Publications

• The Population-Specific Impact of Neandertal Introgression on Human Disease , Michael Dannemann, Genome Biology and Evolution, Volume 13, Issue 1, January 2021, evaa250, https://doi.org/10.1093/gbe/evaa250
• Harnessing pluripotent stem cells as models to decipher human evolution, Michael Dannemann, Irene Gallego Romero, first published: 20 April 2021, https://doi.org/10.1111/febs.15885
• Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution? Evan K. Irving-Pease, Rasa Muktupavela, Michael Dannemann, Fernando Racimo. Frontiers in Genetics –  Evolutionary and Population Genetics, Volume, first published August, 2021, https://doi.org/10.3389/fgene.2021.703541
• Detection of Neanderthal Adaptively Introgressed Genetic Variants that Modulate Reporter Gene Expression in Human Immune Cells. Jagoda, E., Xue, J.R., Reilly, S.K., Dannemann, M., Racimo, F., Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P.C., Capellini, T.D. Molecular Biology and Evolution. First published October 2021,  https://doi.org/10.1093/molbev/msab304
• Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas. Linda Ongaro, Mayukh Mondal, Rodrigo Flores, Davide Marnetto, Ludovica Molinaro, Marta E Alarcón-Riquelme, Andrés Moreno-Estrada, Nedio Mabunda, Mario Ventura, Kristiina Tambets, Garrett Hellenthal, Cristian Capelli, Toomas Kivisild, Mait Metspalu, Luca Pagani, Francesco Montinaro,  Human Molecular Genetics, Volume 30, Issue 22, 15 November 2021, Pages 2123–2134, https://doi.org/10.1093/hmg/ddab177
• Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes. 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, Scietific Reports 11, 21088 (2021). https://doi.org/10.1038/s41598-021-00123-x
• Revisiting the out of Africa event with a deep-learning approach. Francesco Montinaro; Vasili Pankratov; Burak Yelmen; Burak Yelmen; Luca Pagani; Luca Pagani; Mayukh Mondal, The American Journal of Human Genetics 108, no 11, November 4^th 2021, pages 2037-2051, https://doi.org/10.1016/j.ajhg.2021.09.006
• Chronology of natural selection in Oceanian genomes. Brucato, Nicolas, Mathilde André, Georgi Hudjashov, Mayukh Mondal, Murray P. Cox, Matthew Leavesley, and François-Xavier Ricaut, IScience 25, no 7, June 30, 2022, https://doi.org/10.1016/j.isci.2022.104583
• Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul. Brucato, Nicolas, Mathilde André, Roxanne Tsang, Lauri Saag, Jason Kariwiga, Kylie Sesuki, Teppsy Beni, William Pomat, John Muke, and Vincent Meyer, Molecular Biology and Evolution, Volume 38, Issue 11, November 2021, Pages 5107-5121, https://doi.org/10.1093/molbev/msab238
• Ancestral Genomic Contributions to Complex Traits in Contemporary Europeans. 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, Current Biology, Volume 32, Issue 6, p1412-1419, March 28, 2022, https://doi.org/10.1016/j.cub.2022.01.046
• Phylogenetic History of Patrilineages Rare in Northern and Eastern Europe from Large-Scale Re-Sequencing of Human Y-Chromosomes. Ilumäe, Anne-Mai, Helen Post, Rodrigo Flores, Monika Karmin, Hovhannes Sahakyan, Mayukh Mondal, Francesco Montinaro, Lauri Saag, Concetta Bormans, and Luisa Fernanda Sanchez, European Journal of Human Genetics, 29, p1510–1519, May 7, 2021, https://doi.org/10.1038/s41431-021-00897-8
• Improving Selection Detection with Population Branch Statistic on Admixed Populations. Burak Yelmen, Davide Marnetto, Ludovica Molinaro, Rodrigo Flores, Mayukh Mondal, Luca Pagani, Genome Biology and Evolution, Volume 13, Issue 4, April 2021, https://doi.org/10.1093/gbe/evab039
• Climatic windows for human migration out of Africa in the past 300,000 years. Robert M Beyer, Mario Krapp, Anders Eriksson, Andrea Manica, Nature Communications volume 12, Article number: 4889 (2021), https://doi.org/10.1038/s41467-021-24779-1
• Genetic architecture of gene regulation in Indonesian populations identies QTLs associated with local ancestry and archaic introgression. 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, American Journal of Human Genetics, Volume 109, Issue 1, p50-65, January 6, 2022, https://doi.org/10.1016/j.ajhg.2021.11.017
• Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes. 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, Transl Psychiatry 12, 433 (2022). https://doi.org/10.1038/s41398-022-02196-2
• Long-range regulatory effects of Neandertal DNA in modern humans. Danat Yermakovich, Vasili Pankratov, Urmo Võsa, Bayazit Yunusbayev, Estonian Biobank Research Team, Michael Dannemann. Genetics, Volume 223, Issue 3, March 2023, iyac188, https://doi.org/10.1093/genetics/iyac188
• Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels. 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. Nat Commun 15, 3352 (2024). https://doi.org/10.1038/s41467-024-47735-1
• Using fecal immunochemical tubes for the analysis of the gut microbiome has the potential to improve colorectal cancer screening. Kertu Liis Krigul, Oliver Aasmets, Kreete Lüll, Tõnis Org, Elin Org. Sci Rep 11, 19603 (2021). https://doi.org/10.1038/s41598-021-99046-w
• Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection. Vasili Pankratov, Milyausha Yunusbaeva, Sergei Ryakhovsky, Maksym Zarodniuk, Estonian Biobank Research Team & Bayazit Yunusbayev Nat Commun 13, 7069 (2022). https://doi.org/10.1038/s41467-022-34461-9
• Differences in local population history at the finest level: the case of the Estonian population. 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. Eur J Hum Genet 28, 1580–1591 (2020). https://doi.org/10.1038/s41431-020-0699-4
• The genetic legacy of the expansion of Bantu-speaking peoples in Africa. 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 Steyn, …Carina M. Schlebusch, Nature 625, 540–547 (2024). https://doi.org/10.1038/s41586-023-06770-6
• Genome-wide association study of obstructive sleep apnoea in the Million Veteran Program uncovers genetic heterogeneity by sex. 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, eBioMedicine, Volume 90, April 2023, 104536, https://doi.org/10.1016/j.ebiom.2023.104536
• HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases. 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. Commun Biol 6, 1113 (2023). https://doi.org/10.1038/s42003-023-05496-5