Centre for Genomics, Evolution and Medicine
The Centre for Genomics, Evolution, and Medicine was founded in 2018 through an ERA Chair grant (no 810645) under the Horizon 2020 programme with the aim to bring together expertise and research in the fields of genomics, evolutionary biology and biomedicine. The aim of the research unit is to integrate expertise in three key areas: ancient genomics, personalized medicine, and medical genomics. By combining these research directions, the unit seeks to advance its objectives through a multidisciplinary approach and international collaborations.
Contact: michael.dannemann@ut.ee CV Google Scholar
Research groups
Interdisciplinary research in genomics
The research in the group focuses on how past climates, diets, and pathogens have shaped genetic diversity and their role in common diseases. The group uses an interdisciplinary approach that combines mathematical modeling with environmental, genomic and health data to study the effects of gene-environment interactions on variation in human complex traits and the role of past environmental changes and demographic processes in the evolution of these traits.
The research group is led by Associate Professor of Interdisciplinary Research in Genomics Anders Eriksson.
Anders Eriksson received his PhD from the University of Gothenburg 2005. Following his PhD, he conducted postdocs at University of Cambridge and King Abdullah University of Science and Technology (Saudi Arabia). Between 2017-2019 he worked as Lecturer at King’s College London, Department of Medical Genomics. In 2019, he established his independent research group within cGEM at the Institute of Genomics, University of Tartu. He was the head of cGEM 2019-2023.
Bioinformatics and medical genomics
The research group uses experimental assays based on stem cell systems to test the functional potential of candidate variants. The primary goal is the assessment of the regulatory and functional potential of candidate variants to improve our understanding of their evolutionary history.
The research group is co-led by Associate Professor’s of Bioinformatics and Medical Genomics Tõnis Org and Irene Gallego Romero.
Tõnis Org received his PhD from the University of Tartu Medical Faculty in 2010. Following his PhD, he conducted a postdoc at University of California Los Angeles (USA) from 2010 to 2015. Since 2015 he been working at the Institute of Molecular and Cell Biology, University of Tartu where he is currently Associate Professor of Biotechnology. Since 2021, he holds a part time Associate Professor of Bioinformatics and Medical Genomics position in cGEM.
His research combines novel method development with functional genomics and stem cell biology to understand tissue specific gene regulation.
Irene Gallego Romero...
Evolutionary Genomics
The research group combines genomic and phenotypic datasets to explore the role of past evolutionary processes on phenotypic variation in present-day populations. One primary research direction aims at deciphering the impact of past admixture with Neandertals and Denisovans on present-day human traits.
The research group is led by Associate Professor of Evolutionary Genomics Michael Dannemann.
Michael Dannemann received his PhD from the University of Leipzig and the Max Planck Institute for Evolutionary Anthropology, Leipzig in 2014. Following his PhD, he conducted a postdoc at the Max Planck Institute for Evolutionary Anthropology from 2014 to 2019. In 2020, he established his independent research group within cGEM at the Institute of Genomics, University of Tartu. Starting in 2024, he became the head of cGEM.
Centre members
Anders Eriksson, PhD, Associate Professor of Interdisciplinary Research in Genomics
Research interests: Evolutionary Genomics, Statistical and Population Genetics, Gene-Environment Interaction
Main areas of expertise: Population genomics, mathematical modelling of stochastic processes, evolutionary biology
Tõnis Org, PhD, Associate Professor of Bioinformatics and Medical Genomics
Research interests: Cell Biology, Molecular Biology, Medical Genomics
Irene Gallego Romero, PhD, Associate Professor of Bioinformatics and Medical Genomics
Research interests: Functional and Evolutionary Genomics, Comparative Transciptomics, Denisovan Admixture
Danat Yermakovich, PhD, Junior Research Fellow of Evolutionary Genetics
Research interests: Archaic Introgression, Human Phenotype Evolution
Vasili Pankratov, PhD, Research Fellow of Computational and Medical Genomics
Research interests: Human Evolutionary and Medical Genomics, Demographic Modelling
PhD students
Ivan Kuznetsov, MSc (Bioengineering or Bioinformatics)
Research interests: Behavioural genetics, human population genetics
Supervisors: Vasili Pankratov, Luca Pagani, Francesco Montinaro
Rita Kreevan, MSc (Gene Technology)
Research interests: Functional genomics, medical genomics
Supervisors: Irene Gallego Romero, Michael Dannemann, Tōnis Org, Anders Eriksson
Rutvi Rajpara, MSc (Bioinformatics)
Research interests: Pathogen-driven human evolution, Archaic admixture, Signatures of selection, Immune response genetics.
Supervisors: Michael Dannemann, Irene Gallego Romero, Kaia Palm
Jose Rodrigo Flores, MSc (Computer Science)
Research interests: Evolutionary Genomics, Selection and Adaptation
Supervisors: Anders Eriksson, Liisa Loog
MSc students
Kirill Nitsenko
Research interests: Disentangling the archaic source population in the genomes of present-day Oceanian populations
Supervisors: Michael Dannemann, Danat Yermakovich, Monika Karmin
Stepan Strelchenko
Research interests: Gene-environment interactions in body mass variation
Supervisor: Anders Eriksson
BSc students
Roza Rostam Nejad
Research interests: The role of Neandertal DNA in antiinflammatory processes in present-day humans
Supervisor: Michael Dannemann
Liene Gutmāne
Research interests: The role of Neandertal DNA on immune responses in present-day humans
Supervisors: Michael Dannemann, Danat Yermakovich
Other staff
Annika Trei
Senior Laboratory Assistant
Anita Ligere, BSc (Science and Technology)
Research interests: Past episodes of selection on immune response loci in present-day humans
Supervisors: Michael Dannemann, Danat Yermakovich
Alumni
Mathilde Frédérique E André
- PhD degree defended in 2023: New Guinea, a hotspot for Human evolution: settlement history and adaptation in northern Sahul / Anatoomiliselt kaasaegse inimese evolutsioon asustamise, arhailiste inimlastega segunemise ja kohastumuste ajalugu
- Supervisors: Mayukh Mondal, Francois-xavier Ricaut
Mayukh Mondal
- Post-doc of evolutionary and population genomics, 2020 to 2023
Johann Koobas
- Bacholer degree defended in 2023: The Pleiotropic Effects of Neanderthal DNA in Present-Day Asian Populations
Collaborations
- Charité, Berlin
- Copenhagen University
- Harvard University
- Max Planck Institute for Evolutionary Anthropology
- Melbourne (SVI)
- Protobios
- Toulouse University
- University of California, Berkeley
Major publications
Dannemann, M., The Population-Specific Impact of Neandertal Introgression on Human Disease, Genome Biology and Evolution, Volume 13, Issue 1, January 2021, evaa250, https://doi.org/10.1093/gbe/evaa250
Dannemann, M. and Gallego Romero, I. (2022), Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J, 289: 2992-3010. https://doi.org/10.1111/febs.15885
Marnetto, D., Pankratov, V., Mondal, M., Montinaro, F., Pärna, K., Vallini, L., Molinaro, L., Saag, L., Loog, L., Montagnese, S., Costa, R., Estonian Biobank Research Team, Metspalu, M., Eriksson, A., Pagani, L. Ancestral genomic contributions to complex traits in contemporary Europeans, Current Biology, Volume 31, Issue 6, 28. March 2022, 1412-1219. https://doi.org/10.1016/j.cub.2022.01.046
Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, et al. (2022) Denisovan introgression has shaped the immune system of present-day Papuans. PLOS Genetics 18(12): e1010470. https://doi.org/10.1371/journal.pgen.1010470
Dannemann, M., Milaneschi, Y., Yermakovich, D. et al. Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes. Transl Psychiatry 12, 433 (2022). https://doi.org/10.1038/s41398-022-02196-2
Danat Yermakovich, Vasili Pankratov, Urmo Võsa, Bayazit Yunusbayev, Estonian Biobank Research Team , Michael Dannemann, Long-range regulatory effects of Neandertal DNA in modern humans, Genetics, Volume 223, Issue 3, March 2023, iyac188, https://doi.org/10.1093/genetics/iyac188
André, M., Brucato, N., Hudjasov, G. et al. Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels. Nat Commun 15, 3352 (2024). https://doi.org/10.1038/s41467-024-47735-1
Pankratov, V., Yunusbaeva, M., Ryakhovsky, S. et al. Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection. Nat Commun 13, 7069 (2022). https://doi.org/10.1038/s41467-022-34461-9
Pankratov, V., Montinaro, F., Kushniarevich, A. et al. Differences in local population history at the finest level: the case of the Estonian population. Eur J Hum Genet 28, 1580–1591 (2020). https://doi.org/10.1038/s41431-020-0699-4
Ivan A. Kuznetsov, Estonian Biobank Research Team, Mait Metspalu, Uku Vainik, Luca Pagani, Francesco Montinaro, Vasili Pankratov, Assessing the impact of 20th century internal migrations on the genetic structure of Estonia, bioRxiv 2023.10.25.564036; doi: https://doi.org/10.1101/2023.10.25.564036
D. Yermakovich, M. André, N. Brucato, J. Kariwiga, M. Leavesley, V. Pankratov, M. Mondal, F. Ricaut, M. Dannemann, Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations, Proc. Natl. Acad. Sci. U.S.A., 121 (26) e2405889121, https://doi.org/10.1073/pnas.2405889121 (2024).
Mayukh Mondal, Mathilde André, Ajai K. Pathak, Nicolas Brucato, François-Xavier Ricaut, Mait Metspalu, Anders Eriksson, Resolving out of Africa event for Papua New Guinean population using neural network, bioRxiv 2024.09.19.613861; doi: https://doi.org/10.1101/2024.09.19.613861
Participation in consortia and working groups
- TRANSPAN
- CorEUStem COST action
