Part of Bia’s PhD project was the analysis of HAR1 evolution. HAR1 is the fastest evolving sequence in the human genome and is part of two overlapping long non-coding RNAs. Bia’s paper “Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1” describes in which order the 18 human-specific substitutions occurred and how they gradually changed the secondary structure of HAR1 into its human-specific form. She found that HAR1 is becoming more stable during human evolution. Her analysis methods are implemented in the software “MutationOrder”, which is publicly available and can be used for exploring the evolution of other RNA structures.
This project was a collaboration with Dan Tulpan. He won the Biovis design contest on visualizing RNA structure evolution that we co-designed at the ISMB conference in 2015. He joined our project after the contest and provided valuable visualization and scientific input to our paper.
Marko, a highly talented student from Belgrade, Serbia is joining our group for an internship. He is interested in the molecular causes of psychiatric disorders. During his half a year internship he will explore the evolution of long non-coding RNAs involved in psychiatric disorders.
Our paper “A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma” was published in PLoS Computational Biology.
This was a collaborative work with the group of Eivind Almaas in Trondheim, Norway, lead by his PhD student Andre Voigt. We developed a method that allows for comparing networks and identifying links that are conserved, specific, or differential to networks (“CSD method”).
The third PEB conference took place in Bialowieza, Poland, in the Fall 2017. After PEB at CIBIO in Porto and in Belgrade, Serbia, this was another very successful and fun conference. We heard many interesting talks and enjoined well-prepared bioinformatics hands-on workshops. Thanks to Agnieszka and everybody involved in the organization!
In the end, EVOP alumni from Huddersfield decided to organize the next PEB conference in the UK. More information will follow.
I accepted the position in the Spring 2017 and am now professor at the Freie Universität Berlin since 1st of July 2017.
After being professor for Bioinformatics at the University of Hohenheim for about 1.5 years, I am now starting my new group in Berlin. I am fulfilling the professorship for Human Biology at the Institute for Biology.
One last time in Leipzig: Our programming course will take place in March next year. You can still apply for it until the end of this year. More information about the course are here: http://evop.bioinf.uni-leipzig.de.
Late but not forgotten: Alvaro defended his PhD this August. Congratulations to an excellent thesis and defense!
The next Programming for Evolutionary Biology (PEB) Conference will take place in Belgrade, from September 7th-12th.
The website is already online and you can already register for it: http://pebconference.info/
This conference was initiated by students of our third Programming for Evolutionary Biology course, but is now open to everybody. The first PEB conference took place at CIBIO (Vila do Conde, Portugal) last year and has really been a big success and a lot of fun. Besides your scientific contributions, the organizers convinced several outstanding speakers to give plenary talks. There will also be a couple of workshops, which will allow you to further improve your programming skills. And, last but not least, I’m expecting a superb leisure program in and around Belgrade. And all of this again for a very reasonable price of 200 Euro, which includes conference materials, accommodation in double, shared rooms (7-12.09.2016), meals, and leisure.
Since space is limited, register for the Belgrade event as soon as possible!
With this work we aimed at obtaining more insights into the gene regulatory networks of the human prefrontal cortex, which is important for cognitive abilities. Analyzing multiple independent genome-wide expression datasets from healthy individuals we realized that the transcription factor networks derived from them are considerably different. Here we focussed on the network links that were consistently observed across the different datasets by building a consensus network. This allowed us to identify a network module consisting of many transcription factors with known importance for brain development and functions. Our work not only suggests how these transcription factors are interacting and what common target genes of them might be, but also identified not yet characterized transcription factors that seem to be excellent new candidates for playing important roles in the human prefrontal cortex. We hope that with this line of research we will in the long run be able to help uncovering the molecular basis of human cognitive skills.
Stefano, you made it! Congratulations, Dr. Berto!