We have published an invited headline review in the Journal of the Royal Society Interface on the Construction, comparison and evolution of networks in life sciences and other disciplines. Our paper describes how biological networks change over time – in relatively short scales like during signal transduction and in relatively long scales like during development and evolution. We give a comprehensive overview about existing methods for analyzing such network changes. Moreover, we take a survey across non-biological sciences to explore how they investigate network changes. Our survey includes also some entertaining examples on the evolution of cooking recipes and the Marvel Universe.
Headline review in Interface
PhD position on expression patterns in Alzheimer’s disease
We are offering a fully funded PhD position in our lab to work on the analysis of gene expression differences between brain of Alzheimer’s patients and controls. The focus will be on mono-allelically expressed genes to test the hypothesis that they are involved in establishing cellular diversity and selective vulnerability.
See the complete advertisement here: PhD_AlzheimerExpressionSignatures
PhD position on brain development and evolution available
We have acquired funding for a PhD position within a project that investigates a relationship between brain size and cognitive abilities in rodents from Chernobyl. We are interested in deciphering molecular signatures that determine differences in brain size and behavior.
See the complete advertisement here: PhD_BrainEvolution
Postdoc position on Human Evolution in my lab
We currently have an opening for a postdoc, with some flexibility about the actual research topic. The postdoc is expected to propose and develop a research project that fits to the general interests of the group. Requirements for the position are a Dr. rer. nat. or PhD in Biology or Bioinformatics or another relevant field. The ideal candidate would have a strong interest in human evolution and expertise within multiple of the following areas: conducting research with induced pluripotent stem cells, differentiation into neuronal cells, CRISPR/Cas9, functional investigation of transcription factors and non-coding RNAs, ChIP-Seq, ChIRP-Seq, RNA-Seq, gene regulatory networks, computational analysis of –omics data, R, Python, network analysis.
See the complete advertisement here: Postdoc_HumanEvolution.
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.
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.
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: email@example.com.
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!
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.
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.