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Assoz. Prof. Dr. Martin Kuhlwilm

T: +43-1-4277-54730

martin.kuhlwilm@univie.ac.at

https://admixture.univie.ac.at/

Winter term 2025

300031 SE Departmentseminar Evolutionäre Anthropologie

300072 UE Applications of admixture genomics

300075 VO Computational genomics approaches to evolution and human history

Summer term 2025

300005 SE Machine Learning in Population Genetics

300048 UE Sequencing bioinformatics for beginners

300222 VO Scientific methods and applications in human evolution

300223 VO Evolutionary Genomics and Admixture

Winter term 2024

300031 SE Departmentseminar Evolutionäre Anthropologie

300072 UE Applications of admixture genomics

300075 VO Computational genomics approaches to evolution and human history

301849 UE Scientific Practice in Molecular Microbiology, Ecology or Immunobiology

550001 UE Sequencing data analysis and genomics

Han, S. J., Riyahi, S., Huang, X., & Kuhlwilm, M. (2025). A curated dataset of great ape genome diversity. Scientific Data, 12, Article 1835. https://doi.org/10.1038/s41597-025-06124-z

Huang, X., Chen, S., Hackl, J., & Kuhlwilm, M. (2025). SAI: A Python Package for Statistics for Adaptive Introgression. Molecular Biology and Evolution, 42, Article msaf295. https://doi.org/10.1093/molbev/msaf295

Pigott, E. M., Cheshmedzhieva, K., Zeller, E., van der Sluis, L. G., Chowdhury, M. P., Gianni, M., Végh, E., Uthmeier, T., Chabai, V., Patou-Mathis, M., Šimková, P. G., Voglmayr, J. N., Weber, G. W., Pinhasi, R., Timmermann, A., Kuhlwilm, M., Douka, K., & Higham, T. (2025). A new late Neanderthal from Crimea reveals long-distance connections across Eurasia. Proceedings of the National Academy of Sciences, 122(45), e2518974122. https://doi.org/10.1073/pnas.2518974122

Huang, X., Hackl, J. A. L., & Kuhlwilm, M. (2025). Decoding genomic landscapes of introgression. Trends in Genetics, 41, 1096–1108. Advance online publication. https://doi.org/10.1016/j.tig.2025.07.001

Kuhlwilm, M., Boeckx, C., & Moriano, J. (2025). Palaeogenomics: A window into the genetic basis of derived traits in Homo sapiens. In The Oxford Handbook of Approaches to Language Evolution Oxford University Press. https://doi.org/10.1093/oxfordhb/9780192886491.013.12

Llanos-Lizcano, A., Hämmerle, M., Sperduti, A., Sawyer, S., Zagorc, B., Özdoğan, K. T., Guellil, M., Cheronet, O., Kuhlwilm, M., Pinhasi, R., & Gelabert, P. (2025). Intra-individual variability in ancient plasmodium DNA recovery highlights need for enhanced sampling. Scientific Reports, 15, Article 757. Advance online publication. https://doi.org/10.1038/s41598-024-85038-z

PERE, GELABERT., Bickle, P. F., Hofmann, D., Teschler-Nicola, M. E., Anders, A., Huang, X., Hämmerle, M., Olalde, I., Fournier, R., Ringbauer, H., Akbari, A., Cheronet, O., Lazaridis, I., Broomandkhoshbacht, N., Fernandes, D. M., Buttinger, K., Callan, K., Candilio, F., Morante, G. B., ... Reich, D. (2025). Social and genetic diversity in first farmers of central Europe. Nature Human Behaviour, 9(1), 53-64. Article 19544. https://doi.org/10.1038/s41562-024-02034-z

Hämmerle, M., Guellil, M., Trgovec-Greif, L., Cheronet, O., Sawyer, S., Ruiz-Gartzia, I., Lizano, E., Rymbekova, A., Gelabert, P., Bernardi, P., Han, S., Rattei, T., Schuenemann, V. J., Marques-Bonet, T., Guschanski, K., Calvignac-Spencer, S., Pinhasi, R., & Kuhlwilm, M. (2024). Screening great ape museum specimens for DNA viruses. Scientific Reports, 14(1), Article 29806. https://doi.org/10.1038/s41598-024-80780-w

Han, S., Filippo, C. D., Parra, G., Meneu, J. R., Laurent, R., Frandsen, P., Hvilsom, C., Gronau, I., Marques-Bonet, T., Kuhlwilm, M., & Andrés, A. M. (2024). Deep genetic substructure within bonobos. Current Biology, 34(22), 5341-5348.e3. https://doi.org/10.1101/2024.07.01.601523, https://doi.org/10.1016/j.cub.2024.09.043

Hämmerle, M., Rymbekova, A., Gelabert, P., Sawyer, S., Cheronet, O., Bernardi, P., Calvignac-Spencer, S., Kuhlwilm, M., Guellil, M., & Pinhasi, R. (2024). Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak. Emerging infectious diseases, 30(4), 815-817. https://doi.org/10.3201/eid3004.231546

Kuderna, L. F. K., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., Cox, A. J., Gao, H., Kumar, A., Aguet, F., Christmas, M. J., Clawson, H., Haeussler, M., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., ... Farh, K. K.-H. (2024). Identification of constrained sequence elements across 239 primate genomes. Nature, 625(7996), 735-742. https://doi.org/10.1038/s41586-023-06798-8

Huang, X., Rymbekova, A., Dolgova, O., Lao, O., & Kuhlwilm, M. (2024). Harnessing deep learning for population genetic inference. Nature Reviews. Genetics, 25(1), 61–78. https://doi.org/10.1038/s41576-023-00636-3

Pawar, H., Rymbekova, A., Cuadros-Espinoza, S., Huang, X., Manuel, M. D., Valk, T. V. D., Lobon, I., Alvarez-Estape, M., Haber, M., Dolgova, O., Han, S., Esteller-Cucala, P., Juan, D., Ayub, Q., Garcia, R. B., Kelley, J., Cornejo, O. E., Lao, O., Andrés, A. M., ... Kuhlwilm, M. (2023). Ghost admixture in eastern gorillas. Nature Ecology & Evolution, 7(9), 1503-1514. https://doi.org/10.1038/s41559-023-02145-2

Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., Vries, D. D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A., ... Bonet, T. M. (2023). A global catalog of whole-genome diversity from 233 primate species. Science, 380(6648), 906-913. https://doi.org/10.1126/science.abn7829

Sørensen, E. F., Harris, R. A., Zhang, L., Raveendran, M., Kuderna, L. F. K., Walker, J. A., Storer, J. M., Kuhlwilm, M., Fontsere, C., Seshadri, L., Bergey, C. M., Burrell, A. S., Bergman, J., Phillips-Conroy, J. E., Shiferaw, F., Chiou, K. L., Chuma, I. S., Keyyu, J. D., Fischer, J., ... Rogers, J. (2023). Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science, 380(6648), Article eabn8153. https://doi.org/10.1126/science.abn8153

Gao, H., Hamp, T., Ede, J., Schraiber, J. G., McRae, J., Singer-Berk, M., Yang, Y., Dietrich, A. S. D., Fiziev, P., Kuderna, L. F. K., Sundaram, L., Wu, Y., Adhikari, A. N., Field, Y., Batzoglou, S., Aguet, F., Lemire, G., Reimers, R., Balick, D., ... Rossi, R. V. (2023). The landscape of tolerated genetic variation in humans and primates. Science, 380(6648), Article eabn8197. https://doi.org/10.1126/science.abn8197

Bentley, B. P., Carrasco-Valenzuela, T., Ramos, E. K. D. S., Pawar, H., Arantes, L. S., Alexander, A., Banerjee, S., Masterson, P., Kuhlwilm, M., Pippel, M., Mountcastle, J., Haase, B., Uliano-Silva, M., Formenti, G., Howe, K., Chow, W., Tracey, A., Sims, Y., Pelan, S., ... Komoroske, L. M. (2023). Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences, 120(7), Article e2201076120. https://doi.org/10.1073/pnas.2201076120

Huang, X., Kruisz, P., & Kuhlwilm, M. (2022). sstar: A Python package for detecting archaic introgression from population genetic data with S*. Molecular Biology and Evolution, 39(11), Article msac212. https://doi.org/10.1101/2022.03.10.483765, https://doi.org/10.1093/molbev/msac212

Andirkó, A., Moriano, J., Vitriolo, A., Kuhlwilm, M., Testa, G., & Boeckx, C. (2022). Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens. Scientific Reports, 12(1), Article 9937. https://doi.org/10.1038/s41598-022-13589-0

Fontsere, C., Kuhlwilm, M., Morcillo-Suarez, C., Alvarez-Estape, M., Lester, J. D., Gratton, P., Schmidt, J. M., Dieguez, P., Aebischer, T., Álvarez-Varona, P., Agbor, A., Angedakin, S., Assumang, A. K., Ayimisin, E. A., Bailey, E., Barubiyo, D., Bessone, M., Carretero-Alonso, A., Chancellor, R., ... Marques-Bonet, T. (2022). Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics, 2(6), Article 100133. https://doi.org/10.1016/j.xgen.2022.100133