Nowick Lab

We are currently running our fifth “Programming for Evolutionary Biology” course in Leipzig. We are taking the students of our course on a tour on analyzing Next-Generation-Sequencing data, genome annotation, population genomics, phylogenomics, gene expression evolution, biological networks, and other topics, while teaching how to work with Unix systems and programming in R and Python.

Our paper on the evolution of binding sites of the transcription factor GABPa has been accepted for publication in MBE. This work was originally started by Robert Querfurth at the Max-Planck-Institute for Molecular Genetics in Berlin. Alvaro and I got excited about this project and happily accepted to get involved in it.

In this work we identified binding sites of GABPa by ChIP-Seq and then used a comparative genomics approach to determine which binding sites are human specific. Interestingly, many of these sites were found to be significantly enriched near genes important for the brain and central nervous system, but also for other functions, such as breast development and energy metabolism, which might provide some clues for the evolution of functions and phenotypes that are unique to humans. Our work received some attention in the international press.

This nice figure was painted by Manjusha Chintalapati as a suggestion for a cover figure.

When we started writing this paper we were inspired by the debate about the question of how much of the human genome is functional. Estimates for that proportion range from 5% to 90%, a huge difference that obviously cannot be reconciled by more data. We think that this difference rather reflects diversity in the conception of what function is. We start by discussing examples of biological functions that are not covered by any of the common definitions of function and end by arguing that any biological meaningful interpretations of function depend on the specific theoretical and measurement context.

Laubichler_TheoryBioscience
Manfred D. Laubichler · Peter F. Stadler · Sonja J. Prohaska · Katja Nowick

Registration just opened for the 4th Programming for Evolutionary Biology course. Based on our very successful previous courses we again put together a comprehensive program for learning programming skills to perform analysis of genomics and evolutionary data. Check out our curriculum for 2015 and why to apply for our course. And don’t forget the most important reason for coming to our course: It’s a lot of fun!

Our local newspaper published an article about us and two more research groups who received together over one million Euro to investigate the functions of long non-coding RNAs in the human nervous system. Our main goal is to understand how these RNAs contributed to the evolution of the human brain.

Many greetings from Bogota, where we are currently holding our first Programming for Evolutionary Biology course in the Americas. Clara Isabel Bermúdez Santana and her TAs Cristian, Alejandro, and Diego, as well as her students from the Universidad Nacional de Colombia are super welcoming hosts for us!

Aida Andres and I have put together a special journal issue with papers on human evolution for the journal Current Opinion in Genetics & Development. Inviting the authors for 19 articles, editing, and coordinating this special issue has been an exciting experience and I’m happy to see that our special issue is now published. Please enjoy a fascinating collection of papers. You can find a summary of all papers in our Editorial.

Thanks a lot to everybody who has contributed to this issue!

In our paper Hoehe et al. on “Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes” published in Nature Communications we describe the extent of sequence variation that exists between the two alleles of human individuals. Surprisingly, many genes in our genome harbor sequence variants that can manifest in the amino acid sequence, thus increase the repertoire of proteins that can be expressed in human cells.

This project was lead by Dr. Margret Hoehe from the Max-Planck-Institute for Molecular Genetics in Berlin, Germany.

When we compared the secondary structures of the non-coding RNA HAR1 between primate species and wanted to represent our results at Bia’s poster at the ISMB conference this year, we realized that it is quite challenging to find a good visualization that supports a comparison between structures. In a pub in Boston, Jan Aerts, Bia Walter, Henrike Indrischek, and I sketched this challenge on a napkin. Gratefully, Ryo Sakai and Eamonn Maguire developed our idea into the official design contest for the BioVis conference 2015 in Dublin. We are very excited to see what solutions the contestants will come up with.

Sandra and Lisa, both turned their projects into very interesting and well-conducted Masters theses. Sandra worked on the “Evolutionary comparison of KAP1 binding sites between humans and chimpanzees” and Lisa on the “Functional characterization of ZNF542 and ZEB2 in primates”. The results of both projects gave us new insights in functional differences between TF genes of humans and other primates.