the Center for Genomics, Evolution and Medicine

Deliverables

Research Strategy: cGEM 2025

A longterm research strategy for cGEM provided by ERA Chair holder and the team in cohesion with cGEM staff

Long-Term Research Strategy: cGEM 2035

Project website and visual identity package

A comprehensive project website about the objectives, progress and achievements (including Open Access publications), involved research groups, and events (summer schools, conferences and courses) will be established along with visual identity

Publications

Phylogenetic History of Patrilineages Rare in Northern and Eastern Europe from Large-Scale Re-Sequencing of Human Y-Chromosomes

Author(s): Ilumäe, Anne-Mai, Helen Post, Rodrigo Flores, Monika Karmin, Hovhannes Sahakyan, Mayukh Mondal, Francesco Montinaro, Lauri Saag, Concetta Bormans, and Luisa Fernanda Sanchez
Published in: European Journal of Human Genetics, Issue 29, no 10, 2021, Page(s) 1510-19, ISSN 1018-4813
Publisher: Natue Publishing Group
DOI: 10.1038/s41431-021-00897-8

Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?

Author(s): Evan K. Irving-Pease, Rasa Muktupavela, Michael Dannemann, Fernando Racimo
Published in: Frontiers in Genetics, Issue 12, 2021, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2021.703541

Genetic architecture of gene regulation in Indonesian populations identies QTLs associated with local ancestry and archaic introgression!

Author(s): Heini M Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, Chelzie Crenna Darusallam, Mait Metspalu, Herawati Sudoyo, Murray P Cox*, Irene Gallego Romero*, Nicholas E Banovich*
Published in: American Journal of Human Genetics, Issue 109 (1), 2022, Page(s) 50-65, ISSN 0002-9297
Publisher: University of Chicago Press
DOI: 10.1016/j.ajhg.2021.11.017

Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection

Author(s): Pankratov, Vasili; Yunusbaeva, Milyausha; Ryakhovsky, Sergei; Zarodniuk, Maksym; Metspalu, Andres; Nelis, Mari; Milani, Lili; Magi, Reedik; Esko, Tonu; Yunusbayev, Bayazit
Published in: Nature Communications, Issue 13 (1), 2022, Page(s) ARTN 7069, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34461-9

Revisiting the out of Africa event with a deep-learning approach

Author(s): Francesco Montinaro; Francesco Montinaro; Vasili Pankratov; Burak Yelmen; Burak Yelmen; Luca Pagani; Luca Pagani; Mayukh Mondal
Published in: The American Journal of Human Genetics, Issue 108, no 11, 2021, Page(s) 2037-51, ISSN 1537-6605
Publisher: Cell Press
DOI: 10.1016/j.ajhg.2021.09.006

The Population-Specific Impact of Neandertal Introgression on Human Disease

Author(s): Michael Dannemann
Published in: Genome Biology and Evolution, Issue 13/1, 2021, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evaa250

Long-range regulatory effects of Neandertal DNA in modern humans

Author(s): Danat Yermakovich, Vasili Pankratov, Urmo Võsa, Bayazit Yunusbayev, Estonian Biobank Research Team, Michael Dannemann
Published in: Genetics, Issue 223 (3), 2023, Page(s) iyac188, ISSN 1943-2631
Publisher: Oxford Academic Press
DOI: 10.1093/genetics/iyac188

Genome-wide association study of obstructive sleep apnoea in the Million Veteran Program uncovers genetic heterogeneity by sex

Author(s): Tamar Sofer; Nuzulul Kurniansyah; Michael Murray; Yuk-Lam Ho; Erik Abner; Tõnu Esko; Jennifer E. Huffman; Kelly Cho; Peter W.F. Wilson; Daniel J. Gottlieb; Andres Metspalu; Lili Milani; Tõnu Esko; Reedik Mägi; Mari Nelis; Georgi Hudjashov
Published in: eBioMedicine, Issue 3, 2023, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2023.104536

Differences in local population history at the finest level: the case of the Estonian population

Author(s): Vasili Pankratov, Francesco Montinaro, Alena Kushniarevich, Georgi Hudjashov, Flora Jay, Lauri Saag, Rodrigo Flores, Davide Marnetto, Marten Seppel, Mart Kals, Urmo Võsa, Cristian Taccioli, Märt Möls, Lili Milani, Anto Aasa, Daniel John Lawson, Tõnu Esko, Reedik Mägi, Luca Pagani, Andres Metspalu, Mait Metspalu
Published in: European Journal of Human Genetics, Issue 28 (11), 2020, Page(s) 1580-1591, ISSN 1018-4813
Publisher: Natue Publishing Group
DOI: 10.1038/s41431-020-0699-4

The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Author(s): Cesar A. Fortes-Lima, Concetta Burgarella, Rickard Hammarén, Anders Eriksson, Mário Vicente, Cecile Jolly, Armando Semo, Hilde Gunnink, Sara Pacchiarotti, Leon Mundeke, Igor Matonda, Joseph Koni Muluwa, Peter Coutros, Terry S. Nyambe, Justin Cirhuza Cikomola, Vinet Coetzee, Minique de Castro, Peter Ebbesen, Joris Delanghe, Mark Stoneking, Lawrence Barham, Marlize Lombard, Anja Meyer, Maryna Stey
Published in: Nature, Issue 625, 2023, Page(s) 540-547, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-06770-6

Chronology of Natural Selection in Oceanian Genomes

Author(s): Brucato, Nicolas, Mathilde André, Georgi Hudjashov, Mayukh Mondal, Murray P. Cox, Matthew Leavesley, and François-Xavier Ricaut
Published in: IScience, Issue 25, no 7, 2022, Page(s) 104583, ISSN 2589-0042
Publisher: Cell press
DOI: 10.1016/j.isci.2022.104583

Improving Selection Detection with Population Branch Statistic on Admixed Populations

Author(s): Yelmen, Burak, Davide Marnetto, Ludovica Molinaro, Rodrigo Flores, Mayukh Mondal, and Luca Pagani
Published in: Genome Biology and Evolution, Issue 13, no 4, 2021, Page(s) evab039, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab039

Ancestral Genomic Contributions to Complex Traits in Contemporary Europeans

Author(s): Davide Marnetto, Vasili Pankratov, Mayukh Mondal, Francesco Montinaro, Katri Pärna, Leonardo Vallini, Ludovica Molinaro, Lehti Saag, Liisa Loog, Sara Montagnese, Rodolfo Costa; Estonian Biobank Research Team; Mait Metspalu, Anders Eriksson, Luca Pagani
Published in: Current Biology, Issue 32, no 6, 2022, Page(s) 1412-19, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2022.01.046

Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes

Author(s): Michael Dannemann, Yuri Milaneschi, Danat Yermakovich, Victoria Stiglbauer, Hanna Maria Kariis, Kristi Krebs, Manuel A Friese, Christian Otte, Estonian Biobank Research Team, Kelli Lehto, Brenda WJH Penninx, Janet Kelso, Stefan M Gold
Published in: Translational Psychiatry, Issue 12, 2022, Page(s) no 433, ISSN 2158-3188
Publisher: Nature Publishing Group
DOI: 10.1038/s41398-022-02196-2

Climatic windows for human migration out of Africa in the past 300,000 years

Author(s): Robert M Beyer, Mario Krapp, Anders Eriksson, Andrea Manica
Published in: Nature Communications, Issue 12 (1), 2022, Page(s) 4889, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24779-1

Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes

Author(s): Jayant Mahadevan; Ajai Kumar Pathak; Alekhya Vemula; Ravi Kumar Nadella; Biju Viswanath; Sanjeev Jain; Accelerator Program for Discovery in Brain disorders using Stem cells (ADBS) Consortium; Meera Purushottam; Mayukh Mondal
Published in: Scientific Reports, Issue Volume 11, 2021, Page(s) Article number: 21088, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-00123-x

Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas.

Author(s): Linda Ongaro; Mayukh Mondal; Rodrigo Flores; Davide Marnetto; Ludovica Molinaro; Marta E. Alarcón-Riquelme; Andrés Moreno-Estrada; Nédio Mabunda; Mario Ventura; Kristiina Tambets; Garrett Hellenthal; Cristian Capelli; Cristian Capelli; Toomas Kivisild; Mait Metspalu; Luca Pagani; Luca Pagani; Francesco Montinaro; Francesco Montinaro
Published in: Human Molecular Genetics, Issue 30, no. 22, 2021, Page(s) 2123–34, ISSN 0964-6906
Publisher: Oxford University Press
DOI: 10.1093/hmg/ddab177

Detection of Neanderthal Adaptively Introgressed Genetic Variants that Modulate Reporter Gene Expression in Human Immune Cells

Author(s): Evelyn Jagoda, James R Xue, Steven K Reilly, Michael Dannemann, Fernando Racimo, Emilia Huerta-Sanchez, Sriram Sankararaman, Janet Kelso, Luca Pagani, Pardis C Sabeti, Terence D Capellini
Published in: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab304

Using fecal immunochemical tubes for the analysis of the gut microbiome has the potential to improve colorectal cancer screening

Author(s): Kertu Liis Krigul, Oliver Aasmets, Kreete Lüll, Tõnis Org, Elin Org
Published in: Scientific Reports, Issue 11, 2021, Page(s) 19603, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-99046-w

HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

Author(s): Guillaume Butler-Laporte, Joseph Farjoun, Tomoko Nakanishi, Tianyuan Lu, Erik Abner, Yiheng Chen, Michael Hultström, Andres Metspalu, Lili Milani, Reedik Mägi, Mari Nelis, Georgi Hudjashov, Estonian Biobank Research Team, Satoshi Yoshiji, Yann Ilboudo, Kevin Y. H. Liang, Chen-Yang Su, Julian D. S. Willet, Tõnu Esko, Sirui Zhou, Vincenzo Forgetta, Daniel Taliun & J. Brent Richards
Published in: Communications Biology, Issue 6 (1113), 2023, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-023-05496-5

Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul

Author(s): Brucato, Nicolas, Mathilde André, Roxanne Tsang, Lauri Saag, Jason Kariwiga, Kylie Sesuki, Teppsy Beni, William Pomat, John Muke, and Vincent Meyer
Published in: Molecular Biology and Evolution, Issue 38, no 11, 2021, Page(s) 5107-21, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab238

Harnessing pluripotent stem cells as models to decipher human evolution

Author(s): Michael Dannemann, Irene Gallego Romero
Published in: The FEBS Journal, 2021, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.15885

Effect of RNA m6A methyltransferase activation by a low molecular weight compound on anxiety- and depression-related behaviours, monoamine neurochemistry and striatal gene expression in the rat

Author(s): Margus Kanarik, Kristi Liiver, Marianna Školnaja, Indrek Teino, Tõnis Org, Karita Laugus, Ruth Shimmo, Mati Karelson, Mart Saarma, Jaanus Harro
Published in: bioRxiv, Issue preprint, 2024, ISSN 2692-8205
Publisher: Cold Sping Harbour Laboratory
DOI: 10.1101/2024.01.08.574593

HLA allele-calling using whole-exome sequencing identifies 129 novel associations in 11 autoimmune diseases: a multi-ancestry analysis in the UK Biobank

Author(s): Guillaume Butler-Laporte, Joseph Farjoun, Tomoko Nakanishi, Tianyuan Lu, Erik Abner, Yiheng Chen, Michael Hultström, Andres Metspalu, Lili Milani, Reedik Mägi, Mari Nelis, Georgi Hudjashov, Estonian Biobank Research Team, Satoshi Yoshiji, Yann Ilboudo, Kevin YH Liang, Chen-Yang Su, Julian DS Willet, Tõnu Esko, Sirui Zhou, Vincenzo Forgetta, Daniel Taliun, J Brent Richards
Published in: medRxiv, Issue preprint, 2023
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.01.15.23284570

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Author(s): Danat Yermakovich, Mathilde André, Nicolas Brucato, Jason Kariwiga, Matthew Leavesley, Vasili Pankratov, Mayukh Mondal, François-Xavier Ricaut, Michael Dannemann
Published in: bioRxiv, Issue prerpint, 2024, ISSN 2692-8205
Publisher: Gold Spring Harbour Laboratory
DOI: 10.1101/2024.01.14.575483

Assessing the impact of 20th century internal migrations on the genetic structure of Estonia

Author(s): Ivan A. Kuznetsov, Estonian Biobank Research Team, Mait Metspalu, Uku Vainik, Luca Pagani, Francesco Montinaro, Vasili Pankratov
Published in: bioRxiv, Issue prerpint, 2023
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.10.25.564036

Cell atlas of the regenerating human liver after portal vein embolization

Author(s): Agnieska Brazovskaja, Tomás Gomes, Christiane Körner, Zhisong He, Theresa Schaffer, Julian Connor Eckel, René Hänsel, Malgorzata Santel, Timm Denecke, Michael Dannemann, Mario Brosch, Jochen Hampe, Daniel Seehofer, Georg Damm, J Gray Camp, Barbara Treutlein
Published in: bioRxiv, Issue preprint, 2022, Page(s) 2021.06. 03.444016, ISSN 2692-8205
Publisher: Gold Spring Harbor Laboratory
DOI: 10.1101/2021.06.03.444016

Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Author(s): Mathilde Andre, Nicolas Brucato, Georgi Hudjasov, Vasili Pankratov, Danat Yermakovich, Rita Kreevan, Jason Kariwiga, John Muke, Anne Boland, Jean-Francois Deleuze, Vincent Meyer, Nicholas Evans, Murray P Cox, Matthew Leavesley, Michael Dannemann, Tonis Org, Mait Metspalu, Mayukh Mondal, Francois-Xavier Ricaut
Published in: bioRxiv, Issue preprint, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.15.520226

Deliverables

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