[BBC] Fwd: Still some seats available for BioSB Course Comparative Genomics: from evolution to function - November 21-25, 2016 in Nijmegen

[Celia van Gelder]

*BioSB Course Comparative Genomics: from evolution to function
(3rd edition) *
*Date:* November 21-25, 2016
*Location*: CMBI, Radboudumc, Nijmegen, the Netherlands
*Course coordinators:*  Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap
Heringa (VU),  Celia van Gelder (BioSB)
*Course website*: http://biosb.nl/education/course-portfolio/
course-comparative-genomics/
*Registration:* http://biosb.nl/education/course-portfolio/
enrollment-comparative-genomics-from-evolution-to-function-course-2016/
*More information*: education at biosb.nl


*Course description*
Comparative genomics between species and between types of data facilitates
the understanding of what these data really reflect about the underlying
biological processes. Comparative genomics therewith relies on a solid
understanding of basic elements of Bioinformatics like homology and
orthology. Moreover it is important to know the assumptions and heuristics
of bioinformatic methods for comparative genomics and hence we aim to let
participants develop an understanding of why these methods sometimes fail
(or misdetect) as a consequence of a variety of biological /evolutionary
causes, and in which situations which method is most appropriate. The first
two days of the course provide a basis for the course with the aim to move
“beyond blast” in terms of the most sensitive homology searches, domain
level analysis of protein evolution as well as more fine grained
definitions of relatedness as can be obtained from the proper
interpretation of gene trees (i.e. various levels of orthology). This
foundation is used to discuss in the three following days in more detail
three topics: (1) the study of functional and evolutionary consequence of
(genome) duplications, (2) the evolution of interactions and complexes and
(3) the prediction and evolution of genomic regulatory elements and of RNA
structures

*Target audience*

The course is intended for PhD students and master students in
bioinformatics or geneticists and experimental biologists with a strong
interest in evolution of the eukaryotes. It is especially relevant to
students who want to compare various types of genomics data between
species. Participants are expected to have some hands on experience with
tools like blast, constructing multiple sequence alignments and
phylogenetic trees, and in addition to have some familiarity with concepts
such as orthology, synteny and protein domains.

*Programme*

*Monday November 21: Distant homology and protein domains (lecturer Jaap
Heringa)*
Topics & Tools: Divergent and convergent evolution, (multiple) sequence
alignment, psiblast, jackhmmer, hhsearch, pfam, homology and function,
undetected orthology from failure to detect homology, paralogs and function
specificity prediction


*Tuesday Nov 22: Small scale orthology and large scale databases (lecturers
Martijn Huynen, Berend Snel)*Topics & Tools: tree reconciliation, relation
between homology and orthology, ensembl compara, COGs, inparalogs vs
outparalogs, fusion and fission

*Wednesday Nov 23: Comparative Interactomics (lecturers Jaap Heringa,
Martijn Huynen/John van Dam)*
Topics & Tools: network alignment, phylogenetic profiles, biogrid,
cytoscape, Bayesian data integration, neofunctionalization vs
subfunctionalization

*Thursday Nov 24 : Genome duplications (lecturer Berend Snel)*
Topics & Tools: yeast gene order browser, synteny, consequences of genome
duplications, timing of duplications, ensembl biomart

*Friday Nov 25: Finding functional elements in DNA and RNA sequences,
Biased gene conversion (lecturer Martijn Huynen)*
Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs
sampling, RNA secondary structure prediction based on sequences and on
experimental data, biased gene conversion & positive selection.

*BioSB Education Programme*

This course is part of the Education Programme of BioSB, the Netherlands
Bioinformatics and Systems Biology research school, which offers training
and education for in bioinformatics and systems biology.
More information about BioSB can be found at www.biosb.nl.

*More information*

For more information about the course you can contact Celia van Gelder
at *education at biosb.nl
<education at biosb.nl>*.







-- 

Dr. Celia W.G. van Gelder

Programme Manager Learning DTL/ELIXIR-NL Training
Education Manager BioSB

tel. +31613375327
e-mail: celia.van.gelder at dtls.nl
websites:  www.dtls.nl, www.biosb.nl
skype: celia.van.gelder

Postal address:
DTL
PO Box 19245
3501 DE Utrecht
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