Ants, Bees, Genomes & Evolution @ Queen Mary University London

Teaching: Data Science, Bioinformatics & Evolutionary Genomics

Courses Yannick has taught on include: Evolution, Ecological and Evolutionary Genomics, Genome Bioinformatics, Research Frontiers, Research Methods.

Much of the material we use is QMUL's QMPlus content management system. Some of is also on GitHub or below.

Genome Bioinformatics (Masters)

This module from the QMUL's Bioinformatics MSc covers the essential aspects of next generation sequence analysis, including genome assembly, variant calling and population genetics. Also covers essential computer skills needed for bioinformatics, such as Linux and using our high performance computing cluster.

Learning how to program in R

As biology is becoming a data science its increasingly important to be able to wrangle large datasets. We use variations of the following for QMUL's SBC361 (3rd year Research Methods) and Bio781p (MSc Statistics & Bioinformatics):

Some older stuff

Bioinformatics & Population Genomics

Practicals prepared with Rodrigo Pracana, Julien Roux, Rob Waterhouse and Stefan Schiffels for a 1 week Bioinformatics & Population Genomics course. [Overview slides]. We use similar material for QMUL’s Bioinformatics MSc and our Ecological and Evolutionary Genomics MSc:

Ecological and Evolutionary Genomics

Our students did some great blogging.

2016: Ecoevo @ Wordpress

2015: SBC322 @ Winnower

2014: QMEcoEvoGenomics @ Wordpress


1st year introduction (part of QMUL's BIO113):

2006-2010 stuff from Uni Lausanne:

  • Introduction to microarray analysis: Three hour practical for 3rd year Biology students. Download normalized affimterix data, blindly use Limma to find significant genes, cluster them with TMEV, conduct GO analysis of one cluster… conclude about confounding factors in experimental design.
  • Introduction to BLAST: Two hour practical for 2nd year biology students. Calculate score & evalue of an alignment by hand… compare with true Blast results obtained on NCBI, see that blastp and blastn have different sensitivities. Check some new NCBI blast features.

Semester programming projects: