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2025
Fagernäs, Z., Sieling, S., Troché, G., Bakker, J.K., Olsen, J.V., Welker, F., 2025. Identification and removal of contamination in palaeoproteomic analysis of dental enamel. Scientific Reports 16: 1853, pp. 1-10. https://doi.org/10.1038/s41598-025-31472-6
Fagernäs, Z., Troche, G., Goldberg, P., Hublin, J.-J., McPherron, S.P., Murphe, W.C., Olsen, J.V., Sandgathe, D., Sirakov, N., Soressi, M., Tsanova, T., Turq, A., Wierer, M., Welker, F., Aldeias, V., 2025. New methods on the blocks: taxonomic identification of archaeological bones in resin-embedded sediments through paleoproteomics. PNAS Nexus 4 (10), pgaf289. pp. 1-12. https://doi.org/10.1093/pnasnexus/pgaf289
Dekker, J.A.A., Carli, P., Winter, R.M., Collins, M.J., Dickinson, M.R., Harvey, V.L., Hill, E., Nair, B., Tsutaya, T., Vinas-Caron, L.C., Warinner, W., Welker, F., Fagernäs, Z., 2025. Open science, communication, and collaboration for the future of palaeoproteomics. PCI Archaeology 5, e77. pp. 1-29. https://doi.org/10.24072/pcjournal.576
Arrieta-Donato, E., Tavares-Guzmán, Á., Bravo-Lopez, M., Villa-Islas, V., Castillo-Carbajal, A., Li, W., ... & Sánchez-Quinto, F. (2025). Columbian mammoth mitogenomes from Mexico uncover the species’ complex evolutionary history. Science, 390(6768), pp. 47-52. https://doi.org/10.1126/science.adt9651
Villanea, F. A., Peede, D., Kaufman, E. J., Añorve-Garibay, V., Chevy, E. T., Villa-Islas, V., ... & Huerta-Sánchez, E. (2025). The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science, 389(6762), eadl0882, pp. 1-10. https://doi.org/10.1126/science.adl0882
Madupe, P.P., Koenig, C., Patramanis, I., Rüther, P.L., Hlazo, N., Mackie, M., Tawane, M., Krueger, J., Taurozzi, A.J., Troché, G., Kibii, J., Pickering, R., Dickinson, M., Sahle, Y., Kgotleng, D., Musiba, C., Manthi, F., Bell, L., DuPlessis, M., Gilbert, C., Zipfel, B., Kuderna, L.F.K., Lizano, E., Welker, F., Kyriakidou, P., Cox, J., Mollereau, C., Tokarski, C., Blackburn, J., Ramos-Madrigal, J., Marques-Bonet, T., Penkman, K., Zanolli, C., Schroeder, L., Racimo, F., Olsen, J.V., Ackermann, R.R., Cappellini, E., 2025. Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus. Science 388 (6750), pp. 969-973. https://doi.org/10.1126/science.adt9539
Fagernäs, F., Troché, G., Buylaert, J.-P., Khujageldiev, T., Kurbanov, R., Olsen, J.V., Pedersen, M.W., Welker, F., 2025. Cleaning the dead: optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan. Journal of Archaeological Science, 179, 106228. pp. 1-10. https://doi.org/10.1016/j.jas.2025.106228
McGrath, K., van der Sluis, L.G., Lefebvre, A., Charpentier, A., Rodrigues, A.S.L., Álvarez-Fernández, E., Baleux, F., Berganza, E., Chauvière, F.-X., Dachary, M., Duarte Matías, E., Houmard, C., Marín-Arroyo, A.B., de la Rasilla Vives, V., Tapia, J., Thil, F., Tombret, O., Torres-Iglesias, L., Speller, C., Zazzo, A., Pétillon, J.-M., 2025. Late Palaeolithic whale bone tools reveal humand and whale ecology in the Bay of Biscay. Nature Communications 16: 4646, pp. 1-15. https://doi.org/10.1038/s41467-025-59486-8
Tsutaya, T., Sawafuji, R., Taurozzi, A.J., Fagernäs, Z., Patramanis, I., Troché, G., Mackie, M., Gakuhari, T., Oota, H., Tsai, C.-H., Olsen, J.V., Kaifu, Y., Chang, C.-H., Cappellini, Welker, F., 2025. A male Denisovan mandible from Pleistocene Taiwan. Science 388 (6743), pp. 176-180. https://doi.org/10.1126/science.ads3888
Sümer, A.P., Rougier, H., Villalba-Mouco, V., Huang, Y., Iasi, L.N.M., Essel, E., Bossoms Mesa, A., Furtwaengler, A., Peyrégne, S., de Filippo, C., Rohrlach, A.B., Pierini, F., Mafessoni, F., Fewlass, f., 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., Schüler, T., Hublin, J.-J., Velemínský, P., Brůžek, J., Peter, B.P., Meyer, M., Meller, H., Ringbauer, H., Hajdinjak, M., Prüfer, K., Krause, J., 2025. Earliest modern human genomes constrain timing of Neanderthal admixture. Nature 635, pp. 711-717. https://doi.org/10.1038/s41586-024-08420-x
Welker, F., Ásmundsdóttir, R.D., Mylopotamitaki, D., Torres-Iglesias, L., Villa-Islas, V., Le Meillour, L., Fagernäs, F., 2025. Palaeoproteomic contributions, and current limitations, to understanding Middle and Late Pleistocene human evolution. PaleoAnthropology pp. 321-339. https://doi.org/10.48738/2025.iss2.xxx
Rey-Iglesia, A., Pryor, A.J.E., de Jager, D., Wilson, T., Teeter, M., Margaryan, A., Khaskhanov, R., Le Meillour, L., Troché, G., Welker, F., Szpak, P., Dudin, A.E., Lorenzen, E.D., 2025. Ancient biomolecular anlaysis of 39 mammoth individuals from Kostenki 11-1a elucidates Upper Palaeolithic human resource use. Quaternary Environments and Humans 3(1), 100049. pp. 1-15. https://doi.org/10.1016/j.qeh.2024.100049
2024
Smith, G.M., Ruebens, K., Sinet-Mathiot, V., Welker, F., 2024. Towards a deeper integration of ZooMS and zooarchaeology at Palaeolithic sites: current challenges and future directions. PaleoAnthropology 2024 (2), pp. 186-211.
Xia, H., Zhang, D., Wang, J., Fagernäs, Z., Li, T., Li, Y., Yao, J., Lin, D., Troché, G., Smith, G.M., Chen, X., Cheng, T., Shen, X., Han, Y., Olsen, J.V., Shen, Z., Pei, Z., Hublin, J.-J., Chen, F., Welker, F., 2024. Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave. Nature 632, pp. 108-113. https://doi.org/10.1038/s41586-024-07612-9.
Taurozzi, A., Rüther, P.L., Patramanis, I., Koenig, C., Paterson, R.S., Madupe, P.P., Harkin, F.S., Welker, F., Mackie, M., Ramos-Madrigal, J., Olsen, J.V., Cappellini, E., 2024. Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nature Protocols 19, pp. 2085-2116. https://doi.org/10.1038/s41596-024-00975-3
Chiang, Y., Welker, F., Collins, M.J., 2024. Spectra without stories: reporting 94% dark and unidentified ancient proteomes. Open Research Europe 4: 71, pp. 1-13. https://doi.org/10.12688/openreseurope.17225.1
Hansen, J., Dekker, J., Troché, G., Fagernäs, Z., Saña Segui, M., Welker, F., 2024. A comparative study of commercially available, minimally invasive, sampling methods on Early Neolithic humeri analysed via palaeoproteomics. Journal of Archaeological Science 167: 106002, pp. 1-12. https://doi.org/10.1016/j.jas.2024.106002
Le Meillour, L., Sinet-Mathiot, V., Ásmundsdóttir, R.D., Hansen, J., Mylopotamitaki, D., Troché, G., Xia, H., Herrera Bethencourt, J., Ruebens, K., Smith, G.M., Fagernäs, Z., Welker, F., 2024. Increasing sustainability in palaeoproteomics by optimising digestion times for large-scale archaeological bone analyses. iScience 27: 109432, pp. 1-17. https://doi.org/10.1016/j.isci.2024.109432
Dekker, J., Mylopotamitaki, D., Verbaas, A., McCarthy, M.L., Tange Olsen, M., van den Hurk, Y., Bratttinga, J., Welker, F., 2024. Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands. PCI Archaeology 4: e81, pp. 1-28. https://doi.org/10.24072/pcjournal.451
Ásmundsdóttir, R.D., Hansen, J., Troché, G., Olsen, J.V., Saña Sequi, M., Welker, F., 2024. Early Holocene preservation differences between cortical and trabecular bone proteomes. Journal of Archaeological Science: Reports 57: 104643, pp. 1-10. https://doi.org/10.1016/j.jasrep.2024.104643
Fagernäs, Z., Troché, G., Olsen, J.V., Welker, F., 2024. Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases. Journal of Proteomics 298: 105143, pp. 1-10. https://doi.org/10.1016/j.jprot.2024.105143
Pederzani, S., Britton, K., Trost, M., Fewlass, H., Bourgon, N., McCormack, J., Jaouen, K., Dietl, H., Döhle, H.-J., Kirchner, A., Lauer, T., Le Corre, M., McPherron, S.P., Meller, H., Mylopotamitaki, D., Orschiedt, J., Rougier, J., Ruebens, K., Schüler, T., Sinet-Mathiot, V., Smith, G.M., Talamo, S., Tütken, T., Welker, F., Zavala, E.I., Weiss, M., Hublin, J.-J., 2024. Stable isotopes show Homo sapiens dispersed into cold steppes ∼45,000 years ago at Ilsenhöhle in Ranis, Germany. Nature Ecology and Evolution 8, pp. 578-588. https://doi.org/10.1038/s41559-023-02318-z
Smith, G., Ruebens, K., Zavala, E.I., Sinet-Mathiot, V., Fewlass, H., Pederzani, S., Jaouen, K., Mylopotamitaki, D., Britton, K., Rougier, H., Stahlschmidt, M., Meyer, M., Meller, H., Dietl, H., Orschiedt, J., Krause, J., Schüler, T., McPherron, S.P., Weiss, M., Hublin, J.-J., Welker, F., 2024. The ecology, subsistence and diet of ∼45,000 years-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany Nature Ecology and Evolution 8, pp. 564-577. https://doi.org/10.1038/s41559-023-02303-6
Mylopotamitaki, D., Weiss, M., Fewlass, H., Zavala, E.I., Rougier, H., Sümer, A.P., Hajdinjak, M., Smith, G.M., Ruebens, K., Sinet-Mathiot, V., Pederzani, S., Essel, E., Harking, F.S., Xia, H., Hansen, J., Kirchner, A., Lauer, T., Stahlschmidt, M., Hein, M., Talamo, S., Wacker, L., Meller, H., Dietl, H., Orschiedt, J., Olsen, J.V., Zeberg, H., Prüfer, K., Krause, J., Meyer, M., Welker, F., McPherron, S.P., Schüler, T., Hublin, J.-J., 2024. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 626, pp. 341-346. https://doi.org/10.1038/s41586-023-06923-7
Torres-Iglesias, L., Marín-Arroyo, A.B., Welker, F., de la Rasilla, M., 2024. Using ZooMS to assess archaeozoological insights and unravel human subsistence behaviour at La Viña rock shelter (northern Iberia). Journal of Archaeological Science 161: 105904, pp. 1-13. https://doi.org/10.1016/j.jas.2023.105904
2023
Welker, F., 2023. Protein Tales of the Human Past. 45th Kroonvoordracht. Drukkerij J. Bout & Zn (Huizen, the Netherlands). ISBN: 978-90-829-481-5-8. (lecture book print)
Bae, C.J., Aiello, L.C., Hawks, J., Kaifu, Y., Lindal, J., Martinón-Torres, M., Ni, X., Posth, C., Radović, P., Reed, D., Schroeder, L., Schwartz, J.H., Silcox, M.T., Welker, F., Wu, X.-J., Zanolli, C., Roksandic, M. (2023). Moving away from“the Muddle in the Middle” towards solving the Chibanian puzzle. Evolutionary Anthropology 22011. https://doi.org/10.1002/evan.22011
Le Meillour, L., Zazzo, A., Zirah, S., Tombret, O., Barriel, V., Arthur, K.W., Arthur, J.W., Cauliez, J., Chaix, L., Curtis, M.C., Gifford-Gonzalez, D., Gunn, I., Gutherz, X., Hildebrand, E., Khalidi, L., Millet, M., Mitchell, P., Studer, J., Vila, E., Welker, F., Pleurdeau, D., Lesur, J. (2023). The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa. Royal Society Open Science 10, 231002. https://doi.org/10.6084/m9.figshare.c.6935477
Mylopotamitaki, D., Harking, F.S., Taurozzi, A.J., Fagernäs, Z., Godinho, R.M., Smith, G.M., Weiss, M., Schüler, T., McPherron, S.P., Meller, H., Cascalheira, J., Bicho, N., Olsen, J.V., Hublin, J.-J., Welker, F. (2023). Comparing extraction method efficiency for high-throughput palaeoproteomics bone species identification. Scientific Reports 13, 18345. https://doi.org/10.1038/s41598-023-44885-y
Sinet-Mathiot, V., Rendu, W., Steele, T.E., Spasov, R., Madelaine, S., Renou, S., Soulier, M.-C., Martisius, N.L., Aldeais, V., Endarova, E., Goldberg, P., McPherron, S., Rezek, Z., Sandgathe, D., Sirakov, N., Sirakova, S., Soressi, M., Tsanova, T., Turq, A., Hublin, J.-J., Welker, F., Smith, G.M. (2023). Identifying the unidentified fauna enhances insights into hominin subsistence strategies during the Middle to Upper Palaeolithic transition. Archaeological and Anthropological Sciences, 15: 139, pp. 1-18. https://doi.org/10.1007/s12520-023-01830-4
Bartholdy, B.P., Velsko, I.M., Gur-Arieh, S., Fagernäs, Z., Warinnner, C., Henry, A.G (2023). Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus. bioRxiv (preprint). https://doi.org/10.1101/2023.05.23.541904
Ruebens, K., Smith, G.M., Fewlass, H., Sinet-Mathiot, V., Hublin, J.-J. and Welker, F. (2023). Neanderthal subsistence, taphonomy and chronology at Salzgitter-Lebenstedt (Germany): a multifaceted analysis of morphologically unidentifiable bone. J. Quaternary Sci. 38(4), pp. 471-487. https://doi.org/10.1002/jqs.3499
2022
McCormack, J., Bourgon, N., Sinet-Mathiot, V., Rezek, Z., Smith, G. M., Hublin, J.-J., Dabain, M., & Fewlass, H. (2022). Combining collagen extraction with mineral Zn isotope analyses from a single sample for robust palaeoecological investigations. Archaeological and Anthropological Sciences, 14(7), 137. https://doi.org/10.1007/s12520-022-01601-7
Martisius, N., Spasov, R., Smith, G.M., Endarova, E., Sinet-Mathiot, V., Welker, F., Aldeias, V., Horta, P., Marreiros, J., Rezek, Z., McPherron, S.P., Sirakov, N., Sirakova, S., Tsanova, T., Hublin, J.-J. 2022. Initial Upper Palaeolithic bone technology and personal ornaments at Bacho Kiro Cave (Bulgaria). Journal of Human Evolution 167, 103198. https://doi.org/10.1016/j.jhevol.2022.103198
Demeter, F., Zanolli, C., Westaway, K.E., Joannes-Boyau, R., Duringer, P., Morley, M.W., Welker, F., Rüther, P.L., Skinner, M.M., McColl, H., Gaunitz, C., Vinner, L., Dunn, T.E., Olsen, J.V., Sikora, M., Ponche, J.-L., suzzoni, E., Frangeul, S., Boesch, Q., Antoine, P.-O., Pan, L., Xing, S., Zhao, J.-X., Bailey, R.M., Boualaphane, S., Sichanthongtip, P., Sihanam, D., Patole-Edoumba, E., Aubaile, F., Crozier, F., Bourgon, N., Zachwieja, A., Luangkhoth, T., Souksavatdy, V., Sayavongkhamdy, T., Cappellini, E., Bacon, A.-M., Hublin, J.-J., Willerslev, E., Shackelford, L. 2022. A Middle Pleistocene Denisovan molar from the Annamite Chain of norther Laos. Nature Communications, 13, 2557. https://doi.org/10.1038/s41467-022-29923-z
Bocherens, H., Jaouen, K., Rivals, F., Slon, V., Talamo, S., Welker, F., 2022. Methodological advances in Neanderthal identification, phylogeny, chronology, mobility, climate, and diet, in “Updating Neanderthals“, eds. F. Romagnoli, F. Rivals & S. Benazzi. Academic Press, pp. 303-320. ISBN 978-0-12-821428-2.
Rüther, P., Husic, I.M., Bangsgaard, P., Gregersen, K.M, Pantmann, P., Carvalho, M., Godinho, R.M., Friedl, L., Cascaleheira, J., Taurozzi, A.J., Jørkov, M.L.S., Benedetti, M.M., Haws, J., Bicho, N., Welker, F., Cappellini, E., Olsen, J.V. 2022. SPIN enables high throughput species identification of archaeological bone by proteomics. Nature Communications 13, 3485. https://doi.org/10.1038/s41467-022-30097-x
Ruebens, K., Sinet-Mathiot, V., Talamo, S., Smith, G.M., Welker, F., Hublin, J.-J., McPherron, S.P. 2022. The Late Middle Palaeolithic occupation of Abri du Maras (Layer 1, Neronian, Southeast France): integrating lithic analyses, ZooMS and radiocarbon dating to reconstruct Neanderthal hunting behaviour. Journal of Palaeolithic Archaeology, 5:4. https://doi.org/10.1007/s41982-022-00113-z
2021
Smith, G. M., Spasov, R., Martisius, N. L., Sinet-Mathiot, V., Aldeias, V., Rezek, Z., Ruebens, K., Pederzani, S., McPherron, S. P., Sirakova, S., Sirakov, N., Tsanova, T., & Hublin, J.-J. 2021. Subsistence behavior during the Initial Upper Paleolithic in Europe: Site use, dietary practice, and carnivore exploitation at Bacho Kiro Cave (Bulgaria). Journal of Human Evolution, 161, 103074. https://doi.org/10.1016/j.jhevol.2021.103074
Sinet-Mathiot, V., Martisius, N., Schulz-Kornas, E., van Casteren, A., Tsanova, T.R., Sirakov, N., Spasov, R., Welker, F., Smith, G.M., Hublin, J.-J. 2021. The effect of eraser sampling for proteomic analysis on Palaeolithic bone surface microtopography. Scientifc Reports 11, 23611. https://doi.org/10.1038/s41598-021-02823-w
Talamo, S., Urbanowski, M., Picin, A., Nowaczewska, W.N., Vazzana, A., Binkowski, M., Cercatillo, S., Diakowski, M., Fewlass, H., Marciszak, A., Paleček, D., Richards, M.P., Ryder, C.M., Sinet-Mathiot, V., Smith, G.M., Socah, P., Sponheimer, M., Stefaniak, K., Welker, F., Winter, H., Wiśniewski, A., Żarski, M., Benazzi, S., Nadachowski, A., Hublin, J.-J. 2021. A 41,500 year-old decorated ivory pendant from Stajnia Cave (Poland). Scientific Reports 11, 22078. https://doi.org/10.1038/s41598-021-01221-6
Bacon, A.-M., Bourgon, N., Welker, F., Cappellini, E., Fiorillo, D., Tombret, O., Huong, N.T.M., Tuan, N.A., Sayavonkhamdy, T., Souksavatdy, V., Sichanthongtip, P., Antoine, P.-O., Duringer, P., Ponche, J.-L., Westaway, K., Joannes-Boyau, R., Boesch, Q., Frangeul, S., Patole-Edoumba, E., Zachwieja, A., Shakelford, L., Demeter, F., Hublin, J.-J., Dufour, E. 2021. A multi-proxy approach to exploring Homo sapiens' arrival, environments, and adaptations in Southeast Asia. Scientific Reports, 11, 21080. https://doi.org/10.1038/s41598-021-99931-4
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, Ž., Sirakova, S., Sirakov, N., McPherron, S.P., Tsanova, T., Hublin, J.-J., Peter, B.M., Meyer, M., Skoglund, P., Kelso, J., Pääbo, S., 2021. Initial Upper Palaeolithic humans In Europe had recent Neanderthal ancestry. Nature 592, 253-257. https://doi.org/10.1038/s41586-021-03335-3
Dekker, J., Sinet-Mathiot, V., Spithoven, M., Smit, B., Wilcke, A., Welker, F., Verpoorte, A., Soressi, M., 2021. Human and cervid osseous materials used for barbed point manufacture in Mesolithic Doggerland. Journal of Archaeological Science: Reports 35, 102678. https://doi.org/10.1016/j.jasrep.2020.102678
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