!

Semiparametric regression via penalized splines literature

Interested in semiparametric regression via penalized splines? Take a look here.

Video lectures about genetics (biology)

In addition to YouTube videos about genetics there is also a huge number of video lectures at http://videolectures.net/. There is a lot of material on machine learning, statistics, ..., but also biology - see Introduction to Biology which is a course from MIT. Bellow is a link to first lecture on Genetics given by Lander.

Lecture 6: Genetics 1
Eric Lander

European Master in Animal Breeding and Genetics

Posredujem novico o štipendijah za študij "European Master in Animal Breeding and Genetics". Kratek pregled predmetnikov (Course contents) na spletni strani http://www.emabg.eu pokaže, da je večina predmetov na temo genetike in selekcije na splošno in ločeno po vrstah živali, ki so pomembne za živinorejo. Je pa na voljo tudi nekaj bolj splošnih predmetov, ki bi lahko bili zelo zanimivi - psi in mačke!

Dear all
Scholarships are available for students from EU countries that want to participate in the European Master in Animal Breeding and Genetics (EMABG) starting in August 2009. Deadlines for applications: May 1st 2009. The deadline for non-EU students that want to participate in course starting this year has passed but they can applied before January 15th 2010 for the next academic year. Information on program and scholarships can be found at www.emabg.eu

The European Master in Animal Breeding is accepted by the European Union as an Erasmus Mundus MSc programme for a five-year period starting in 2007. In 2007, 24 students started the program followed by 21 students in 2008. The universities participating in the EM-ABG are Wageningen University (the Netherlands), University of Natural Resources and Applied Life Sciences (Austria), Christian-Albrechts-Universität (Germany), AgroParisTech (France), Swedish University of Agricultural Sciences (Sweden) and The Norwegian University of Life Sciences (Norway). These groups have a long tradition of collaboration and a strong profile in the area of Animal Breeding and Genetics.

For more information and application, please contact:
EM-ABG secretary, Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL 6700 AH Wageningen, The Netherlands, emabg@wur.nl

Kindest regards

Johan van Arendonk
Co-ordinator of EMABG

Course: Selección genómica

Hayes and Gianola will have a course "Selección genómica" from 25-29 May in Valencia. See here for details.

Course: Study of resistance mechanisms in animal infectious diseases course

On behalf of Anne-Sophie Lequarré:

A new session of the well quoted course "Study of resistance mechanisms in animal infectious diseases" will be held one last time at the University of Liège, Belgium from the 16 to the 20 of March 2009 .

This one-week course gives a general introduction to the methods for the identification and exploitation of genetic factors in infectious diseases. It explores the interactions between the genetic diversity of the pathogen and the host in their particular environments. The aim is to integrate the insights of the various disciplines to get a better picture of the genetic basis of resistance to major infectious diseases in livestock.

The course can interest breeders in order to optimize the production in presence of harmful pathogens, biologists to better understand the causes and consequences of co-evolution of the host and its pathogens and of course the epidemiologists.

The course will be taught at a level commensurate with a Master of Science's degree but can also serve as an elective course for researchers wishing to better understand analyses found in the scientific literature. Speakers involved are not only renown scientists but also very good teachers.

The course is supported by EADGENE, a European Network of Excellence on Animal Disease Genomics. Registration prices are quite affordable (250 Euros requested for students or academic personnel). More information can be found at (registration dead-line 15th of February):
http://www.eadgene.info/TrainingCareers/TrainingCourses/EADGENEsupportedc
ourses/StudyofResistanceMechanisms/tabid/242/Default.aspx (please copy whole link into browser or go to http://www.eadgene.info, and follow links within the Training section).

PopG genetic simulation program

Teaching the concepts of population genetics can be tedious and boring if one does not have a feeling for the meaning of the "equations" and "numbers". Students at our department always have problems with these concepts. Therefore, I bundled some R scripts in the DemoPopQuanGen package, but students have a hard time installing the package and running the demos. I guess the learning curve is too steep for the majority of the students.

It seems that the PopG genetic simulation program can do more or less anything we need for the population genetics part. From now on I will use this nice program to show the concepts and I am sure students will like this more than R. Though, it is nice to be able to do some more fancy stuff in R, but one really needs at least some feeling about the programming.

Genomic selection

Last week I have been on a course "Whole genome association and genomic selection" by Ben Hayes. Current course webpage does not (yet) provide course materials (notes and slides), but there are materials from a previous course by Ben - look here.

In a "nutshell" the course was about usage of whole genome data in order to improve (via selection of best individuals) important traits in livestock. Today, we can collect a lot (several thousands), up to 60K for cattle for example) of genotypes with "chip technologies" for a price around 200-300$. After the cleaning of the data, a researcher would estimate effect of each genotype (just additive or maybe even the dominance effect) on the phenotype of individuals. Technically, when we get the genotype data, this data do not represent the exact (functional) genes, but just markers along the whole genome. When we estimate the effect of markers, we try to exploit the possible linkage between the markers and potential genes, which are to a large extent unknown to us. Essential issue with the success of this method is that there is enough linkage disequilibrium between markers and genes. We can achieve that with dense chips. Since there has been an intense selection and strong founder effects in populations of livestock, the re is more linkage disequilibrium and the density of chips in livestock can be lower than in humans. After the estimation of markers effects, we can calculate a genotypic value for any genotyped individual. The essence of this approach has been presented in the paper by Meuwissen et al. (2001). There has been a lot of research/work done since then! There are also quite some important technical details, but this really seems to be a new very hot topic for animal breeding and genetics.

During the course I had an opportunity to disscuss with many people and there seems to be a great intereset for genomic selection in dairy cattle. This is due to the availability of dense chips for cattle and possibility of wide exploitation of semen via artifical insemination. New Zealand, Netherlands, USA are the countries which have already implemented the genomic selection and are already starting to sell the semen of young bulls. The big advantage of genomic selection in dairy cattle is in shortened generation interval. Up to now, potential bulls were preselected from best cows accounting for the breeding values of these cows and inbreeding. Then the semen of this preselected bulls would be used to produce their daughters. Then breeding values of the bulls would be estimated from the phenotypic records (milk yield) of their daughters. Well, the calculation of the breeding values accounts for all possible information from relatives, but the accuracy of breeding values is much dependent on the number of close relatives that have phenotypes. A nice description of these techniques is in the book by Mrode. There are also other books, but the book by Mrode is a very good one for the start. The process from preselecting the bull up to the calculation of breeding values can last around five years.

Besides shortened generation intervals there is also some gain in the accuracy of estimation of genetic values. Up to now animal breeders were mainly exploiting the so called infinitesimall model, where we postulate that there are infinite number of genes and that the effect of gene is negligible. This model is clearly wrong, but has been and still is a very usefull abstraction. Its use has enabled genetic improvement of many economically important traits in agriculture. Since the infinitesimall model is only an abstraction, geneticists were and are still trying hard to find genes that have an effect on various traits. There has been quite a lot of succes in this work, especially for the traits that are under the influence of only few genes. However, for the traits that are continous in the nature there have been only few genes found even though the efforts are substantial. Genomic selection now provides another abstraction. It is again an approximation, but given the abundant genomic data, there are gains in comparison to an infinitesimall model.

With genomic selection animal breeders gain a lot of flexibility and it seems that we will face changes in the organization of breeding programmes. Genomic selection is of course aplicable also for other breeding programmes: beef cattle, sheep, goats, pigs, poultry, ...

ICOTS8 Logo

I like the ICOTS8 Logo.



The description of the logo says:

"The sum of three shifted distributions forms the shape of the three headed mountain Triglav (tri=three, glav=head), the highest mountain in Slovenia and a national pride and symbol of Slovenes. The solid colors correspond to the colors of the Slovenian flag, while the green background is the color of Ljubljana and its symbol: the green dragon.

The three distributions represent students, teachers and researchers, demonstrating that learning, teaching and discovering overlap and progress in harmony."

Encyclopedia of Genetics, Genomics, Proteomics, and Informatics

Springer published new book "Encyclopedia of Genetics, Genomics, Proteomics, and Informatics". Seems great, but way to expensive for me.

Systems biology model

It is quite some time since I have found a course website by Antonio Reverter on quantitative overview of gene expression. His slides are very nice and I guess that the course must be very informative as well as fun. I simply addore his systems biology model picture, which I am shamelesly reproducing here.

Course: Animal Breeding Strategies

Course website - Animal Breeding Strategies. Seems to be related to course material I recently found (link).