Commentary on ncRNA evolution

Have a look at our commentary in Evolutionary Bioinformatics. We provide some background on our tool for testing selection of ncRNA genes, the SSS test. This tool should be useful for any new genome project or biomedical study to gain further insights into the evolution and potential functions of ncRNA genes.

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Paper on GRFs in human populations

Our paper in GBE describes human population differences in genes coding for gene regulatory factors. Surprisingly many of them seem to evolve under positive selection, among them long clusters of KRAB-ZNF genes. Some of the population differences might explain differences in prevalence in psychiatric disorders, such as schizophrenia.

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Postdoc position on evolution of desert rodents

My colleagues and I are announcing a postdoc position to work on the evolution of desert rodents. We are looking for somebody with experience in the analysis of genomics and transcriptomics data. More information is below and here:  http://www.cibio.pt/?p=889.

*** Postdoc in ecological genomics of desert adaptation ***

Post-doctoral position in animal ecological genomics is available at the CIBIO/InBio, Research Centre in Biodiversity and Genetic Resources, University of Porto, Portugal (https://cibio.up.pt/), to work with the BIODESERTS team (https://biodeserts.cibio.up.pt/). Successful applicant will coordinate laboratory work and bioinformatical analyses at CIBIO/InBio, in close collaboration and visits at University of Oulu (https://bit.ly/2KV4epD) and Free University of Berlin (https://bit.ly/2ATA69P). Candidate will have the opportunity to participation in field work in North Africa (https://goo.gl/H1gptJ) investigating unique desert rodents.

This project investigates the effect of past climatic changes on the genomic architecture of adaptation using Sahara desert specialist, Jaculus jaculus. Since the formation of the Sahara, during the Mid-Upper Pliocene, the region went through several climate changes. Those changes influenced habitat structure of recently described cryptic species within Jaculus jaculus. Discovery of divergence in fur coloration and camouflage lead to the hypothesis that Jaculus species specialized to explore divergent habitats. In this project we ask: what is the role of climate changes in shaping the genomic architecture of adaptations to extreme desert conditions, camouflage and habitat specialization?

Funding is available for up to 32 months with renewal after first year of satisfactory performance. Salary level is according to the Portuguese state foundation (gross: 2130 €/month, net: 1480-1560 €/month, plus allowances/social security/insurance).

Qualifications. Candidate should have PhD in biology, or equivalent, with specialization in genomics/transcriptomics, experienced in analytical work (SNP calling, population demography and genomics, sequence mapping, gene expression analysis, network analytics). Knowledge in molecular laboratory work (methods: ddRAD sequencing including museum samples, transcriptome sequencing) is preferred.

Interested candidates should submit: 1) a letter of interest (maximum 1 page), 2) a CV (maximum 3 pages), and 3) a list of publications (indicating publications as first/corresponding author, and those with/without previous supervisors) to: http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=114174. Review of applications will begin immediately and continue until the position is filled. Inquires should be addressed to: boratyns@cibio.up.pt.

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PhD students in Leipzig finished

For almost two years our group was split between the University Leipzig and the Freie Universitaet Berlin. Now PhD students in Leipzig have finished and moved on to their next research groups:

Bia defended in September 2018 and is now a postdoc at Empresa Brasileira de Pesquisa Agropecuária (Embrapa).

Rohit defended in December 2018 and is now a postdoc in Peter Sudmant’s lab at UC Berkeley.

Deisy will defend tomorrow (Good luck, Deisy!) and will start a postdoc in Albert-László Barabasi’s lab at Harvard University.

All the best for all of you!

IMG_20180927_173300

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Ama finished her Master thesis

Ama handed in her Master thesis on the functional evolution of the transcription factor ZEB2. She analyzed RNA-Seq and ChIP-Seq data obtained from three different primate species to detect human specific ZEB2 target genes and functions.

Congratulations, Ama!

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New test for selection of RNA secondary structures

Bia developed a test for selection of non-coding RNAs. Her test uses the RNA secondary structure as proxy for its function. In contrast to previous work, she cannot only asses negative selection but also pinpoint structures with lineage specific changes and signatures of positive selection. We found candidates, that might be involved in the evolution of the human brain and its cognitive functions. Her test, called SSS (“Selection on Secondary Structure”), is available as a from her github repository and is useful for genome-wide assessments of non-coding RNA structural evolution as well as candidate approaches.

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Two new lizard genomes

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.

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wTO package for network analysis

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.

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Paper on human neurogenesis

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.

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Network evolution paper

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.

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