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


November 21-25, 2016


Radboud umc, CMBI, Nijmegen, the Netherlands
Address: Geert Grooteplein Zuid 26-28, 6525 GA  Nijmegen, route 260 (ground floor)
Route description

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 Anton Feenstra)
Topics & Tools: Divergent and convergent evolution, homology and function, paralogs and function specificity prediction, neofunctionalization vs subfunctionalization, detection of subfamily- and function-specific residues

Tuesday Nov 22: Small scale orthology and large scale databases (lecturer Martijn Huynen)
Topics & Tools: relation between homology and orthology, COGs, inparalogs vs outparalogs, fusion and fission, psiblast, jackhmmer, hhsearch, undetected orthology from failure to detect homology

Wednesday Nov 23: Comparative Interactomics (lecturers Jaap Heringa)
Topics & Tools: (multiple) sequence alignment, network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration,

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

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

Daily time schedule

The daily time schedule varies depending on the agenda of the teaching staff, most of the days we will stick to the following schedule.

09:00-10:30 lectures
10.30-11.00 coffee break
11.00-12.30 computer excercises
12:30-13:15 lunch
13.15-15.15 computer excercises
15.15-15.30 coffee/tea break
15.30-16.30 preparation of the literature discussion
16.30-17.00 literature discussion

There will be drinks on Monday November 21st at the end of the course day, so we will stop with the computer exercises 15 minutes earlier.


Papers will be sent to the participants before the course. You are strongly advised to read the papers before the start of the course. On each day we will discuss one set of papers. Each participant will be assigned a Figure to discuss & explain to the rest of the audience.


Registration for the course is closed.

Links to previous editions