Assoz. Prof. Dr. Martin Kuhlwilm

Rymbekova, A, Gelabert, P, Llanos-Lizcano, A, Balakrishnan, K, Hämmerle, M, Han, S, Cheronet, O, Abdykanova, A, Kasymkulov, K, Hrivnyak, M, Eng, JT, Pinhasi, R & Kuhlwilm, M 2026, 'Genomic insights into the Iron Age Saka of Boz-Barmak, Kyrgyzstan', Scientific Reports. https://doi.org/10.1038/s41598-026-62891-8

Stanton, DWG, Bergström, A, Heintzman, PD, van der Valk, T, Carmagnini, A, Ersmark, E, Pawar, H, Sandoval-Velasco, M, Androsov, S, Fedorov, S, Kuhlwilm, M, Nagel, D, Plotnikov, V, Protopopov, A, Shapiro, B, Barnett, R, Sinding, MHS, Marques-Bonet, T, Yamaguchi, N, Gilbert, MTP, Götherström, A, Skoglund, P, Frantz, L & Dalén, L 2026, 'Paleogenomes reveal the evolutionary relationship between modern and cave lions', Cell, vol. 189, no. 14, pp. 4425-4436.e11. https://doi.org/10.1016/j.cell.2026.05.007

Huang, X, Hackl, JAL & Kuhlwilm, M 2025, 'Decoding genomic landscapes of introgression', Trends in Genetics, vol. 41, no. 12, pp. 1096–1108. https://doi.org/10.1016/j.tig.2025.07.001

Huang, X, Chen, S, Hackl, J & Kuhlwilm, M 2025, 'SAI: A Python Package for Statistics for Adaptive Introgression', Molecular Biology and Evolution, vol. 42, no. 12. https://doi.org/10.1093/molbev/msaf295

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

Pigott, EM, Cheshmedzhieva, K, Zeller, E, van der Sluis, LG, Chowdhury, MP, Gianni, M, Végh, E, Uthmeier, T, Chabai, V, Patou-Mathis, M, Šimková, PG, Voglmayr, JN, Weber, GW, 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, vol. 122, no. 45, e2518974122. https://doi.org/10.1073/pnas.2518974122

Llanos-Lizcano, A, Hämmerle, M, Sperduti, A, Sawyer, S, Zagorc, B, Özdoğan, KT, 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, vol. 15, 757. https://doi.org/10.1038/s41598-024-85038-z

PERE, GELABERT, Bickle, PF, Hofmann, D, Teschler-Nicola, ME, Anders, A, Huang, X, Hämmerle, M, Olalde, I, Fournier, R, Ringbauer, H, Akbari, A, Cheronet, O, Lazaridis, I, Broomandkhoshbacht, N, Fernandes, DM, Buttinger, K, Callan, K, Candilio, F, Morante, GB, Curtis, E, Ferry, M, Keating, D, Freilich, S, Kearns, A, Harney, É, Lawson, AM, Mandl, K, Michel, M, Oberreiter, V, Zagorc, B, Oppenheimer, J, Sawyer, S, Schattke, C, Özdoğan, KT, Qiu, L, Workman, JN, Zalzala, F, Mallick, S, Mah, M, Micco, A, Pieler, F, Pavuk, J, Šefčáková, A, Lazar, C, Starović, A, Djuric, M, Škrivanko, MK, Slaus, M, Bedić, Ž, Novotny, F, Szabó, LD, Cserpák-Laczi, O, Hága, T, Szolnoki, L, Hajdú, Z, Mirea, P, Nagy, EG, Virág, ZM, Attila, HM, Horváth, LA, Biró, KT, Domboróczki, L, Szeniczey, T, Jakucs, J, Szelekovszky, M, Farkas, Z, Sztáncsuj, SJ, Tóth, K, Csengeri, P, Pap, I, Patay, R, Putica, A, Vasov, B, Havasi, B, Sebők, K, Raczky, P, Lovász, G, Tvrdy, Z, Rohland, N, Novak, M, Ruttkay, M, Krošláková, M, Batora, J, Paluch, T, Borić, D, Dani, J, Kuhlwilm, M, Palamara, PF, Hajdu, T, Pinhasi, R & Reich, D 2025, 'Social and genetic diversity in first farmers of central Europe', Nature Human Behaviour, vol. 9, no. 1, 19544, pp. 53-64. 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, VJ, Marques-Bonet, T, Guschanski, K, Calvignac-Spencer, S, Pinhasi, R & Kuhlwilm, M 2024, 'Screening great ape museum specimens for DNA viruses', Scientific Reports, vol. 14, no. 1, 29806. https://doi.org/10.1038/s41598-024-80780-w

Han, S, Filippo, CD, Parra, G, Meneu, JR, Laurent, R, Frandsen, P, Hvilsom, C, Gronau, I, Marques-Bonet, T, Kuhlwilm, M & Andrés, AM 2024, 'Deep genetic substructure within bonobos', Current Biology, vol. 34, no. 22, pp. 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, vol. 30, no. 4, pp. 815-817. https://doi.org/10.3201/eid3004.231546

Kuderna, LFK, Ulirsch, JC, Rashid, S, Ameen, M, Sundaram, L, Hickey, G, Cox, AJ, Gao, H, Kumar, A, Aguet, F, Christmas, MJ, Clawson, H, Haeussler, M, Janiak, MC, Kuhlwilm, M, Orkin, JD, Bataillon, T, Manu, S, Valenzuela, A, Bergman, J, Rouselle, M, Silva, FE, Agueda, L, Blanc, J, Gut, M, de Vries, D, Goodhead, I, Harris, RA, Raveendran, M, Jensen, A, Chuma, IS, Horvath, JE, Hvilsom, C, Juan, D, Frandsen, P, Schraiber, JG, de Melo, FR, Bertuol, F, Byrne, H, Sampaio, I, Farias, I, Valsecchi, J, Messias, M, da Silva, MNF, Trivedi, M, Rossi, R, Hrbek, T, Andriaholinirina, N, Rabarivola, CJ, Zaramody, A, Jolly, CJ, Phillips-Conroy, J, Wilkerson, G, Abee, C, Simmons, JH, Fernandez-Duque, E, Kanthaswamy, S, Shiferaw, F, Wu, D, Zhou, L, Shao, Y, Zhang, G, Keyyu, JD, Knauf, S, Le, MD, Lizano, E, Merker, S, Navarro, A, Nadler, T, Khor, CC, Lee, J, Tan, P, Lim, WK, Kitchener, AC, Zinner, D, Gut, I, Melin, AD, Guschanski, K, Schierup, MH, Beck, RMD, Karakikes, I, Wang, KC, Umapathy, G, Roos, C, Boubli, JP, Siepel, A, Kundaje, A, Paten, B, Lindblad-Toh, K, Rogers, J, Marques Bonet, T & Farh, KK-H 2024, 'Identification of constrained sequence elements across 239 primate genomes', Nature, vol. 625, no. 7996, pp. 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, vol. 25, no. 1, pp. 61–78. https://doi.org/10.1038/s41576-023-00636-3

Pawar, H, Rymbekova, A, Cuadros-Espinoza, S, Huang, X, Manuel, MD, Valk, TVD, Lobon, I, Alvarez-Estape, M, Haber, M, Dolgova, O, Han, S, Esteller-Cucala, P, Juan, D, Ayub, Q, Garcia, RB, Kelley, J, Cornejo, OE, Lao, O, Andrés, AM, Guschanski, K, Ssebide, B, Cranfield, M, Tyler-Smith, C, Xue, Y, Prado-Martinez, J, Marques-Bonet, T & Kuhlwilm, M 2023, 'Ghost admixture in eastern gorillas', Nature Ecology & Evolution, vol. 7, no. 9, pp. 1503-1514. https://doi.org/10.1038/s41559-023-02145-2

Kuderna, LFK, Gao, H, Janiak, MC, Kuhlwilm, M, Orkin, JD, Bataillon, T, Manu, S, Valenzuela, A, Bergman, J, Rousselle, M, Silva, FE, Agueda, L, Blanc, J, Gut, M, Vries, DD, Goodhead, I, Harris, RA, Raveendran, M, Jensen, A, Chuma, IS, Horvath, JE, Hvilsom, C, Juan, D, Frandsen, P, Schraiber, JG, Melo, FRD, Bertuol, F, Byrne, H, Sampaio, I, Farias, I, Valsecchi, J, Messias, M, Silva, MNFD, Trivedi, M, Rossi, R, Hrbek, T, Andriaholinirina, N, Rabarivola, CJ, Zaramody, A, Jolly, CJ, Phillips-Conroy, J, Wilkerson, G, Abee, C, Simmons, JH, Fernandez-Duque, E, Kanthaswamy, S, Shiferaw, F, Wu, D, Zhou, L, Shao, Y, Zhang, G, Keyyu, JD, Knauf, S, Le, MD, Lizano, E, Merker, S, Navarro, A, Nadler, T, Khor, CC, Lee, J, Tan, P, Lim, WK, Kitchener, AC, Zinner, D, Gut, I, Melin, AD, Guschanski, K, Schierup, MH, Beck, RMD, Umapathy, G, Roos, C, Boubli, JP, Rogers, J, Farh, KK-H & Bonet, TM 2023, 'A global catalog of whole-genome diversity from 233 primate species', Science, vol. 380, no. 6648, pp. 906-913. https://doi.org/10.1126/science.abn7829

Sørensen, EF, Harris, RA, Zhang, L, Raveendran, M, Kuderna, LFK, Walker, JA, Storer, JM, Kuhlwilm, M, Fontsere, C, Seshadri, L, Bergey, CM, Burrell, AS, Bergman, J, Phillips-Conroy, JE, Shiferaw, F, Chiou, KL, Chuma, IS, Keyyu, JD, Fischer, J, Gingras, M-C, Salvi, S, Doddapaneni, H, Schierup, MH, Batzer, MA, Jolly, CJ, Knauf, S, Zinner, D, Farh, KK-H, Marques-Bonet, T, Munch, K, Roos, C & Rogers, J 2023, 'Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons', Science, vol. 380, no. 6648, eabn8153. https://doi.org/10.1126/science.abn8153

Gao, H, Hamp, T, Ede, J, Schraiber, JG, McRae, J, Singer-Berk, M, Yang, Y, Dietrich, ASD, Fiziev, P, Kuderna, LFK, Sundaram, L, Wu, Y, Adhikari, AN, Field, Y, Batzoglou, S, Aguet, F, Lemire, G, Reimers, R, Balick, D, Janiak, M, Kuhlwilm, M, Orkin, J, Manu, S, Valenzuela, A, Bergman, J, Rousselle, M, Silva, FE, Calpena, LA, Blanc, J, Gut, M, Vries, DD, Goodhead, I, Harris, R, Raveendran, M, Jensen, A, Chuma, I, Horvath, J, Hvilsom, C, Juan, D, Frandsen, P, Melo, FRD, Bertuol, F, Byrne, H, Sampaio, I, Farias, IP, Valsecchi, J, Messias, M, Silva, MNFD, Trivedi, M & Rossi, RV 2023, 'The landscape of tolerated genetic variation in humans and primates', Science, vol. 380, no. 6648, eabn8197. https://doi.org/10.1126/science.abn8197

Bentley, BP, Carrasco-Valenzuela, T, Ramos, EKDS, Pawar, H, Arantes, LS, 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, Wood, J, Yetsko, K, Perrault, J, Stewart, K, Benson, SR, Levy, Y, Todd, E, Shaffer, HB, Scott, P, Henen, B, Murphy, RW, Mohr, D, Scott, AF, Duffy, D, Gemmell, NJ, Suh, A, Winkler, S, Thibaud-Nissen, F, Nery, MF, Marques-Bonet, T, Antunes, A, Tikochinski, Y, Dutton, PH, Fedrigo, O, Myers, E, Jarvis, E, Mazzoni, C & Komoroske, LM 2023, 'Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories', Proceedings of the National Academy of Sciences, vol. 120, no. 7, e2201076120. https://doi.org/10.1073/pnas.2201076120