Center for Molecular Biology (ZMBH), Heidelberg University, Germany
A PhD student positions (3 years with possible extensions) is available immediately in the evolutionary genomics group of Henrik Kaessmann. Applications will be reviewed until the position is filled.
We are seeking highly qualified and enthusiastic applicants with a Master degree, a keen interest in evolutionary questions, and a talent and passion for bioinformatics analyses.
Our lab has been interested in a range of topics related to the origins and evolution of organs in mammals and other vertebrates and the various underlying genomic/molecular changes (see “Selected Publications” below). In the framework of our research, we have generated and analyzed comprehensive genomics (e.g., RNA-seq, ATAC-seq) datasets based on samples from our large organ collections. More recently, we have begun to bring the work of our lab to the level of single cells using state-of-the-art single-cell genomics technologies and bioinformatics procedures.
The PhD student position will be funded by a recently awarded ERC Advanced Grant (VerteBrain – “The Ancestral Vertebrate Brain and its Cellular Diversification During Evolution”). In the framework of this grant, we seek to unravel the molecular origins and evolution of the vertebrate brain and its constituent substructures and cell types. Possible projects involve comparative/bioinformatics analyses of extensive single-cell transcriptomic, epigenomic, and spatial transcriptomics data generated in the lab for key species representing all major vertebrate lineages, ranging from jawless vertebrates, such as the sea lamprey, to mammals, such as platypus and human. The precise projects will be developed together with the candidate, based on their interest.
In our lab, we attach great importance to a highly collaborative and positive team spirit! Indeed, we have various “mini-teams” of dry and wet lab researchers within the lab, who enthusiastically drive projects forward in remarkable ways. We are also particularly fond of the diverse cultural backgrounds of our lab members, which contribute to a very enriching atmosphere.
The language of our institute is English and its members form a highly international group. The ZMBH is located in Heidelberg, a picturesque international city next to the large Odenwald forest and Neckar river. The city offers a very stimulating, diverse and collaborative research environment, with the European Molecular Biology Laboratory (EMBL), German Cancer Research Center (DKFZ), Heidelberg Institute of Theoretical Studies (HITS), and the Max Planck Institute for Medical Research located in close proximity to the University.
For more information on the group and our institute more generally, please refer to our website at the ZMBH (http://www.zmbh.uni-heidelberg.de/Kaessmann/).
Please submit a CV, statement of research interest, and names of three references to: Henrik Kaessmann (h.kaessmann@zmbh.uni-heidelberg.de).
-- Selected publications:
Sarropoulos, I., Sepp, M., Fromel, R., Leiss, K., Trost, N., Leushkin, E., Okonechnikov, K., Joshi, P., Giere, P., Kutscher, L.M., Cardoso-Moreira, M., Pfister, S.M., and Kaessmann, H. (2021) Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science 373: eabg4696.
Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M., and Kaessmann, H. (2021) Alternative splicing during mammalian organ development. Nat. Genet. 53:924-935.
Wang, Z.Y., Leushkin, E., Liechti, A., Ovchinnikova, S., Mossinger, K., Bruning, T., Rummel, C., Grutzner, F., Cardoso-Moreira, M., Janich, P., Gatfield, D., Diagouraga, B., de Massy, B., Gill, M.E., Peters, A.H.F.M., Anders, S., and Kaessmann, H. (2020) Transcriptome and translatome co-evolution in mammals. Nature 588: 642-647.
Cardoso-Moreira M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascencao, K., Rummel, C., Ovchinnikova, S., Mazin, P.V., Xenarios, I., Harshman, K., Mort, M., Cooper, D.N., Sandi, C., Soares, M.J., Ferreira, P.G., Afonso, S., Carneiro, M., Turner, J.M., VandeBerg, J.L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y.E., and Kaessmann H. (2019) Gene expression across mammalian organ development. Nature 571: 505-509.
Sarropoulos, I., Marin, R., Cardoso-Moreira, M., and Kaessmann, H. (2019) Developmental dynamics of lncRNAs across mammalian organs and species. Nature 571: 510-514.
Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grutzner, F., and Kaessmann, H. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508: 488-493.
Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grutzner, F., and Kaessmann, H. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640.
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csardi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F.W., Zeller, U., Khaitovich, P., Grutzner, F., Bergmann, S., Nielsen, R., Paabo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
