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Henrik Kaessmann, Associate Professor

Henrik Kaessmann received his PhD in 2001 from the University of Leipzig after working on the genetic diversity of humans and the great apes in the laboratory of Dr. Svante Pääbo at the University of Munich and subsequently at the Max Planck Institute for Evolutionary Anthropology, Leipzig. For his postdoctoral training, he joined the lab of Dr. Wen-Hsiung Li in the Department of Ecology and Evolution at the University of Chicago, where he worked on the origin of human genes and gene structures. In 2003, he joined the Center for Integrative Genomics as an assistant professor and was appointed associate professor in 2007. In 2005 he was elected as an EMBO Young Investigator, and was awarded a European Research Council Starting Grant in 2009. In 2010, he received the Friedrich Miescher Award from the Swiss Society for Biochemistry and was elected as group leader of the Swiss Institute of Bioinformatics. He was awarded a European Research Council Consolidator Grant in 2013. In 2014, he was elected to EMBO membership.

Keywords: Evolutionary genomics, molecular evolution, transcriptome evolution, new gene origination, adaptive evolution, primates, mammals


Research Summary

Mammals are characterized by specific phenotypic traits that include lactation, hair, and relatively large brains with unique structures. Individual mammalian lineages have, in turn, evolved characteristic traits that distinguish them from others. These include obvious anatomical differences but also differences related to reproduction, life span, cognitive abilities, behavior, and disease susceptibility. The molecular changes (i.e., changes in protein/RNA sequences or expression levels) underlying these phenotypic shifts and the associated selective pressures have only recently begun to be investigated based on an increasing number of available mammalian genomes. Our group performs integrated bioinformatics analyses pertaining to the functional evolution of mammalian genes (and potentially associated phenotypic changes) on the basis of publicly available genomic data as well as data generated by the wet lab unit of the group (e.g., large-scale transcriptome data).

We have been interested in a range of topics related to the functional evolution of genomes from primates (e.g., the emergence of new genes and their functions) and other mammals (e.g., the origin and evolution of mammalian sex chromosomes). In the framework of a recently launched set of projects, a large amount of transcriptome and genome (e.g., epigenome) data are being produced by the wet lab unit of the group for a unique collection of tissues from representative mammals and outgroup species (e.g., birds) using next generation sequencing technologies. Topics of current projects that are based on these data include the origins and/or evolution of protein-coding genes, alternative splicing, microRNAs, long noncoding RNAs, and dosage compensation.


Representative Publications

Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grützner, F., and Kaessmann, H. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature (in press).

Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grützner, F., and Kaessmann, H. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640. URL

Julien, P., Brawand, D., Soumillon, M., Necsulea, A., Liechti, A., Schütz, F., Daish, T., Grützner, F., and Kaessmann, H. (2012) Mechanisms and evolutionary patterns of mammalian and avian dosage compensation PLoS Biol. 5:e1001328. URL

Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F.W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348. URL

Henrichsen, C., Vinckenbosch, N., Zöllner, S., Chaignat, E., Pradervand, S., Frédéric Schütz, Ruedi, M., *Kaessmann, H. and *Reymond, A. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat. Genet. 41: 424-429. URL

Rosso, L., Marques, A. C., Weier, M., Lambert, N., Lambot, M. A., Vanderhaeghen, P., and Kaessmann, H. (2008) Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein. PLoS Biol. 6:e140. URL

Potrzebowski, L., Vinckenbosch, N., Marques, A. C., Chalmel, F., Jegou, B., and Kaessmann, H. (2008) Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes. PLoS Biol. 6:e80. URL

Brawand, D., Wahli, W., and Kaessmann, H. (2008) Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 6: e63. URL

Vinckenbosch, N., Dupanloup, I., and Kaessmann, H. (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl. Acad. Sci. U. S. A. 103: 3220-5. URL

Marques, A. C., Dupanloup, I., Vinckenbosch, N., Reymond, A., and Kaessmann, H. (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3:e357. URL

Burki, F. and Kaessmann, H. (2004) Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat. Genet. 36: 1061-3. URL

*Emerson, J. J., *Kaessmann, H., Betran, E., and Long, M. (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540. URL

Kaessmann, H., Wiebe, V., Weiss, G., and Pääbo, S. (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27: 155-6. URL

Kaessmann, H., Wiebe, V., and Pääbo, S. (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1162. URL

Kaessmann, H., Heissig, F., von Haeseler, A., and Pääbo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. 22: 78-81. URL

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