Recent Department Publications
Last update: May 27th, 2022
2022
Brown, S., Massilani, D., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Stoessel, A., Jope-Street, B., Meyer, M., Kelso, J., Pääbo, S., Higham, T., & Douka, K. (2022). The earliest Denisovans and their cultural adaptation. Nature Ecology & Evolution, 6, 28-35. |
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Coppo, L., Mishra, P., Siefert, N., Holmgren, A., Pääbo, S., & Zeberg, H. (2022). A substitution in the glutathione reductase lowers electron leakage and inflammation in modern humans. Science Advances, 8(1): eabm1148. |
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Gerber, T., Loureiro, C., Schramma, N., Chen, S., Jain, A., Weber, A., Weigert, A., Santel, M., Alim, K., Treutlein, B., & Camp, J. G. (2022). Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium. eLife, 11: e69745. |
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He, Z., Maynard, A., Jain, A., Gerber, T., Petri, R., Lin, H.-C., Santel, M., Ly, K., Dupré, J.-S., Sidow, L., Sanchis Calleja, F., Jansen, S. M. J., Riesenberg, S., Camp, J. G., & Treutlein, B. (2022). Lineage recording in human cerebral organoids. Nature Methods, 19(1), 90-99.
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Hopkins, R. J. A., Hajdinjak, M., Šefčáková, A., Comeskey, D., Devièse, T., & Higham, T. F. G. (2022). Single amino acid radiocarbon dating of two Neanderthals found at Šal’a (Slovakia). Radiocarbon, 64, 87-100. |
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Huffman , J. E., Butler-Laporte , G., Khan , A., Pairo-Castineira, E., Drivas, T. G., Peloso, G. M., Nakanishi , T., COVID-19 Host Genetics Initiative, Ganna, A., Verma, A., Baillie , J. K., Kiryluk, K., Richards , J. B., & Zeberg, H. (2022). Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19. Nature Genetics, 54, 125-127. |
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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. (2022). Detection of Neanderthal adaptively introgressed genetic variants that modulate reporter gene expression in human immune cells. Molecular Biology and Evolution, 39(1): msab304. |
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Krumm, J., Sekine, K., Samaras, P., Brazovskaja, A., Breunig, M., Yasui, R., Kleger, A., Taniguchi, H., Wilhelm, M., Treutlein, B., Camp, J. G., & Kuster, B. (2022). High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Reports, 38: 110604. |
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Le Duc, D., Velluva, A., Cassatt-Johnstone, M., Olsen, R.-A., Baleka, S., Lin, C.-C., Lemke, J. R., Southon, J. R., Burdin, A., Wang, M.-S., Grunewald, S., Rosendahl, W., Joger, U., Rutschmann, S., Hildebrandt, T. B., Fritsch, G., Estes, J. A., Kelso, J., Dalén, L., Hofreiter, M., Shapiro, B., & Schöneberg, T. (2022). Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow. Science Advances, 8(5). |
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Liu, Q., Iqbal, M. F., Yaqub, T., Firyal, S., Zhao, Y., Stoneking, M., & Li, M. (2022). The transmission of human mitochondrial DNA in four-generation pedigrees (advance online). Human Mutation. |
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Massilani, D., Morley, M. W., Mentzer, S. M., Aldeias, V., Vernot, B., Miller, C., Stahlschmidt, M., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Conard, N. J., Wurz, S., Henshilwood, C. S., Vasquez, J., Essel, E., Nagel, S., Richter, J., Nickel, B., Roberts, R. G., Pääbo, S., Slon, V., Goldberg, P., & Meyer, M. (2022). Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proceedings of the National Academy of Sciences, 119(1): e2113666118. |
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Nebe, M., Kehr, S., Schmitz, S., Breitfeld, J., Lorenz, J., Le Duc, D., Stadler, P. F., Meiler, J., Kiess, W., Garten, A., & Kirstein, A. S. (2022). Small integral membrane protein 10 like 1 downregulation enhances differentiation of adipose progenitor cells. Biochemical and Biophysical Research Communications, 604, 57-62. |
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Peter, B. M. (2022). A geometric relationship of F2, F3 and F4-statistics with principal component analysis. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1852): 20200413. |
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Riesenberg, S., Helmbrecht, N., Kanis, P., Maricic, T., & Pääbo, S. (2022). Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage. Nature Communications, 13: 489. |
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Rocha, J. L., Vaz Pinto, P., Siegismund, H. R., Meyer, M., Jansen van Vuuren, B., Veríssimo, L., Ferrand, N., & Godinho, R. (2022). African climate and geomorphology drive evolution and ghost introgression in sable antelope (advance online). Molecular Ecology. |
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Zavala, E. I., Ayinuer-Petri, A., Richter, J., Nickel, B., Vernot, B., & Meyer, M. (2022). Quantifying and reducing cross‐contamination in single‐ and multiplex hybridization capture of ancient DNA (advance online). Molecular Ecology Resources. |
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Zavala, E. I., Thomas, J. T., Sturk-Andreaggi, K., Daniels-Higginbotham, J., Meyers, K. K., Barrit-Ross, S., Ayinuer-Petri, A., Richter, J., Nickel, B., Berg, G. E., McMahon, T. P., Meyer, M., & Marshall, C. (2022). Ancient DNA methods improve forensic DNA profiling of Korean War and World War II unknowns. Genes, 13(129). |
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Zeberg, H. (2022). The major genetic risk factor for severe COVID-19 is associated with protection against HIV. Proceedings of the National Academy of Sciences of the United States of America, 119(9): e2116435119. |
Open Access2021
Alpaslan-Roodenberg, S., Anthony, D., Babiker, H., Bánffy, E., Booth, T., Capone, P., Deshpande-Mukherjee, A., Eisenmann, S., Fehren-Schmitz, L., Frachetti, M., Fujita, R., Frieman, C. J., Fu, Q., Gibbon, V., Haak, W., Hajdinjak, M., Hofmann, K. P., Holguin, B., Inomata, T., Kanzawa-Kiriyama, H., Keegan, W., Kelso, J., Krause, J., Kumaresan, G., Kusimba, C., Kusimba, S., Lalueza-Fox, C., Llamas, B., MacEachern, S., Mallick, S., Matsumura, H., Morales-Arce, A. Y., Matuzeviciute, G. M., Mushrif-Tripathy, V., Nakatsuka, N., Nores, R., Ogola, C., Okumura, M., Patterson, N., Pinhasi, R., Prasad, S. P. R., Prendergast, M. E., Punzo, J. L., Reich, D., Sawafuji, R., Sawchuk, E., Schiffels, S., Sedig, J., Shnaider, S., Sirak, K., Skoglund, P., Slon, V., Snow, M., Soressi, M., Spriggs, M., Stockhammer, P. W., Szécsényi-Nagy, A., Thangaraj, K., Tiesler, V., Tobler, R., Wang, C.-C., Warinner, C., Yasawardene, S., & Zahir, M. (2021). Ethics of DNA research on human remains: Five globally applicable guidelines. Nature, 599, 41-46. |
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Berger, C., Heyne, H. O., Heiland, T., Dommel, S., Höfling, C., Guiu-Jurado, E., Lorenz, J., Roßner, S., Dannemann, M., Kelso, J., Kovacs, P., Blüher, M., & Klöting, N. (2021). A novel compound heterozygous leptin receptor mutation causes more severe obesity than in Lepr mice. Journal of Lipid Research, 62: 100105. |
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Bokelmann, L., Nickel, O., Maricic, T., Pääbo, S., Meyer, M., Borte, S., & Riesenberg, S. (2021). Point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP. Nature Communications, 12(1): 1467. |
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Carlhoff, S., Duli, A., Nägele, K., Nur, M., Skov, L., Sumantri, I., Oktaviana, A. A., Hakim, B., Burhan, B., Syahdar, F. A., McGahan, D. P., Bulbeck, D., Perston, Y. L., Newman, K., Saiful, A. M., Ririmasse, M., Chia, S., Hasanuddin, Pulubuhu, D. A. T., Suryatman, Supriadi, Jeong, C., Peter, B. M., Prüfer, K., Powell, A., Krause, J., Posth, C., & Brumm, A. (2021). Genome of a middle Holocene hunter-gatherer from Wallacea. Nature, 596, 543-547. |
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Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A.-M.-S., Harmant, C., Laurent, R., Verdu, P., Laval, G., Boland, A., Olaso, R., Deleuze, J.-F., Valentin, F., Ko, Y.-C., Jakobsson, M., Gessain, A., Excoffier, L., Stoneking, M., Patin, E., & Quintana-Murci, L. (2021). Genomic insights into population history and biological adaptation in Oceania. Nature, 592(7855), 583-589. |
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COVID-19 Host Genetics initiative, including authors, Zeberg, H., Niemi, M. E. K., Karjalainen, J., Liao, R. G., Neale, B. M., Daly, M., Ganna, A., Pathak, G. A., Andrews, S. J., Kanai, M., Veerapen, K., Fernandez-Cadenas, I., Schulte, E. C., Striano, P., Marttila, M., Minica, C., Marouli, E., Karim, M. A., Wendt, F. R., Savage, J., Sloofman, L., Butler-Laporte, G., Kim, H.-N., Kanoni, S., Okada, Y., Byun, J., Han, Y., Uddin, M. J., Smith, G. D., Willer, C. J., Buxbaum, J. D., Mehtonen, J., Finucane, H., Cordioli, M., Martin, A. R., Zhou, W., Pasaniuc, B., Julienne, H., Aschard, H., Shi, H., Yengo, L., Polimanti, R., Ghoussaini, M., Schwartzentruber, J., Dunham, I., Chwialkowska, K., Francescatto, M., Trankiem, A., Balaconis, M. K., Davis, L., Lee, S., Priest, J., Renieri, A., Sankaran, V. G., van Heel, D., Deelen, P., Richards, J. B., Nakanishi, T., Biesecker, L., Kerchberger, V. E., Baillie, J. K., Mari, F., Bernasconi, A., Baillie, S. C., Canakoglu, A., Wolford, B., Faucon, A., Dutta, A. K., Schurmann, C., Harry, E., Birney, E., Nguyen, H., Nasir, J., Kaunisto, M., Solomonson, M., Dueker, N., Vadgama, N., Limou, S., Rahmouni, S., Mbarek, H., Darwish, D., Uddin, M. M., Albertos, R., Pérez-Tur, J., Li, R., Folkersen, L., Moltke, I., Koelling, N., Teumer, A., Kousathanas, A., Utrilla, A., Verdugo, R. A., Zárate, R., Medina-Gómez, C., Gómez-Cabrero, D., Carnero-Montoro, E., Cadilla, C. L., Moreno-Estrada, A., Garmendia, A., Moya, L., Sedaghati-Khayat, B., Boua, P. R., Favé, M.-J., Francioli, L., Lemaçon, A., Migeotte, I., Patel, S., Varnai, R., Szentpeteri, J. L., Sipeky, C., Colombo, F., von Hohenstaufen, K., Lio, P., Vallerga, C., Wang, Q., Tanigawa, Y., Im, H., Han, C., Song, H., Lim, J., Lee, Y., Kim, S., Im, S., Atanasovska, B., Ahmad, H. F., Boer, C., Jansen, P., Franke, L., Kaja, E., Pasko, D., Kennis-Szilagyi, I., Kornilov, S. A., Prijatelj, V., Prokić, I., Sivanadhan, I., Perumal, S., Esmaeeli, S., Pearson, N. M., Auton, A., Shelton, J. F., Shastri, A. J., Filshtein-Sonmez, T., Coker, D., Symons, A., Esparza-Gordillo, J., Aslibekyan, S., O’Connell, J., Ye, C., Weldon, C. H., Perera, M., O’Leary, K., Tuck, M., O’Brien, T., Meltzer, D., O’Donnell, P., Nutescu, E., Yang, G., Alarcon, C., Herrmann, S., Mazurek, S., Banagan, J., Hamidi, Z., Barbour, A., Raffat, N., Moreno, D., Friedman, P., Ferwerda, B., van de Beek, D., Brouwer, M. C., Vlaar, A. P. J., Wiersinga, W. J., Posthuma, D., Tissink, E., Zwinderman, K. H. A., Uffelmann, E., van Agtmael, M., Algera, A. G., van Baarle, F., Bax, D., Beudel, M., Jan Bogaard, H., Bomers, M., Bonta, P. I., Bos, L., Botta, M., de Brabander, J., de Bree, G., de Bruin, S., Bugiani, M., Bulle, E., Chouchane, O., Cloherty, A., Dongelmans, D., Elbers, P., Fleuren, L., Geerlings, S., Geerts, B., Geijtenbeek, T., Girbes, A., Goorhuis, B., Grobusch, M. P., Hafkamp, F., Hagens, L., Hamann, J., Harris, V., Hemke, R., Hermans, S. M., Heunks, L., Hollmann, M., Horn, J., Hovius, J. W., de Jong, D. M., Koning, R., van Mourik, N., Nellen, J., Nossent, E. J., Paulus, F., Peters, E., van der Poll, T., Preckel, B., Prins, J. M., Raasveld, J., Reijnders, T., Schinkel, M., Schultz, M. J., Schuurman, A., Sigaloff, K., Smit, M., Stijnis, C. S., Stilma, W., Teunissen, C., Thoral, P., Tsonas, A., van der Valk, M., Veelo, D., de Vries, H., van Vugt, M., Wouters, D., Minnaar, R. P., Kromhout, A., van Uffelen, J. K. W., Wolterman, R. A., Roberts, G., Park, D., Ball, C. A., Coignet, M., McCurdy, S., Knight, S., Partha, R., & Rhead, B. (2021). Mapping the human genetic architecture of COVID-19. Nature, 600(7889), 472-477. |
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Devièse, T., Abrams, G., Hajdinjak, M., Pirson, S., De Groote, I., Di Modica, K., Toussaint, M., Fischer, V., Comeskey, D., Spindler, L., Meyer, M., Semal, P., & Higham, T. (2021). Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proceedings of the National Academy of Sciences, 118(12): e2022466118. |
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Devièse, T., Abrams, G., Hajdinjak, M., Pirson, S., De Groote, I., Di Modica, K., Toussaint, M., Fischer, V., Comeskey, D., Spindler, L., Meyer, M., Semal, P., & Higham, T. (2021). Reply to Van Peer: Direct radiocarbon dating and ancient genomic analysis reveal the true age of the Neanderthals at Spy Cave. Proceedings of the National Academy of Sciences of the United States of America, 118(26): e2107116118. |
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Essel, E., Korlević, P., & Meyer, M. (2021). A method for the temperature-controlled extraction of DNA from ancient bones. Biotechniques, 71(1), 383-387. |
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Evans, B. J., Peter, B., Melnick, D. J., Andayani, N., Supriatna, J., Zhu, J., & Tosi, A. J. (2021). Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution. Proceedings of the Royal Society B: Biological Sciences, 288(1960): 20211756. |
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Fleck, J. S., Sanchís-Calleja, F., He, Z., Santel, M., Boyle, M. J., Camp, J. G., & Treutlein, B. (2021). Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases. Cell Stem Cell, 28, 1148-1159. |
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Gjermeni, E., Kirstein, A. S., Kolbig, F., Kirchhof, M., Bundalian, L., Katzmann, J. L., Laufs, U., Blüher, M., Garten, A., & Le Duc, D. (2021). Obesity – an update on the basic pathophysiology and review of recent therapeutic advances. Biomolecules, 11(10): 1426. |
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Guo, S., Huang, S., Jiang, X., Hu, H., Han, D., Moreno, C. S., Fairbrother, G. L., hughes, D. A., Stoneking, M., & Khaitovich, P. (2021). Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn. BMC Genomics, 22: 286. |
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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., Meyer, M., Skoglund, P., Kelso, J., & Pääbo, S. (2021). Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature, 592, 253-257. |
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Hodgkins, J., Orr, C. M., Gravel-Miguel, C., Riel-Salvatore, J., Miller, C. E., Bondioli, L., Nava, A., Lugli, F., Talamo, S., Hajdinjak, M., Cristiani, E., Romandini, M., Meyer, D., Drohobytsky, D., Kuester, F., Pothier-Bouchard, G., Buckley, M., Mancini, L., Baruffaldi, F., Silvestrini, S., Arrighi, S., Keller, H. M., Griggs, R. B., Peresani, M., Strait, D. S., Benazzi, S., & Negrino, F. (2021). An infant burial from Arma Veirana in northwestern Italy provides insights into funerary practices and female personhood in early Mesolithic Europe. Scientific Reports, 11: 23735. |
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Hou, Q.-Q., Xiao, Q., Sun, X.-Y., Ju, X.-C., & Luo, Z.-G. (2021). TBC1D3 promotes neural progenitor proliferation by suppressing the histone methyltransferase G9a. Science Advances, 7: eaba8053. |
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Iasi, L. N., Ringbauer, H., & Peter, B. (2021). An extended admixture pulse model reveals the limitations to human-Neandertal introgression dating. Molecular Biology and Evolution, 38(11), 5156-5174. |
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Jauss, R.-T., Nowack, A., Walden, S., Wolf, R., Schaffer, S., Schellbach, B., Bonkowski, M., & Schlegel, M. (2021). To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies. European Journal of Protistology, 80: 125805. |
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Kirstein, A. S., Kehr, S., Nebe, M., Hanschkow, M., Barth, L. A., Lorenz, J., Penke, M., Breitfeld, J., Le Duc, D., Landgraf, K., Körner, A., Kovacs, P., Stadler, P. F., Kiess, W., & Garten, A. (2021). PTEN regulates adipose progenitor cell growth, differentiation, and replicative aging. Journal of Biological Chemistry, 297(2): 100968. |
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Kutanan, W., Liu, D., Kampuansai, J., Srikummool, M., Srithawong, S., Shoocongdej, R., Sangkhano, S., Ruangchai, S., Pittayaporn, P., Arias, L., & Stoneking, M. (2021). Reconstructing the human genetic history of mainland Southeast Asia: Insights from genome-wide data from Thailand and Laos. Molecular Biology and Evolution, 38(8), 3459-3477. |
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Kyrousi, C., O’Neill, A. C., Brazovskaja, A., He, Z., Kielkowski, P., Coquand, L., Di Giaimo, R., D’ Andrea, P., Belka, A., Forero Echeverry, A., Mei, D., Lenge, M., Cruceanu, C., Buchsbaum, I. Y., Khattak, S., Fabien, G., Binder, E., Elmslie, F., Guerrini, R., Baffet, A. D., Sieber, S. A., Treutlein, B., Robertson, S. P., & Cappello, S. (2021). Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nature Communications, 12(1): 6298. |
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Le Duc, D., Hentschel, J., Neuser, S., Stiller, M., Meier, C., Jäger, E., Abou Jamra, R., Platzer, K., Monecke, A., Ziemer, M., Markovic, A., Bläker, H., & Lemke, J. R. (2021). In cis TP53 and RAD51C pathogenic variants may predispose to sebaceous gland carcinomas. European Journal of Human Genetics, 29, 489-494. |
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Lin, H.-C., He, Z., Ebert, S., Schörnig, M., Santel, M., Nikolova, M. T., Weigert, A., Hevers, W., Kasri, N. N., Taverna, E., Camp, J. G., & Treutlein, B. (2021). NGN2 induces diverse neuron types from human pluripotency. Stem Cell Reports, 16, 2118-2127. |
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Lin, T.-Y., Gerber, T., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Grosser, L., Shibata, E., Treutlein, B., & Tanaka, E. M. (2021). Fibroblast dedifferentiation as a determinant of successful regeneration. Developmental Cell, 56(10), 1541-1551.e6. |
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Mafessoni, F., Lachmann, M., & Gokhale, C. S. (2021). On the fitness of informative cues in complex environments. Journal of Theoretical Biology, 527: 110819. |
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Maricic, T., Helmbrecht, N., Riesenberg, S., Macak, D., Kanis, P., Lackner, M., Pugach-Matveeva, A. D., & Pääbo, S. (2021). Comment on “Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment”. Science, 374(6565), 269. |
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Martinón-Torres, M., d’Errico, F., Santos, E., Álvaro Gallo, A., Amano, N., Archer, W., Armitage, S. J., Arsuaga, J. L., de Castro, B., María, J., Blinkhorn, J., Crowther, A., Douka, K., Dubernet, S., Faulkner, P., Fernández-Colón, P., Kourampas, N., González García, J., Larreina, D., Le Bourdonnec, F.-X., MacLeod, G., Martín-Francés, L., Massilani, D., Mercader, J., Miller, J. M., Ndiema, E., Notario, B., Pitarch Martí, A., Prendergast, M. E., Queffelec, A., Rigaud, S., Roberts, P., Shoaee, M. J., Shipton, C., Simpson, I., Boivin, N., & Petraglia, M. D. (2021). Earliest known human burial in Africa. Nature, 593(7857), 95-100. |
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Matsumae, H., Ranacher, P., Savage, P. E., Blasi, D. E., Currie, T. E., Koganebuchi, K., Nishida, N., Sato, T., Tanabe, H., Tajima, A., Brown, S., Stoneking, M., Shimizu, K. K., Oota, H., & Bickel, B. (2021). Exploring correlations in genetic and cultural variation across language families in northeast Asia. Science Advances, 7(34): eabd9223. |
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Mora-Bermúdez, F., Taverna, E., & Huttner, W. B. (2021). From stem and progenitor cells to neurons in the developing neocortex: Key differences among hominids (advance online). The FEBS Journal. |
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Nakanishi, T., Pigazzini, S., Degenhardt, F., Cordioli, M., Butler-Laporte, G., Maya-Miles, D., Bujanda, L., Bouysran, Y., Niemi, M. E., Palom, A., Ellinghaus, D., Khan, A., Martínez-Bueno, M., Rolker, S., Amitrano, S., Tato, L. R., Fava, F., FinnGen, (HGI), T.-C.-1.-H.-G.-I., Spinner, C. D., Prati, D., Bernardo, D., Garcia, F., Darcis, G., Fernández-Cadenas, I., Holter, J. C., Banales, J. M., Frithiof, R., Kiryluk, K., Duga, S., Asselta, R., Pereira, A. C., Romero-Gómez, M., Nafría-Jiménez, B., Hov, J. R., Migeotte, I., Renieri, A., Planas, A. M., Ludwig, K. U., Buti, M., Rahmouni, S., Alarcón-Riquelme, M. E., Schulte, E. C., Franke, A., Karlsen, T. H., Valenti, L., Zeberg, H., Richards, J. B., & Ganna, A. (2021). Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality. The Journal of Clinical Investigation, 131(23). |
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Overcast, I., Ruffley, M., Rosindell, J., Harmon, L., Borges, P. A. V., Emerson, B. C., Etienne, R. S., Gillespie, R., Krehenwinkel, H., Mahler, D. L., Massol, F., Parent, C. E., Patiño, J., Peter, B., Week, B., Wagner, C., Hickerson, M. J., & Rominger, A. (2021). A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities. Molecular Ecology Resources, 21(8), 2782-2800. |
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Pakendorf, B., & Stoneking, M. (2021). The genomic prehistory of peoples speaking Khoisan languages. Human Molecular Genetics, 30(2), R49-R55. |
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Parker, C. E., Bos, K. I., Haak, W., & Krause, J. (2021). Optimized bone sampling protocols for the retrieval of ancient DNA from archaeological remains. Journal of Visualized Experiments, 177: e63250. |
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Picin, A., Benazzi, S., Blasco, R., Hajdinjak, M., Helgen, K. M., Hublin, J.-J., Rosell, J., Skoglund, P., Stringer, C., & Talamo, S. (2021). Comment on “A global environmental crisis 42,000 years ago”. Science, 374(6570): eabi8330. |
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Pugach, I., Hübner, A., Hung, H.-c., Meyer, M., Carson, M. T., & Stoneking, M. (2021). Ancient DNA from Guam and the peopling of the Pacific. Proceedings of the National Academy of Sciences, 118(1): e202211211. |
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Reinscheid, R. K., Mafessoni, F., Lüttjohann, A., Jüngling, K., Pape, H.-C., & Schulz, S. (2021). Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality. Peptides, 138: 170506. |
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Schörnig, M., & Taverna, E. (2021). A closer look to the evolution of neurons in humans and apes using stem-cell-derived model systems. Frontiers in Cell and Developmental Biology, 9: 661113. |
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2020
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Bokelmann, L., Glocke, I., & Meyer, M. (2020). Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. Genome Research, 30(10), 1449-1457. |
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Braadbaart, F., Reidsma, F., Roebroeks, W., Chiotti, L., Slon, V., Meyer, M., Théry-Parisot, I., van Hoesel, A., Nierop, K., Kaal, J., van Os, B., & Marquer, L. (2020). Heating histories and taphonomy of ancient fireplaces: A multi-proxy case study from the Upper Palaeolithic sequence of Abri Pataud (Les Eyzies-de-Tayac, France). Journal of Archaeological Science: Reports, 33: 102468. |
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Cauret, C. M. S., Gansauge, M.-T., Tupper, A. S., Furman, B. L. S., Knytl, M., Song, X., Greenbaum, E., Meyer, M., & Evans, B. J. (2020). Developmental systems drift and the drivers of sex chromosome evolution. Molecular Biology and Evolution, 37(3), 799-808. |
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Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J., & Camp, J. G. (2020). Human stem cell resources are an inroad to Neandertal DNA functions. Stem Cell Reports, 15, 214-225. |
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Evans, B. J., Gansauge, M.-T., Tocheri, M. W., Schillaci, M. A., Sutikna, T., Jatmiko, Saptomo, E. W., Klegarth, A., Tosi, A. J., Melnick, D. J., & Meyer, M. (2020). Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. Journal of Human Evolution, 146: 102852. |
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Fellows Yates, J. A., Andrades Valtueña, A., Vågene, A. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-López, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., & Warinner, C. G. (2020). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8: 31. |
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Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M. (2020). Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nature Protocols, 15, 2279-2300. |
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Gunnarsdottir, E. D., & Stoneking, M. (2020). Genetic Landscape of Present-Day Hunter-Gatherer Groups. In T. Güldemann ( |
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Kutanan, W., Shoocongdej, R., Srikummool, M., Hübner, A., Suttipai, T., Srithawong, S., Kampuansai, J., & Stoneking, M. (2020). Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand. European Journal of Human Genetics, 28, 1563-1579. |
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Liu, D., Duong, N. T., Ton, N. D., Van Phong, N., Pakendorf, B., Van Hai, N., & Stoneking, M. (2020). Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity. Molecular Biology and Evolution, 37(9): msaa099, pp. 2503-2519. |
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Maricic, T., Nickel, O., Ayinuer-Petri, A., Essel, E., Gansauge, M.-T., Kanis, P., Macak, D., Riesenberg, S., Bokelmann, L., Zeberg, H., Meyer, M., Borte, S., & Pääbo, S. (2020). A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2. PLoS One, 15(12): e0244824. |
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Massilani, D., Skov, L., Hajdinjak, M., Gunchinsuren, B., Tseveendorj, D., Yi, S., Lee, J., Nagel, S., Nickel, B., Devièse, T., Higham, T., Meyer, M., Kelso, J., Peter, B., & Pääbo, S. (2020). Denisovan ancestry and population history of early East Asians. Science, 370(6516), 579-583. |
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Miller, A. J., Yu, Q., Czerwinski, M., Tsai, Y.-H., Conway, R. F., Wu, A., Holloway, E. M., Walker, T., Glass, I. A., Treutlein, B., Camp, J. G., & Spence, J. R. (2020). In vitro and in vivo development of the human airway at single-cell resolution. Developmental Cell, 53(1): e6, pp. 117-128. |
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Parker, E. C., Rohrlach, A. B., Friederich, S., Nagel, S., Meyer, M., Krause, J., Bos, K. I., & Haak, W. (2020). A systematic investigation of human DNA preservation in medieval skeletons. Scientific Reports, 10(1): 18225. |
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Pedro, N., Brucato, N., Fernandes, V., André, M., Saag, L., Pomat, W., Besse, C., Boland, A., Deleuze, J.-F., Clarkson, C., Sudoyo, H., Metspalu, M., Stoneking, M., Cox, M. P., Leavesley, M., Pereira, L., & Ricaut, F.-X. (2020). Papuan mitochondrial genomes and the settlement of Sahul. Journal of Human Genetics, 65(875), 887. |
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2019
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. (2019). The current genomic landscape of Western South America: Andes, Amazonia, and Pacific Coast. Molecular Biology and Evolution, 36(12), 2698-2713. |
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Bozek, K., Khrameeva, E. E., Reznick, J., Omerbašić, D., Bennett, N. C., Lewin, G. R., Azpurua, J., Gorbunova, V., Seluanov, A., Regnard, P., Wanert, F., Marchal, J., Pifferi, F., Aujard, F., Liu, Z., Shi, P., Pääbo, S., Schröder, F., Willmitzer, L., Giavalisco, P., & Khaitovich, P. (2019). Publisher correction: Lipidome determinants of maximal lifespan in mammals. Scientific Reports, 9(1): 6972. |
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Devièse, T., Massilani, D., Yi, S., Comeskey, D., Nagel, S., Nickel, B., Ribechini, E., Lee, J., Tseveendorj, D., Gunchinsuren, B., Meyer, M., Pääbo, S., & Higham, T. (2019). Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia. Nature Communications, 10(10): 274. |
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Douka, K., Brown, S., Higham, T., Pääbo, S., Derevianko, A., & Shunkov, M. (2019). FINDER project: collagen fingerprinting (ZooMS) for the identification of new human fossils. Antiquity, 93(367): e1. |
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Evans, B. J., Gansauge, M.-T., Stanley, E. L., Furman, B. L. S., Cauret, C. M. S., Ofori-Boateng, C., Gvoždík, V., Streicher, J. W., Greenbaum, E., Tinsley, R. C., Meyer, M., & Blackburn, D. C. (2019). Xenopus fraseri: Mr. Fraser, where did your frog come from? PLoS One, 14(9): e0220892. |
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2016
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Hughes, D. A., Kircher, M., He, Z., Guo, S., Fairbrother, G. L., Moreno, C. S., Khaitovich, P., & Stoneking, M. (2015). Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology, 16: 54. |
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Korlević, P., Gerber, T., Gansauge, M.-T., Hajdinjak, M., Nagel, S., Ayinuer-Petri, A., & Meyer, M. (2015). Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques, 59(2), 87-93. |
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Li, M., Schröder, R., Ni, S., Madea, B., & Stoneking, M. (2015). Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proceedings of the National Academy of Sciences of the United States of America, 112(8), 2491-2496. |
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Macholdt, E., Slatkin, M., Pakendorf, B., & Stoneking, M. (2015). New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa. American Journal of Physical Anthropology, 156(4), 661-664. |
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MacLarnon, A. M., Sommer, V., Goffe, A. S., Higham, J. P., Lodge, E., Tkaczynski, P. J., & Ross, C. (2015). Assessing adaptability and reactive scope: Introducing a new measure and illustrating its use through a case study of environmental stress in forest-living baboons. General and Comparative Endocrinology, 215, 10-24. |
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Prüfer, K., & Meyer, M. (2015). Comment on “Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans”. Science, 347(6224), 835-835. |
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Pugach, I., & Stoneking, M. (2015). Genome-wide insights into the genetic history of human populations. Investigative Genetics, 6: 6. |
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Savage, P. E., Matsumae, H., Oota, H., Stoneking, M., Currie, T. E., Tajima, A., Gillan, M., & Brown, S. (2015). How 'circumpolar' is Ainu music? Musical and genetic perspectives on the history of the Japanese archipelago. Ethnomusicology Forum, 24(3), 443-467. |
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Sawyer, S., Renaud, G., Viola, B., Hublin, J.-J., Gansauge, M.-T., Shunkov, M. V., Derevianko, A. P., Prüfer, K., Kelso, J., & Pääbo, S. (2015). Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proceedings of the National Academy of Sciences of the United States of America, 112(51), 15696-15700. |
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Valverde, G., Zhou, H., Lippold, S., de Filippo, C., Tang, K., Herráez, D. L., Li, J., & Stoneking, M. (2015). A novel candidate region for genetic adaptation to high altitude in Andean populations. PLoS One, 10(5): e0125444. |
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Vaughan, A. E., Brumwell, A. N., Xi, Y., Gotts, J. E., Brownfield, D. G., Treutlein, B., Tan, K., Tan, V., Liu, F. C., Looney, M. R., Matthay, M. A., Rock, J. R., & Chapman, H. A. (2015). Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature, 517(7536), 621-625. |
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Weiß, C. L., Dannemann, M., Prüfer, K., & Burbano, H. A. (2015). Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data. eLife, 4: e10005. |
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White, L., Romagné, F., Müller, E., Erlebach, E., Weihmann, A., Parra, G., Andrés, A. M., & Castellano, S. (2015). Genetic adaptation to levels of dietary selenium in recent human history. Molecular Biology and Evolution, 32(6), 1507-1518. |
2014
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Barbieri, C., Güldemann, T., Naumann, C., Gerlach, L., Berthold, F., Nakagawa, H., Mpoloka, S. W., Stoneking, M., & Pakendorf, B. (2014). Unraveling the complex maternal history of Southern African Khoisan populations. American Journal of Physical Anthropology, 153(3), 435-448. |
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Barbieri, C., Vicente, M., Oliveira, S., Bostoen, K., Rocha, J., Stoneking, M., & Pakendorf, B. (2014). Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa. PLoS One, 9(6): e9911. |
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Benazzi, S., Peresani, M., Talamo, S., Fu, Q., Mannino, M. A., Richards, M. P., & Hublin, J.-J. (2014). A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy. Journal of Human Evolution, 66(1), 89-94. |
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Bozek, K., Wei, Y., Yan, Z., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Pieszek, R., Sherwood, C. C., Hof, P. R., Ely, J. J., Steinhauser, D., Bangsbo, J., Willmitzer, L., Hansson, O., Call, J., Giavalisco, P., & Khaitovich, P. (2014). Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biology, 12(5): e1001871. |
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Brown, S., Savage, P. E., Ko, A.-M.-S., Stoneking, M., Ko, Y.-C., Loo, J.-H., & Trejaut, J. A. (2014). Correlations in the population structure of music, genes and language. Proceedings of the Royal Society of London. Series B: Biological Sciences, 281(1774): 20132072. |
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Carneiro, M., Albert, F. W., Afonso, S., Pereira, R. J., Burbano, H. A., Campos, R., Melo-Ferreira, J., Blanco-Aguiar, J. A., Villafuerte, R., Nachman, M. W., Good, J. M., & Ferrand, N. (2014). The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genetics, 10(8): e1003519. |
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Carneiro, M., Rubin, C.-J., Palma, F. D., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J. M., Barrell, D., Bolet, G., Boucher, S., Burbano, H. A., Campos, R., Chang, J. L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R. G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J. M., Lander, E. S., Ferrand, N., Lindblad-Toh, K., & Andersson, L. (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, 345(6200), 1074-1079. |
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Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., Dabney, J., Siebauer, M. F., White, L., Burbano, H. A., Renaud, G., Stenzel, U., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J., Andrés, A. M., & Pääbo, S. (2014). Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences of the United States of America, 111(18), 6666-6671. |
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Dabney, J., Meyer, M., & Pääbo, S. (2014). Ancient DNA damage. In E. C. Friedberg, S. J. Elledge, A. R. Lehmann, T. Lindahl, & M. Muzi-Falconi ( |
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Deelen, P., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L. C., Hottenga, J. J., Karssen, L. C., Estrada, K., Kreiner-Møller, E., Rivadeneira, F., van Setten, J., Gutierrez-Achury, J., Westra, H.-J., Franke, L., van Enckevort, D., Dijkstra, M., Byelas, H., van Duijn, C. M., Genome of the Netherlands Consortium, including authors, Stoneking, M., Li, M., & others, de Bakker, P. I. W., Wijmenga, C., & Swertz, M. A. (2014). Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'. European Journal of Human Genetics, 22(11), 1321-1326. |
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Delfin, F. S., Ko, A.-M.-S., Li, M., Gunnarsdóttir, E. D., Tabbada, K. A., Salvador, J. M., Calacal, G. C., Sagum, M. S., Datar, F. A., Padilla, S. G., Ungria, M. C. A. D., & Stoneking, M. (2014). Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region. European journal of human genetics, 22(2), 228-237. |
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Duggan, A. T., & Stoneking, M. (2014). Recent developments in the genetic history of East Asia and Oceania. Current Opinion in Genetics & Development, 29, 9-14. |
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Duggan, A. T., Evans, B., Friedlaender, F. R., Friedlaender, J. S., Koki, G., Merriwether, D. A., Kayser, M., & Stoneking, M. (2014). Maternal history of Oceania from complete mtDNA genomes: Contrasting ancient diversity with recent homogenization due to the Austronesian expansion. The American Journal of Human Genetics, 94(5), 721-733. |
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Engelken, J., Carnero-Montoro, E., Pybus, M., Andrews, G. K., Lalueza-Fox, C., Comas, D., Sekler, I., de la Rasilla, M., Rosas, A., Stoneking, M., Valverde, M. A., Vicente, R., & Bosch, E. (2014). Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PLoS Genetics, 10(2): e1004128. |
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Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Ayinuer-Petri, A., Prüfer, K., de Filippo, C., Meyer, M., Zwyns, N., Salazar García, D. C., Kuzmin, Y. V., Keates, S. G., Kosintsev, P. A., Razhev, D. I., Richards, M. P., Peristov, N. V., Lachmann, M., Douka, K., Higham, T. F. G., Slatkin, M., Hublin, J.-J., Reich, D., Kelso, J., Viola, B., & Pääbo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514(7523), 445-449. |
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Gansauge, M.-T., & Meyer, M. (2014). Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research, 24(9), 1543-1549. |
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Gerth, M., Gansauge, M.-T., Weigert, A., & Bleidorn, C. (2014). Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic. Nature Communications, 5: 5117. |
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Giuliani, C., Barbieri, C., Li, M., Bucci, L., Monti, D., Passarino, G., Luiselli, D., Franceschi, C., Stoneking, M., & Garagnani, P. (2014). Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. Aging, 6(6), 454-467. |
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Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J., Pääbo, S., Meshorer, E., & Carmel, L. (2014). Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science, 344(6183), 523-527. |
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Guo, J., Tan, J., Yang, Y., Zhou, H., Hu, S., Hashan, A., Bahaxar, N., Xu, S., Weaver, T. D., Jin, L., Stoneking, M., & Tang, K. (2014). Variation and signatures of selection on the human face. Journal of Human Evolution, 75, 143-152. |
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Gustavino, B., Meschini, R., Franzetti, G., Gratton, P., Allegrucci, G., & Sbordoni, V. (2014). Genotoxicity testing for radon exposure: Dolichopoda (Orthoptera, Rhaphidophoridae) as potential bio-indicator of confined environments. Current Zoology, 60(2), 299-307. |
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He, Z., Bammann, H., Han, D., Xie, G., & Khaitovich, P. (2014). Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA, 20(7), 1103-1111. |
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