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

Date: November 21-25, 2016
Location: Radboudumc, Nijmegen, the Netherlands

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.

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

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

Daytime schedule
09:00-10:30   lectures
10.30-11.00   coffee break
11.00-12.00   discussion preparation
12.00-12.30   discussion and evaluation
12:30-13:30   lunch
13:30-16:30   computer exercises and wrap-up

Details can be found at
Please register here