BioSB Course Comparative Genomics: from evolution to function (3rd edition)

November 21-25, 2016

CMBI, Radboudumc, Nijmegen, the Netherlands

Course coordinators:
Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU),  Celia van Gelder (BioSB)

Course website:


More information:
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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.

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

More information:
For more information about the course you can contact Celia van Gelder at
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