Preliminary programme

Saturday (16.09)
16:30-21           Trip from Warsaw Chopin Airport to Białowieża
21:00                 Welcome reception

Sunday (17.09)

10:15-10:30    Welcome and opening of Third PEB meeting
10:30-11:15    opening lecture, Bogdan Jaroszewicz Białowieża Forest – an unique natural lab of biological sciences
11:15-12:00    plenary talk, Mark Blaxter “There’s a bug in my genome!” – new tools for assembly and annotation of genomes from neglected organisms.
12:00-12:20    coffee break
12:20-12:40    Ana Lokmer: Protists in the gut – our lost friends? (Using metagenomic data to examine the effect of protists on the gut microbiota)
12:40-13:00    Szymon Drobniak MHC vs. gut microbiota in birds: a draft of a research project
13:00-13:15    Sponsor’s talk. Bartłomiej Drop (LabJot): NEBNext: Library Preparation for Next Generation Sequencing
13:15-14:30    lunch
15:00- 18:00   excursion to the Strict Reserve
after 18:30     bioinfo stock exchange
20:00               dinner

Monday (18.09)

10:00-10:45     plenary talk, Stuart JE Baird: Compression population genomics
10:45-11:20     coffee break
11:20-11:40     Claudius Kerth: The history of a hybrid zone
11:40-12:00    Maria Luisa Martin Cerezo European phylogeography of Apodemus flavicollis and Apodemus sylvaticus using ddRADseq.
12:00-12:20     Agnieszka Kloch Evolution of the components of the immune system in the wild: role for intronic variance
12:20-13:30    bioinfo stock exchange
13:30-14:30     lunch break
14:30-16:30     pararell workshops: Przemek Biecek: ggplot / Olek Michalski: Data manipulation in R
16:30-17:00     coffee break
17:00-19:00     pararell workshops: Przemek Biecek: ggplot / Olek Michalski: Data manipulation in R
19:00               dinner /

Tuesday (19.09)

10-10:45          plenary talk, Katja Nowick KRAB-ZNF and lncRNA genes as potential drivers of the evolution of species and phenotypic innovations
10:45-11:20     coffee break
11:20-11:40     Alvaro Perdomo-Sabogal A landscape of positively selected gene regulatory factors in three human populations
11:40-12:00     Carlos Garcia Network analysis of inbreeding depression in Drosophila melanogaster
12:00-12:20     Hollie Marshall The Role of Methylation in the Reproductive Status of Bumblebee Workers
12:20-12:40     Marina Silva From Palaeolithic foragers to Bronze Age conquerors
12:40-14:00     lunch break
14:00-16:00    workshop: Claudius Kerth, Unix for bioinformatics
16:00-19:00     bioinfo stock exchange
19:30                gala dinner

Wednesday (20.09)

9:30-14:00    Coming back to Warsaw

Plenary talks

Mark Blaxter
Mark Blaxter
Mark studies genomics of nematodes and other, less popular species, such as Tardigrates. He is the right person to ask when you struggle with assembling a genome of absolutely non-model species.

“There’s a bug in my genome!” – new tools for assembly and annotation of genomes from neglected organisms.

The ever decreasing cost of generating raw genome sequence data has opened out genomics to a very wide audience. However, with great power comes great responsibility, and working on organisms that have been isolated from the wild, that are not inbred, and that are not very big, means that extra caution has to be taken in genome assembly and analysis. In particular, wild caught and small organisms are intimately associated with a microbiome – the bacteria, archaea, fungi, protozoans and other organisms that live in or on the species of interest. Further genomes can be introduced during sample processing (including human contamination). It is essential that sequences from these organisms are not mistakenly incorporated into the genome estimate for the target species, as they will result in erroneous claims of acquisition of new genes and new functions by horizontal gene transfer. We aim to identify and isolating sequences from different organisms early in the genome assembly and annotation process, so that the “true” genome of the target species can be identified, and also so that we understand, partially, the microbiome it is associated with. To do this, we have developed a series of tools for screening primary genome data to identify contaminants and cobionts, and tools to interrogate genes to affirm their origins. I will illustrate this with the instructive tale of the tardigrade Hypsibius dujardini, which, despite first announcements, has a rather normal genome, and our analyses of nematode genomes.

Katja Nowick, University of Leipzig
KatjaKatja studies primates, H. sapiens included, and she is particularly interested in the role of transcription factors.




KRAB-ZNF and lncRNA genes as potential drivers of the evolution of species and phenotypic innovations

Understanding the molecular basis of species evolution and the evolution of phenotypic innovations is a fascinating endeavor. Fast evolving genes and gene regulatory differences are among the hottest factors discussed for driving such evolutionary changes. I will introduce two families of genes that are both, fast evolving and involved in gene regulation, namely genes coding for KRAB-ZNF proteins and for long non-coding RNAs (lncRNAs).
KRAB-ZNFs are transcription factors with Krüppel-type zinc finger domains and a Krüppel-associated box. They are regulating genes involved in developmental processes, brain functions, the immune system, and probably an array of other functions, so that molecular changes in KRAB-ZNF genes can create phenotypic differences related to these functions. We have recently proposed that they can also create hybrid incompatibilities, thus drive speciation. In addition, they have been shown to suppress endogenous retroviruses, with which they seem to battle an evolutionary arms race. I will present how we currently investigate evolutionary functional differences between great ape KRAB-ZNF genes.
LncRNAs represent a recently discovered and largely unexplored family of molecules. There are more lncRNA genes than genes coding for proteins. It is currently unknown, how many lncRNAs are functional, but at least for some lncRNAs their secondary structure is key for determining their function. With this in mind, we developed a framework for testing whether a lncRNA is evolving under positive or negative selection. This test can provide candidates for further functional studies to discover the role of lncRNAs in the evolution of species and phenotypic innovations.

Stuart J.E. Baird, Czech Academy of Sciences
StuartStuart is interested in many aspects of evolutionary genetics, and his particular interest is what happens in a hybrid zone.




Data visualisation in R using ggplot2

Przemysław Biecek, University of Warsaw / Warsaw Technical University
PrzemekPrzemek is an R enthusiast, he uses R for his research, he develops packages, and the loves teaching R.



Data manipulation in R

Olek Michalski,
You get along with R but you’re still using Excell/Calc to create a pivot table or when you need to quickly create a new column in the dataframe that combines some other columns from your data? This workshop is right for you.


Advanced Unix for Bioinformatics

Claudius Kerth, Univeristy of Sheffield

If you have any suggestion of a workshop, please let us know using the contact form.