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Postdoc and PhD student positions (dry/wet lab): De novo gene birth and human evolution

Center for Molecular Biology (ZMBH), Heidelberg University, Germany

Postdoc and PhD student positions (3 years with possible extensions) are available immediately in the evolutionary genomics group of Henrik Kaessmann. Applications will be reviewed until the positions are filled.

We are seeking highly qualified and enthusiastic applicants with a keen interest in evolutionary questions and a talent and passion for experimental molecular/cellular work and/or bioinformatics analyses (i.e., both joint and distinct dry/wet lab projects are possible).

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 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. We have also started to experimentally assess the evolutionary impact of selected genomic changes.

The positions will be funded by a recently awarded grant from the NOMIS Foundation (https://nomisfoundation.ch/). In the framework of this grant, we seek to unravel the evolutionary impact of a particularly intriguing class of new genes: protein-coding genes that arose “from scratch” (i.e., from previously noncoding DNA sequence) during evolution – so-called de novo genes. Specifically, we will investigate the prevalence and functional roles of de novo genes in organ development across primates and thus shed light on the molecular evolution underlying the unique biology of humans, in particular that of the brain.

The work will rely on the generation and analyses of translatome (ribosome profiling) data across a unique set of prenatal developmental tissue samples, and the experimental characterization of selected de novo genes in state-of-the-art in vitro organoid systems, ex vivo fetal tissue cultures, and in vivo transgenic mouse models. Notably, the work will be carried out in the framework of collaborations with the labs of Barbara Treutlein (ETH, Basel), Gray Camp (Roche, Basel), and Svante Pääbo (MPI, Leipzig).

Experience in evolutionary and/or developmental biology and/or any of the aforementioned experimental techniques/models are a plus. The individual projects will be developed together with the candidates, based on their respective interests and dry/wet lab skills.

Note that people interested in other topics covered in our lab are also highly welcome to apply (funding is available for strong candidates).

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).

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Selected publications:

Murat, F., Mbengue, N., Boeg Winge, S., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Riera Belles, M., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S., Marques-Bonet, T., Grützner, F., Almstrup, K., Heide Schierup, M., Kaessmann, H. (2022) The molecular evolution of spermatogenesis across mammals. Nature (in press)

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.