Publications

My Google Scholar

* indicates authors with equal contributions

References

1.

Massilani, D., Peyrégne, S., Iasi, L. N. M., Filippo, C. de, Mafessoni, F., Bossoms Mesa, A., Sümer, A. P., Swiel, Y., Popli, D., Silverman, S., Boyle, M. J., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Higham, T., Douka, K., Meyer, M., Zeberg, H., Kelso, J. & Pääbo, S. A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals. Proceedings of the National Academy of Sciences 123, e2534576123 (2026).

2.

Sümer, A. P., Rougier, H., Villalba-Mouco, V., Huang, Y., Iasi, L. N. M., Essel, E., Bossoms Mesa, A., Furtwaengler, A., Peyrégne, S., Filippo, C. de, Rohrlach, A. B., Pierini, F., Mafessoni, F., Fewlass, H., Zavala, E. I., Mylopotamitaki, D., Bianco, R. A., Schmidt, A., Zorn, J., Nickel, B., Patova, A., Posth, C., Smith, G. M., Ruebens, K., Sinet-Mathiot, V., Stoessel, A., Dietl, H., Orschiedt, J., Kelso, J., Zeberg, H., Bos, K. I., Welker, F., Weiss, M., McPherron, S. P., Schüler, T., Hublin, J.-J., Velemínský, P., Brůžek, J., Peter, B. M., Meyer, M., Meller, H., Ringbauer, H., Hajdinjak, M., Prüfer, K. & Krause, J. Earliest modern human genomes constrain timing of Neanderthal admixture. Nature 638, 711–717 (2025).

3.

Baruch, O., Levy, A. A. & Mafessoni, F. A multi-omics approach to identify deleterious mutations in plants. (2024) doi:10.1101/2024.08.22.609273.

4.

Ben-Tov*, D., Mafessoni*, F., Cucuy, A., Honig, A., Melamed-Bessudo, C. & Levy, A. A. Uncovering the dynamics of precise repair at CRISPR/Cas9-induced double-strand breaks. Nature Communications 15, 5096 (2024).

5.

Tramacere, A. & Mafessoni, F. Cognitive Twists: The Coevolution of Learning and Genes in Human Cognition. Review of Philosophy and Psychology 15, 189–217 (2024).

6.

Dahan-Meir, T., Ellis, T. J., Mafessoni, F., Sela, H., Rudich, O., Manisterski, J., Avivi-Ragolsky, N., Raz, A., Feldman, M., Anikster, Y., Nordborg, M. & Levy, A. A. 36-year study reveals stability of a wild wheat population across microhabitats. Molecular Ecology 33, e17512 (2024).

7.

Samach*, A., Mafessoni*, F., Gross*, O., Melamed-Bessudo, C., Filler-Hayut, S., Dahan-Meir, T., Amsellem, Z., Pawlowski, W. P. & Levy, A. A. CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements. The Plant Cell koad209 (2023) doi:10.1093/plcell/koad209.

8.

Tkaczynski*, P. J., Mafessoni*, F., Girard-Buttoz, C., Samuni, L., Ackermann, C. Y., Fedurek, P., Gomes, C., Hobaiter, C., Löhrich, T., Manin, V., Preis, A., Valé, P. D., Wessling, E. G., Wittiger, L., Zommers, Z., Zuberbuehler, K., Vigilant, L., Deschner, T., Wittig, R. M. & Crockford, C. Shared community effects and the non-genetic maternal environment shape cortisol levels in wild chimpanzees. Communications Biology 6, 565 (2023).

9.

Li, L.-F., Zhang, Z.-B., Wang, Z.-H., Li, N., Sha, Y., Wang, X.-F., Ding, N., Li, Y., Zhao, J., Wu, Y., Gong, L., Mafessoni, F., Levy, A. A. & Liu, B. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. Molecular Plant 15, 488–503 (2022).

10.

Mafessoni, F., Lachmann, M. & Gokhale, C. S. On the fitness of informative cues in complex environments. Journal of Theoretical Biology 527, 110819 (2021).

11.

Vernot, B., Zavala, E. I., Gómez-Olivencia, A., Jacobs, Z., Slon, V., Mafessoni, F., Romagné, F., Pearson, A., Petr, M., Sala, N., Pablos, A., Aranburu, A., Castro, J. M. B. de, Carbonell, E., Li, B., Krajcarz, M. T., Krivoshapkin, A. I., Kolobova, K. A., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Grote, S., Essel, E., Herráez, D. L., Nagel, S., Nickel, B., Richter, J., Schmidt, A., Peter, B., Kelso, J., Roberts, R. G., Arsuaga, J.-L. & Meyer, M. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science (New York, N.Y.) 372, eabf1667 (2021).

12.

Reinscheid, R. K., Mafessoni, F., Lüttjohann, A., Jüngling, K., Pape, H.-C. & Schulz, S. Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality. Peptides 138, 170506 (2021).

13.

Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., Essel, E., Nagel, S., Nickel, B., Richter, J., Moldovan, O. T., Constantin, S., Endarova, E., Zahariev, N., Spasov, R., Welker, F., Smith, G. M., Sinet-Mathiot, V., Paskulin, L., Fewlass, H., Talamo, S., Rezek, Z., Sirakova, S., Sirakov, N., McPherron, S. P., Tsanova, T., Hublin, J.-J., Peter, B. M., Meyer, M., Skoglund, P., Kelso, J. & Pääbo, S. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 592, 253–257 (2021).

14.

Trucchi*, E., Gratton*, P., Mafessoni*, F., Motta, S., Cicconardi, F., Mancia, F., Bertorelle, G., D’Annessa, I. & Di Marino, D. Population Dynamics and Structural Effects at Short and Long Range Support the Hypothesis of the Selective Advantage of the G614 SARS-CoV-2 Spike Variant. Molecular Biology and Evolution 38, 1966–1979 (2021).

15.

Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., Schierup, M. H. & Stefansson, K. The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes. Nature 582, 78–83 (2020).

16.

Mafessoni, F., Grote, S., Filippo, C. de, Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., Skoglund, P., Krivoshapkin, A. I., Derevianko, A. P., Meyer, M., Kelso, J., Peter, B., Prüfer, K. & Pääbo, S. A high-coverage Neandertal genome from Chagyrskaya Cave. Proceedings of the National Academy of Sciences 117, 15132–15136 (2020).

17.

Barbieri, C., Barquera, R., Arias, L., Sandoval, J. R., Acosta, O., Zurita, C., Aguilar-Campos, A., Tito-Álvarez, A. M., Serrano-Osuna, R., Gray, R. D., Mafessoni, F., Heggarty, P., Shimizu, K. K., Fujita, R., Stoneking, M., Pugach, I. & Fehren-Schmitz, L. The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast. Molecular Biology and Evolution 36, 2698–2713 (2019).

18.

Bokelmann, L., Hajdinjak, M., Peyrégne, S., Brace, S., Essel, E., Filippo, C. de, Glocke, I., Grote, S., Mafessoni, F., Nagel, S., Kelso, J., Prüfer, K., Vernot, B., Barnes, I., Pääbo, S., Meyer, M. & Stringer, C. A genetic analysis of the Gibraltar Neanderthals. Proceedings of the National Academy of Sciences of the United States of America 116, 15610–15615 (2019).

19.

Peyrégne, S., Slon, V., Mafessoni, F., Filippo, C. de, Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Cabec, A. L., Wehrberger, K., Conard, N. J., Kind, C. J., Posth, C., Krause, J., Abrams, G., Bonjean, D., Modica, K. D., Toussaint, M., Kelso, J., Meyer, M., Pääbo, S. & Prüfer, K. Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. Science Advances 5, eaaw5873 (2019).

20.

Mafessoni, F. & Lachmann, M. The complexity of understanding others as the evolutionary origin of empathy and emotional contagion. Scientific Reports 9, 5794 (2019).

21.

Mafessoni, F. Encounters with archaic hominins. Nature Ecology & Evolution 3, 14–15 (2019).

22.

Douka, K., Slon, V., Jacobs, Z., Ramsey, C. B., Shunkov, M. V., Derevianko, A. P., Mafessoni, F., Kozlikin, M. B., Li, B., Grün, R., Comeskey, D., Devièse, T., Brown, S., Viola, B., Kinsley, L., Buckley, M., Meyer, M., Roberts, R. G., Pääbo, S., Kelso, J. & Higham, T. Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave. Nature 565, 640 (2019).

23.

Mafessoni, F., Prasad, R. B., Groop, L., Hansson, O. & Prüfer, K. Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets. Genome Biology and Evolution 10, 2697–2708 (2018).

24.

Slon*, V., Mafessoni*, F., Vernot*, B., Filippo, C. de, Grote, S., Viola, B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., Douka, K., Higham, T., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K. & Pääbo, S. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature 561, 113 (2018).

25.

Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crevecoeur, I., Semal, P., Soressi, M., Talamo, S., Hublin, J.-J., Gušić, I., Kućan, Ž., Rudan, P., Golovanova, L. V., Doronichev, V. B., Posth, C., Krause, J., Korlević, P., Nagel, S., Nickel, B., Slatkin, M., Patterson, N., Reich, D., Prüfer, K., Meyer, M., Pääbo, S. & Kelso, J. Reconstructing the genetic history of late Neanderthals. Nature 555, 652–656 (2018).

26.

Mafessoni, F. & Prüfer, K. Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans. Proceedings of the National Academy of Sciences 114, E10256–E10257 (2017).

27.

Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., Rasilla, M. de la, Lalueza-Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., Stewart, J. R., Derevianko, A. P., Jacobs, Z., Li, B., Roberts, R. G., Shunkov, M. V., Lumley, H. de, Perrenoud, C., Gušić, I., Kućan, Ž., Rudan, P., Aximu-Petri, A., Essel, E., Nagel, S., Nickel, B., Schmidt, A., Prüfer, K., Kelso, J., Burbano, H. A., Pääbo, S. & Meyer, M. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017).

28.

Mafessoni, F. & Lachmann, M. Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones. Genetics 201, 1581–1589 (2015).

29.

Banti*, V., Mafessoni*, F., Loreti, E., Alpi, A. & Perata, P. The heat-inducible transcription factor HsfA2 enhances anoxia tolerance in Arabidopsis. Plant Physiology 152, 1471–1483 (2010).