Nowick Lab

Rohit published his results on the comparison of two lizard genomes: Lacerta viridis and Lacerta bilineata. He sequenced both genomes with Illumina and PacBio, performed de-novo assemblies. The high quality assemblies allowed him to assess genome divergence, structural variations, and gene flow between the two species. This was a collaborative project with Martin Schlegel, Peter Stadler, Rui Faria, and Klaus Henle.

Deisy turned our method for calculating weighted topological overlap (wTO) networks into an R package and published it in BMC Bioinformatics. The method was developed by Eivind Almaas for describing a transcription factor network in the prefrontal cortex of humans and chimpanzees. It is especially useful, when gene interactions can be positive or negative, such as in regulatory networks. The R package implements this wTO method and allows further for calculating p-values for each link and consensus networks. It thus produces networks with much reduced noise.

Our group contributed to a research project of Volker Busskamp’s lab on the role of miR-124 during human neurogenesis. Deisy uncovered a transcription factor network that is involved in the differentiation of neurons from induced pluripotent stem cells and determined how this network is changed when miR-124 is not present. The work is published in Cell Systems.

Stefano’s paper on the evolution of the transcription factor network in the primate prefrontal cortex has been published in GBE. While the functional output of that network seems to be conserved across the investigated primates, the network has evolved more links on the human lineage, indicating higher complexity and cooperativity between transcription factors in humans. We suggest that human specific network changes have contributed to the evolution of cognitive skills.

After six successful editions of our Programming for Evolutionary Biology course in Leipzig, we are currently running the first edition at the FU. The outline and philosophy of the course stayed the same; just the location changed. We, organizers, lecturers, speakers, and TAs, are happy and with continued motivation to run this one-of-a-kind course. The IT support team has done a great job in preparing the venue and computers for our course and everything is working pretty flawlessly. Thanks!

We are welcoming the second postdoc in our group! Alvaro came with us from Leipzig to continue as a postdoc. Vladi is from the university of Belgrade. He will be 50% in our group and spend 50% of his time to support the new Bioinformatics Solution Center of the FU Berlin.

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.