31.01.2015 - 14:08
A  A

Recent Department Publications

Last update: January 31st, 2015

Print version (PDF)


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. doi: 10.1002/ajpa.22441
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. doi: 10.1371/journal.pone.0099117
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. doi: 10.1016/j.jhevol.2013.09.009
Cao, Q., Didelot, X., Wu, Z., Li, Z., He, L., Li, Y., Ni, M., You, Y., Lin, X., Li, Z., Gong, Y., Zheng, M., Zhang, M., Liu, J., Wang, W., Bo, X., Falush, D., Wang, S., & Zhang, J. (2014). Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis (Advance online). Gut. doi: 10.1136/gutjnl-2014-307345
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. doi: 10.1371/journal.pgen.1003519
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. doi: 10.1126/science.1253714
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., Brajković, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J. F., 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. doi: 10.1073/pnas.1405138111
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, de Bakker, P. I. W., Wijmenga, C., Swertz, M. A., Stoneking, M., & Li, M. (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. doi: 10.1038/ejhg.2014.19
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. doi: 10.1038/ejhg.2013.122
Duggan, A. T. (2014). Investigations of the settlement and demographic history of Oceania through whole mitochondrial genome sequence analysis. PhD Thesis, Univ., Leipzig.
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. doi: 10.1016/j.gde.2014.06.010
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. doi: 10.1016/j.ajhg.2014.03.014
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. doi: 10.1371/journal.pgen.1004128
Francioli, L. C., Menelaou, A., Pulit, S. L., van Dijk, F., Palamara, P. F., Elbers, C. C., Neerincx, P. B. T., Ye, K., Guryev, V., Kloosterman, W. P., Deelen, P., Abdellaoui, A., van Leeuwen, E. M., van Oven, M., Vermaat, M., Li, M., Laros, J. F. J., Karssen, L. C., Kanterakis, A., Amin, N., Hottenga, J. J., Lameijer, E.-W., Kattenberg, M., Dijkstra, M., Byelas, H., van Setten, J., van Schaik, B. D. C., Bot, J., Nijman, I. J., Renkens, I., Marschall, T., Schönhuth, A., Hehir-Kwa, J. Y., Handsaker, R. E., Polak, P., Sohail, M., Vuzman, D., Hormozdiari, F., van Enckevort, D., Mei, H., Koval, V., Moed, M. H., van der Velde, K. J., Rivadeneira, F., Estrada, K., Medina-Gomez, C., Isaacs, A., McCarroll, S. A., Beekman, M., de Craen, A. J. M., Suchiman, H. E. D., Hofman, A., Oostra, B., Uitterlinden, A. G., Willemsen, G., Study, L. C., Platteel, M., Veldink, J. H., van den Berg, L. H., Pitts, S. J., Potluri, S., Sundar, P., Cox, D. R., Sunyaev, S. R., den Dunnen, J. T., Stoneking, M., de Knijff, P., Kayser, M., Li, Q., Li, Y., Du, Y., Chen, R., Cao, H., Li, N., Cao, S., Wang, J., Bovenberg, J. A., Pe'er, I., Slagboom, P. E., van Duijn, C. M., Boomsma, D. I., van Ommen, G.-J.-B., de Bakker, P. I. W., Swertz, M. A., Wijmenga, C., & Genome of the Netherlands Consortium, The (2014). Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics, 46(8), 818-825. doi: 10.1038/ng.3021
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. F., Viola, B., & Pääbo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514, 445-449. doi: 10.1038/nature13810
Gansauge, M.-T., & Meyer, M. (2014). Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research, 24, 1543-1549. doi: 10.1101/gr.174201.114
Gerth, M., Gansauge, M.-T., Weigert, A., & Bleidorn, C. (2014). Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic. Nature Communications, 5: 5117. doi: 10.1038/ncomms6117
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. Retrieved from http://www.impactaging.com/papers/v6/n6/full/100661.html.
Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014). Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science, 344(6183), 523-527. doi: 10.1126/science.1250368
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. doi: 10.1016/j.jhevol.2014.08.001
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. doi: 10.1261/rna.043075.113
Hellenthal, G., Busby, G. B. J., Band, G., Wilson, J. F., Capelli, C., Falush, D., & Myers, S. (2014). A genetic atlas of human admixture history. Science, 373(6172), 747-751. doi: 10.1126/science.1243518
Henne, K., Li, J., Stoneking, M., Kessler, O., Schilling, H., Sonanini, A., Conrads, G., & Horz, H.-P. (2014). Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies. BMC Evolutionary Biology, 14: 190. doi: 10.1186/s12862-014-0190-3
Heyn, P., Kircher, M., Dahl, A., Kelso, J. F., Tomancak, P., Kalinka, A. T., & Neugebauer, K. M. (2014). The earliest transcribed zygotic genes are short, newly evolved and different across species. Cell Reports, 6(2), 285-292. doi: 10.1016/j.celrep.2013.12.030
Heyne, H. O., Lautenschläger, S., Nelson, R., Besnier, F., Rotival, M., Cagan, A., Kozhemyakina, R., Plyusnina, I. Z., Trut, L., Carlborg, Ö., Petretto, E., Kruglyak, L., Pääbo, S., Schöneberg, T., & Albert, F. W. (2014). Genetic influences on brain gene expression in rats selected for tameness and aggression. Genetics, 198(3), 1277-1290. doi: 10.1534/genetics.114.168948
Horn, S. (2014). TERT-Promoter-Mutationen im familiären und sporadischen Melanom. In Lebendige Wissenschaft: Spitzenforschung in der Dermatologie - Innovationen und Auszeichnungen 2014 (pp. 52-57). Lampertheim: Alpha-Informations-GmbH.
Horn, S., Prost, S., Stiller, M., Makowiecki, D., Kuznetsova, T., Benecke, N., Pucher, E., Hufthammer, A. K., Schouwenburg, C., Shapiro, B., & Hofreiter, M. (2014). Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Molecular Ecology, 23(7), 1717-1729. doi: 10.1111/mec.12691
Hu, H. Y., He, L., & Khaitovich, P. (2014). Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes. BMC Genomics, 15: 457. doi: 10.1186/1471-2164-15-457
Kelso, J. F., & Prüfer, K. (2014). Ancient humans and the origin of modern humans. Current Opinion in Genetics & Development, 29, 133-138. doi: 10.1016/j.gde.2014.09.004
Key, F. M., Teixeira, J. C., de Filippo, C., & Andrés, A. M. (2014). Advantageous diversity maintained by balancing selection in humans. Current Opinion in Genetics & Development, 29, 45-51. doi: 10.1016/j.gde.2014.08.001
Key, F.-M., Peter, B., Dennis, M. Y., Huerta-Sanchez, E., Tang, W., Prokunina-Olsson, L., Nielsen, R., & Andrés, A. M. (2014). Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of Interferon Lambda 4 (IFNL 4). PLoS Genetics, 10(10): e1004681. doi: 10.1371/journal.pgen.1004681
Khrameeva, E. E., Bozek, K., He, L., Yan, Z., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J. F., Pääbo, S., Giavalisco, P., Lachmann, M., & Khaitovich, P. (2014). Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications, 5: 3584. doi: 10.1038/ncomms4584
Ko, A.-M.-S., Chen, C.-Y., Fu, Q., Delfin, F. S., Li, M., Chiu, H.-L., Stoneking, M., & Ko, Y.-C. (2014). Early Austronesians: Into and out of Taiwan. The American Journal of Human Genetics, 94(3), 426-436. doi: 10.1016/j.ajhg.2014.02.003
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., Berger, B., Economou, C., Bollongino, R., Fu, Q., Bos, K. I., Nordenfelt, S., Li, H., de Filippo, C., Prüfer, K., Sawyer, S., Posth, C., Haak, W., Hallgren, F., Fornander, E., Rohland, N., Delsate, D., Francken, M., Guinet, J.-M., Wahl, J., Ayodo, G., Babiker, H. A., Bailliet, G., Balanovska, E., Balanovsky, O., Barrantes, R., Bedoya, G., Ben-Ami, H., Bene, J., Berrada, F., Bravi, C. M., Brisighelli, F., Busby, G. B. J., Cali, F., Churnosov, M., Cole, D. E. C., Corach, D., Damba, L., van Driem, G., Dryomov, S., Dugoujon, J.-M., Fedorova, S. A., Romero, I. G., Gubina, M., Hammer, M., Henn, B. M., Hervig, T., Hodoglugil, U., Jha, A. R., Karachanak-Yankova, S., Khusainova, R., Khusnutdinova, E., Kittles, R., Kivisild, T., Klitz, W., Kučinskas, V., Kushniarevich, A., Laredj, L., Litvinov, S., Loukidis, T., Mahley, R. W., Melegh, B., Metspalu, E., Molina, J., Mountain, J., Näkkäläjärvi, K., Nesheva, D., Nyambo, T., Osipova, L., Parik, J., Platonov, F., Posukh, O., Romano, V., Rothhammer, F., Rudan, I., Ruizbakiev, R., Sahakyan, H., Sajantila, A., Salas, A., Starikovskaya, E. B., Tarekegn, A., Toncheva, D., Turdikulova, S., Uktveryte, I., Utevska, O., Vasquez, R., Villena, M., Voevoda, M., Winkler, C. A., Yepiskoposyan, L., Zalloua, P., Zemunik, T., Cooper, A., Capelli, C., Thomas, M. G., Ruiz-Linares, A., Tishkoff, S. A., Singh, L., Thangaraj, K., Villems, R., Comas, D., Sukernik, R., Metspalu, M., Meyer, M., Eichler, E. E., Burger, J., Slatkin, M., Pääbo, S., Kelso, J. F., Reich, D., & Krause, J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513, 409-413. doi: 10.1038/nature13673
Lee, C.-H., Chiang, S.-L., Ko, A.-M.-S., Hua, C.-H., Tsai, M.-H., Warnakulasuriya, S., Ibrahim, S. O., Sunarjo, Zain, R. B., Ling, T.-Y., Huang, C.-L., Lane, H.-Y., Lin, C.-C., & Ko, Y.-C. (2014). Betel-quid dependence domains and syndrome associated with betel-quid ingredients among chewers: An Asian multi-country evidence. Addiction, 109(7), 1194-1204. doi: 10.1111/add.12530
Li, J., Quinque, D., Horz, H.-P., Li, M., Rzhetskaya, M., Raff, J. A., Hayes, M. G., & Stoneking, M. (2014). Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa. BMC Microbiology, 14: 316. doi: 10.1186/s12866-014-0316-1
Lindskog, C., Kuhlwilm, M., Davierwala, A., Fu, N., Hegde, G., Uhlén, M., Navani, S., Pääbo, S., & Pontén, a. F. (2014). Analysis of candidate genes for lineage-specific expression changes in humans and primates. Journal of Proteome Research, 13(8), 3596-3606. doi: 10.1021/pr500045f
Lippold, S., Xu, H., Ko, A., Li, M., Renaud, G., Butthoff, A., Schröder, R., & Stoneking, M. (2014). Human paternal and maternal demographic histories: Insights from high-resolution Y chromosome and mtDNA sequences. Investigative Genetics, 5: 13. doi: 10.1186/2041-2223-5-13
Lipson, M., Loh, P.-R., Patterson, N., Moorjani, P., Ko, Y.-C., Stoneking, M., Berger, B., & Reich, D. (2014). Reconstructing Austronesian population history in Island Southeast Asia. Nature Communications, 5: 4689. doi: 10.1038/ncomms5689
Macholdt, E., Lede, V., Barbieri, C., Mpoloka, S. W., Chen, H., Slatkin, M., Pakendorf, B., & Stoneking, M. (2014). Tracing pastoralist migrations to Southern Africa with lactase persistence alleles. Current Biology, 24(8), 875-879. doi: 10.1016/j.cub.2014.03.027
Macholdt, E., Slatkin, M., Pakendorf, B., & Stoneking, M. (2014). New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa (advance online). American Journal of Physical Anthropology. doi: 10.1002/ajpa.22675
Malaspinas, A.-S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P. F., Sagredo, F. S., Rasmussen, S., Gonçalves, V. F., Albrechtsen, A., Allentoft, M. E., Johnson, P. L., Li, M., Reis, S., Bernardo, D. V., DeGiorgio, M., Duggan, A. T., Bastos, M., Wang, Y., Stenderup, J., Moreno-Mayar, J. V., Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G. J., Orlando, L., Price, T. D., Jensen, J. D., Nielsen, R., Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M. M., Neves, W. A., Kayser, M., Higham, T., Stoneking, M., Pena, S. D., & Willerslev, E. (2014). Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology, 24(21), R1035-R1037. doi: 10.1016/j.cub.2014.09.078
Meyer, M., Fu, Q., Ayinuer-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., & Pääbo, S. (2014). A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 505(7483), 403-406. doi: 10.1038/nature12788
Mitchell, K. J., Pratt, R. C., Watson, L. N., Gibb, G. C., Llamas, B., Kasper, M., Edson, J., Hopwood, B., Male, D., Armstrong, K. N., Meyer, M., Hofreiter, M., Austin, J., Donnellan, S. C., Lee, M. S. Y., Phillips, M. J., & Cooper, A. (2014). Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31(9), 2322-2330. doi: 10.1093/molbev/msu176
Nigst, P. R., Haesaerts, P., Damblon, F., Frank-Fellner, C., Mallol, C., Viola, B., Götzinger, M., Niven, L., Trnka, G., & Hublin, J.-J. (2014). Early modern human settlement of Europe north of the Alps occurred 43,500 years ago in a cold steppe-type environment. Proceedings of the National Academy of Sciences of the United States of America, 111(40), 14394-14399. doi: 10.1073/pnas.1412201111
Nogueiro, I., Teixeira, J., Amorim, A., Gusmão, L., & Alvarez, L. (2014). Echoes from Sepharad: Signatures on the maternal gene pool of crypto-Jewish descendants (advance online). European journal of human genetics. doi: 10.1038/ejhg.2014.140
O'Brien, J., Didelot, X., Iqbal, Z., Amenga-Etego, L., Ahiska, B., & Falush, D. (2014). A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics, 197(3), 925-937. doi: 10.1534/genetics.114.161299
Oven, M. v., Brauer, S., Choi, Y., Ensing, J., Schiefenhövel, W., Stoneking, M., & Kayser, M. (2014). Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea. European journal of human genetics, 22, 1393-1403. doi: 10.1038/ejhg.2014.38
Pääbo, S. (2014). Neanderthal man: In search of lost genomes. New York: Basic Books.
Pääbo, S. (2014). The human condition: A molecular approach. Cell, 157(1), 216-226. doi: 10.1016/j.cell.2013.12.036
Pfefferle, D., Kazem, A. J. N., Brockhausen, R. R., Ruiz-Lambides, A., & Widdig, A. (2014). Monkeys spontaneously discriminate their unfamiliar paternal relatives under natural conditions using facial cues. Current Biology, 24(15), 1806-1810. doi: 10.1016/j.cub.2014.06.058
Pickrell, J. K., Patterson, N., Loh, P.-R., Lipson, M., Berger, B., Stoneking, M., Pakendorf, B., & Reich, D. (2014). Ancient west Eurasian ancestry in southern and eastern Africa. Proceedings of the National Academy of Sciences of the United States of America, 111(7), 2632 -2637. doi: 10.1073/pnas.1313787111
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M. F., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J. F., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49. doi: 10.1038/nature12886
Pybus, M., Dall'Olio, G. M., Luisi, P., Uzkudun, M., Carreño-Torres, A., Pavlidis, P., Laayouni, H., Bertranpetit, J., & Engelken, J. (2014). 1000 genomes selection browser 1.0: A genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research, 42(D1), D903-D909. doi: 10.1093/nar/gkt1188
Racimo, F., Kuhlwilm, M., & Slatkin, M. (2014). A test for ancient selective sweeps and an application to candidate sites in modern humans (advance online). Molecular Biology and Evolution. doi: 10.1093/molbev/msu255
Renaud, G., LaFave, M. C., Liang, J., Wolfsberg, T. G., & Burgess, S. M. (2014). trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags. BMC Bioinformatics, 15: 329. doi: 10.1186/1471-2105-15-329
Renaud, G., Stenzel, U., & Kelso, J. F. (2014). leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Research (London), 42(18): e141. doi: 10.1093/nar/gku699
Renaud, G., Stenzel, U., Maricic, T., Wiebe, V., & Kelso, J. F. (2014). deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach (advance online). Bioinformatics. doi: 10.1093/bioinformatics/btu719
Rieux, A., Eriksson, A., Li, M., Sobkowiak, B., Weinert, L. A., Warmuth, V., Ruiz-Linares, A., Manica, A., & Balloux, F. (2014). Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution, 31(10), 2780-2792. doi: 10.1093/molbev/msu222
Romagné, F., Santesmasses, D., White, L., Sarangi, G. K., Mariotti, M., Hübler, R., Weihmann, A., Parra, G., Gladyshev, V. N., Guigó, R., & Castellano, S. (2014). SelenoDB 2.0: Annotation of selenoprotein genes in animals and their genetic diversity in humans. Nucleic Acids Research, 42(D1), D437-D443. doi: 10.1093/nar/gkt1045
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J. F., Pääbo, S., Patterson, N., & Reich, D. (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature, 507, 354-357. doi: 10.1038/nature12961
Schreiweis, C., Bornschein, U., Burguière, E., Kerimoglu, C., Schreiter, S., Dannemann, M., Goyal, S., Rea, E., French, C. A., Puliyadi, R., Groszer, M., Fisher, S. E., Mundry, R., Winter, C., Hevers, W., Pääbo, S., Enard, W., & Graybiel, A. M. (2014). Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. Proceedings of the National Academy of Sciences of the United States of America, 111(39), 14253-14258. doi: 10.1073/pnas.1414542111
Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014). Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 111(6), 2229-2234. doi: 10.1073/pnas.1318934111
Stiller, M., Molak, M., Prost, S., Rabeder, G., Baryshnikov, G., Rosendahl, W., Münzel, S., Bocherens, H., Grandal-d'Anglade, A., Hilpert, B., Germonpré, M., Stasyk, O., Pinhasi, R., Tintori, A., Rohland, N., Mohandesan, E., Ho, S. Y., Hofreiter, M., & Knapp, M. (2014). Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231. doi: 10.1016/j.quaint.2013.09.023
The SIGMA Type 2 Diabetes Consortium (2014). Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature, 506, 97-101. doi: 10.1038/nature12828
Tu, H.-P., Ko, A.-M.-S., Chiang, S.-L., Lee, S.-S., Lai, H.-M., Chung, C.-M., Huang, C.-M., Lee, C.-H., Kuo, T.-M., Hsieh, M.-J., & Ko, Y.-C. (2014). Joint effects of alcohol consumption and ABCG2 Q141K on chronic tophaceous gout risk. Journal of Rheumatology, 41(4), 749-758. doi: 10.3899/jrheum.130870
Vilardell, M., Parra, G., & Civit, S. (2014). WISCOD: A statistical web-enabled tool for the identification of significant protein coding regions. BioMed Research International, 2014: 282343. doi: 10.1155/2014/282343
Weigert, A., Helm, C., Meyer, M., Nickel, B., Arendt, D., Hausdorf, B., Santos, S. R., Halanych, K. M., Purschke, G., Bleidorn, C., & Struck, T. H. (2014). Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution, 31(6), 1391-1401. doi: 10.1093/molbev/msu080
Wunderlich, S., Kircher, M., Vieth, B., Haase, A., Merkert, S., Beier, J., Göhring, G., Glage, S., Schambach, A., Curnow, E. C., Pääbo, S., Martin, U., & Enard, W. (2014). Primate iPS cells as tools for evolutionary analyses. Stem Cell Research, 12(3), 622-629. doi: 10.1016/j.scr.2014.02.001
Yahara, K., Didelot, X., Ansari, M. A., Sheppard, S. K., & Falush, D. (2014). Efficient inference of recombination hot regions in bacterial genomes. Molecular Biology and Evolution, 31(6), 1593-1605. doi: 10.1093/molbev/msu082
Zhao, G., Guo, S., Somel, M., & Khaitovich, P. (2014). Evolution of human longevity uncoupled from caloric restriction mechanisms. PLoS One, 9(1): e84117. doi: 10.1371/journal.pone.0084117


Barbieri, C., Butthoff, A., Bostoen, K., & Pakendorf, B. (2013). Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia. European journal of human genetics: EJHG; the official journal of the European Society of Human Genetics, 21, 430-436. doi: 10.1038/ejhg.2012.192
Barbieri, C., Vicente, M., Rocha, J., Mpoloka, S. W., Stoneking, M., & Pakendorf, B. (2013). Ancient substructure in early mtDNA lineages of southern Africa. American Journal of Human Genetics, 92, 285-292. doi: 10.1016/j.ajhg.2012.12.010
Bedaso, Z. K., Wynna, J. G., Alemseged, Z., & Geraads, D. (2013). Dietary and paleoenvironmental reconstruction using stable isotopes of herbivore tooth enamel from middle Pliocene Dikika, Ethiopia: Implication for Australopithecus afarensis habitat and food resources. Journal of Human Evolution, 64(1), 21-38. doi: 10.1016/j.jhevol.2012.05.015
Brandariz-Fontes, C., Leonard, J. A., Vega-Pla, J. L., Backström, N., Lindgren, G., Lippold, S., & Rico, C. (2013). Y-Chromosome Analysis in Retuertas Horses. PLoS One, 8(5): e64985. doi: 10.1371/journal.pone.0064985
Brown, S., Savage, P. E., Ko, A.-M.-S., Stoneking, M., Ko, Y.-C., Loo, J.-H., & Trejaut, J. A. (2013). Correlations in the population structure of music, genes and language. Proceedings of the Royal Society of London. Series B: Biological Sciences, 281(1774): 20132072. doi: 10.1098/rspb.2013.2072
Bruche, S., Gusset, M., Lippold, S., Barnett, R., Eulenberger, K., Junhold, J., Driscoll, C. A., & Hofreiter, M. (2013). A genetically distinct lion (Panthera leo) population from Ethiopia. European Journal of Wildlife Research, 59(2), 215-225. doi: 10.1007/s10344-012-0668-5
Bryk, J., Somel, M., Lorenc, A., & Teschke, M. (2013). Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus). Ecology and Evolution, 3(3), 558-568. doi: 10.1002/ece3.447
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., & Meyer, M. (2013). Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences of the United States of America, 110(39), 15758-15763. doi: 10.1073/pnas.1314445110
Dabney, J., Meyer, M., & Pääbo, S. (2013). Ancient DNA damage. Cold Spring Harbor Perspectives in Biology, 5(7): a012567. doi: 10.1101/cshperspect.a012567
Donaldson-Matasci, M. C., Bergstrom, C. T., & Lachmann, M. (2013). When unreliable cues are good enough. American Naturalist, 182(3), 313-327. doi: 10.1086/671161
Duggan, A. T., & Stoneking, M. (2013). A highly unstable recent mutation in human mtDNA. American Journal of Human Genetics, 92(2), 279-284. doi: 10.1016/j.ajhg.2012.12.004
Ferreira, Z., Hurle, B., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Gonder, M. K., Stone, A. C., Tishkoff, S., Swanson, W. J., NISC Comparative Sequencing Program, Green, E. D., Clark, A. G., & Seixas, S. (2013). Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biology and Evolution, 5(12), 2512-2523. doi: 10.1093/gbe/evt198
Ferreira, Z., Seixas, S., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Swanson, W. J., Clark, A. G., Green, E. D., & Hurle, B. (2013). Reproduction and immunity-driven natural selection in the human WFDC locus. Molecular Biology and Evolution, 30(4), 938-950. doi: 10.1093/molbev/mss329
Fu, Q. (2013). Tracing human prehistory with genetic data of ancient and modern humans. PhD Thesis, Univ., Leipzig.
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J. F., & Pääbo, S. (2013). DNA analysis of an early modern human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences of the United States of America, 110(6), 2223-2227. doi: 10.1073/pnas.1221359110
Fu, Q., Mittnik, A., Johnson, P. L., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., Ronchitelli, A. M., Martini, F., Cremonesi, R. G., Svoboda, J., Bauer, P., Caramelli, D., Castellano, S., Reich, D., Pääbo, S., & Krause, J. (2013). A revised timescale for human evolution based on ancient mitochondrial genomes. Current Biology, 23(7), 553-559. doi: 10.1016/j.cub.2013.02.044
Gansauge, M.-T., & Meyer, M. (2013). Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols, 8(4), 737-748. doi: 10.1038/nprot.2013.038
Good, J. M., Wiebe, V., Albert, F., Burbano, H. A., Kircher, M., Green, R. E., Halbwax, M., André, C., Atencia, R., Fischer, A., & Pääbo, S. (2013). Comparative population genomics of the ejaculate in humans and the great apes. Molecular Biology and Evolution, 30(4), 964-976. doi: 10.1093/molbev/mst005
Grossmann, T., Vaish, A., Franz, J., Schroeder, R., Stoneking, M., & Friederici, A. D. (2013). Emotional voice processing: Investigating the role of genetic variation in the serotonin transporter across development. PLoS One, 8(7): e68377. doi: 10.1371/journal.pone.0068377
Guschanski, K., Krause, J., Sawyer, S., Valente, L. M., Bailey, S., Finstermeier, K., Sabin, R., Gilissen, E., Sonet, G., Nagy, Z. T., Lenglet, G., Mayer, F., & Savolainen, V. (2013). Next-generation museomics disentangles one of the largest primate radiations. Systematic Biology, 62(4), 539-554. doi: 10.1093/sysbio/syt018
Ka, S., Markljung, E., Ring, H., Albert, F. W., Harun-Or-Rashid, M., Wahlberg, P., Garcia-Roves, P. M., Zierath, J. R., Denbow, D. M., Pääbo, S., Siegel, P. B., Andersson, L., & Hallbook, F. (2013). Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight. Physiological Genomics, 45(9), 367-376. doi: 10.​1152/​physiolgenomics.​00078.​2012
Ko, A.-M.-S., Tu, H.-P., Liu, T.-T., Chang, J.-G., Yuo, C.-Y., Chiang, S.-L., Chang, S.-J., Liu, Y.-F., Ko, A.-M.-J., Lee, C.-H., Lee, C.-P., Chang, C.-M., Tsai, S.-F., & Ko, Y.-C. (2013). ALPK1 genetic regulation and risk in relation to gout. International Journal of Epidemiology, 42(2), 466-474. doi: 10.1093/ije/dyt028
Kuhlwilm, M., Davierwala, A., & Pääbo, S. (2013). Identification of putative target genes of the transcription factor RUNX2. PLoS One, 8(12): e83218. doi: 10.1371/journal.pone.0083218
Kunz, M., Dannemann, M., & Kelso, J. (2013). High-throughput sequencing of the melanoma genome. Experimental Dermatology, 22(1), 10-17. doi: 10.1111/exd.12054
Lachmann, M. (2013). The value of information in signals and cues. In U. E. Stegmann (Ed.), Animal Communication Theory: Information and Influence (pp. 357-376). Cambridge: Cambridge University Press. doi: 10.1017/CBO9781139003551.021
Li, J., Nasidze, I., Quinque, D., Li, M., Horz, H.-P., Andre, C., Garriga, R. M., Halbwax, M., Fischer, A., & Stoneking, M. (2013). The saliva microbiome of Pan and Homo. BMC Microbiology, 13: 204. doi: 10.1186/1471-2180-13-204
Li, Z., Bammann, H., Li, M., Liang, H., Yan, Z., Chen, Y.-P.-P., Zhao, M., & Khaitovich, P. (2013). Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains. RNA, 19(12), 1693-1702. doi: 10.1261/rna.039206.113
Maricic, T., Günther, V., Georgiev, O., Gehre, S., Ćurlin, M., Schreiweis, C., Naumann, R., Burbano, H. A., Meyer, M., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Gajović, S., Kelso, J. F., Enard, W., Schaffner, W., & Pääbo, S. (2013). A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Molecular Biology and Evolution, 30(4), 844-852. doi: 10.1093/molbev/mss271
Mazin, P., Xiong, J., Liu, X., Yan, Z., Zhang, X., Li, M., He, L., Somel, M., Yuan, Y., Chen, Y.-P.-P., Li, N., Hu, Y., Fu, N., Ning, Z., Zeng, R., Yang, H., Chen, W., Gelfand, M., & Khaitovich, P. (2013). Widespread splicing changes in human brain development and aging. Molecular Systems Biology, 9: 663. doi: 10.1038/msb.2012.67
Oña Bubach, L. (2013). On the role of resonance in drug failure under HIV treatment interruption. Theoretical Biology & Medical Modelling, 10: 44. doi: 10.1186/1742-4682-10-44
Prado-Martinez, J., Hernando-Herraez, I., Lorente-Galdos, B., Dabad, M., Ramirez, O., Baeza-Delgado, C., Morcillo-Suarez, C., Alkan, C., Hormozdiari, F., Raineri, E., Estellé, J., Fernandez-Callejo, M., Valles, M., Ritscher, L., Schöneberg, T., de la Calle-Mustienes, E., Casillas, S., Rubio-Acero, R., Melé, M., Engelken, J., Caceres, M., Gomez-Skarmeta, J. L., Gut, M., Bertranpetit, J., Gut, I. G., Abello, T., Eichler, E. E., Mingarro, I., Lalueza-Fox, C., Navarro, A., & Marques-Bonet, T. (2013). The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics, 14: 363. doi: 10.1186/1471-2164-14-363
Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O’Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I., Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M. L., Stevison, L., Camprubı´, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J. A., Bergl, R. A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S. A., Mullikin, J. C., Wilson, R. K., Gut, I. G., Gonder, M. K., Ryder, O. A., Hahn, B. H., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schierup, M. H., Hvilsom, C., Andrés, A. M., Wall, J. D., Bustamante, C. D., Hammer, M. F., Eichler, E. E., & Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499, 471-475. doi: doi:10.1038/nature12228
Prüfer, K., Langergraber, K. E., Pääbo, S., & Vigilant, L. (2013). Reply to Gibb and Hills: Divergence times, generation lengths and mutation rates in great apes and humans. Proceedings of the National Academy of Sciences of the United States of America, 110(8): E612. doi: 10.1073/pnas.1222027110
Pugach, I., & Stoneking, M. (2013). Reply to Price and Bird: No inconsistency between the date of gene flow from India and the Australian archaeological record. Proceedings of the National Academy of Sciences of the United States of America, 110(32): E2949. doi: 10.1073/pnas.1307961110
Pugach, I., Delfin, F., Gunnarsdóttir, E., Kayser, M., & Stoneking, M. (2013). Genome-wide data substantiate Holocene gene flow from India to Australia. Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1803-1808. doi: 10.1073/pnas.1211927110
Renaud, G., Kircher, M., Stenzel, U., & Kelso, J. F. (2013). freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics, 29(9), 1208-1209. doi: 10.1093/bioinformatics/btt117
Sheppard, S. K., Didelot, X., Meric, G., Torralbo, A., Jolley, K. A., Kelly, D. J., Bentley, S. D., Maiden, M. C. J., Parkhill, J., & Falush, D. (2013). Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11923-11927. doi: 10.1073/pnas.1305559110
Somel, M., Liu, X., & Khaitovich, P. (2013). Human brain evolution: transcripts, metabolites and their regulators. Nature Reviews Neuroscience, 14(2), 112-127. doi: 10.1038/nrn3372
Stiller, M., & Hofreiter, M. (2013). An ancient DNA perspective on the cave bears from Peştera cu Oase, Romani. In E. Trinkaus, S. Constantin, & J. Zilhão (Eds.), Life and Death at the Peştera cu Oase: a setting for modern human emergence (pp. 159-167). New York: Oxford University Press.
Stoneking, M. (2013). Mitochondrial genome: Evolution. In Encyclopedia of the Life Sciences. Chichester [u.a.]: Wiley. doi: 10.1002/9780470015902.a0005074.pub3
Stoneking, M., & Harvati, K. (2013). Early Old World migrations of Homo sapiens: human biology. In The Encyclopedia of Global Human Migration, P. I. Hoboken, NJ: Wiley-Backwell. doi: 10.1002/9781444351071.wbeghm805
Thalmann, O., Shapiro, B., Cui, P., Schuenemann, V. J., Sawyer, S., Greenfield, D. L., Germonpré, M. B., Sablin, M. V., López-Giráldez, F., Domingo-Roura, X., Napierala, H., Uerpmann, H.-P., Loponte, D. M., Acosta, A. A., Giemsch, L., Schmitz, R. W., Worthington, B., Buikstra, J. E., Druzhkova, A., Graphodatsky, A. S., Ovodov, N. D., Wahlberg, N., Freedman, A. H., Schweizer, R. M., Koepfli, K.-P., Leonard, J. A., Meyer, M., Krause, J., Pääbo, S., Green, R. E., & Wayne, R. K. (2013). Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science, 342(6160), 871-874. doi: 10.1126/science.1243650
Viola, B., & Pääbo, S. (2013). What's new in Central Asia? In M. V. Shunkov, & V. Molodin (Eds.), Fundamental'nye problemy archeologii anthropogii i ėtnografii evrazii: k 70. letiju akademika A. P. Derevjanko = Basic Issues in Archaeology, Anthropology and Ethnography of Eurasia: Festschrift on the occasion of Anatoly Derevianko's 70th birthday (pp. 555-565). Novosibirsk: SB RAS Press.
Yahara, K., Furuta, Y., Oshima, K., Yoshida, M., Azuma, T., Hattori, M., Uchiyama, I., & Kobayashi, I. (2013). Chromosome Painting In Silico in a Bacterial Species Reveals Fine Population Structure. Molecular Biology and Evolution, 30(6), 1454-1464. doi: 10.1093/molbev/mst055


Albert, F. W., Somel, M., Carneiro, M., Aximu-Petri, A., Halbwax, M., Thalmann, O., Blanco-Aguiar, J. A., Plyusnina, I. Z., Trut, L., Villafuerte, R., Ferrand, N., Kaiser, S., Jensen, P., & Pääbo, S. (2012). A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genetics, 8(9): e1002962. doi: 10.1371/journal.pgen.1002962
Ballantyne, K. N., van Oven, M., Ralf, A., Stoneking, M., Mitchell, R. J., van Oorschot, R. A., & Kayser, M. (2012). MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Science International: Genetics, 6(4), 425-436. doi: 10.1016/j.fsigen.2011.08.010
Barbieri, C., Whitten, M., Beyer, K., Schreiber, H., Li, M., & Pakendorf, B. (2012). Contrasting Maternal and Paternal Histories in the Linguistic Context of Burkina Faso. Molecular Biology and Evolution, 29(4), 1213 -1223. doi: 10.1093/molbev/msr291
Burbano, H. A., Green, R. E., Maricic, T., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Kelso, J., Pollard, K. S., Lachmann, M., & Pääbo, S. (2012). Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One, 7(3): e32877. doi: 10.1371/journal.pone.0032877
Carneiro, M., Albert, F. W., Melo-Ferreira, J., Galtier, N., Gayral, P., Blanco-Aguiar, J. A., Villafuerte, R., Nachman, M. W., & Ferrand, N. (2012). Evidence for Widespread Positive and Purifying Selection Across the European Rabbit (Oryctolagus cuniculus) Genome. Molecular Biology and Evolution, 29(7), 1837-1849. doi: 10.1093/molbev/mss025
Carnero-Montoro, E., Bonet, L., Engelken, J., Bielig, T., Martínez-Florensa, M., Lozano, F., & Bosch, E. (2012). Evolutionary and functional evidence for positive selection at the human CD5 immune receptor gene. Molecular Biology and Evolution, 29(2), 811-823. doi: 10.1093/molbev/msr251
Clovis, Y. M., Enard, W., Marinaro, F., Huttner, W. B., & Tonelli, D. D. P. (2012). Convergent repression of Foxp2 3'UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons. Development, 139(18), 3332-3342. doi: 10.1242/dev.078063
Dabney, J., & Meyer, M. (2012). Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques, 52(2), 87-94. doi: 10.2144/000113809
Dannemann, M., Lachmann, M., & Lorenc, A. (2012). 'maskBAD' – a package to detect and remove Affymetrix probes with binding affinity differences. BMC Bioinformatics, 13: 56. doi: 10.1186/1471-2105-13-56
Dannemann, M., Nickel, B., Lizano, E., Burbano, H., & Kelso, J. F. (2012). Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics, 13(Suppl. 3): 116. doi: 10.1186/1471-2164-13-116
Dannemann, M., Prüfer, K., Lizano, E., Nickel, B., Burbano, H. A., & Kelso, J. (2012). Transcription factors are targeted by differentially expressed miRNAs in primates. Genome biology and evolution, 4(4), 552-564. doi: 10.1093/gbe/evs033
de Filippo, C., Bostoen, K., Stoneking, M., & Pakendorf, B. (2012). Bringing together linguistic and genetic evidence to test the Bantu expansion. Proceedings of the Royal Society B: Biological Sciences, 279(1741), 3256-3263. doi: 10.1098/rspb.2012.0318
Delfin, F., Myles, S., Choi, Y., Hughes, D., Illek, R., van Oven, M., Pakendorf, B., Kayser, M., & Stoneking, M. (2012). Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Molecular Biology and Evolution, 29(2), 545-564. doi: 10.1093/molbev/msr186
Didelot, X., Méric, G., Falush, D., & Darling, A. E. (2012). Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics, 13: 256. doi: 10.1186/1471-2164-13-256
Duggan, A. T., Whitten, C. M., Wiebe, V., Crawford, M., Butthoff, A., Spitsyn, V., Makarov, S., Novgorodov, I., Osakovsky, V., & Pakendorf, B. (2012). Investigating the prehistory of Tungusic peoples of Siberia and the Amur-Ussuri region with complete mtDNA genome sequences and Y-chromosomal markers. PLoS One, 8(12): e83570. doi: 10.1371/journal.pone.0083570
Enard, W. (2012). Functional primate genomics - leveraging the medical potential. Journal of Molecular Medicine, 90(5), 471-480. doi: 10.1007/s00109-012-0901-4
Fietz, S. A., Lachmann, R., Brandl, H., Kircher, M., Samusik, N., Schröder, R., Lakshmanaperumal, N., Henry, I., Vogt, J., Riehn, A., Distler, W., Nitsch, R., Enard, W., Pääbo, S., & Huttner, W. B. (2012). Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proceedings of the National Academy of Sciences of the United States of America, 109(29), 11836-11841. doi: 10.1073/pnas.1209647109
Fu, Q., Rudan, P., Pääbo, S., & Krause, J. (2012). Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One, 7(3): e32473. doi: 10.1371/journal.pone.0032473
Gravlund, P., Aaris-Sørensen, K., Hofreiter, M., Meyer, M., Bollback, J. P., & Noe-Nygaar, N. (2012). Ancient DNA extracted from Danish aurochs (Bos primigenius): Genetic diversity and preservation. Annals of Anatomy - Anatomischer Anzeiger, 194(1), 103-111. doi: 10.1016/j.aanat.2011.10.011
Groß, A., Hartung, M., Prüfer, K., Kelso, J., & Rahm, E. (2012). Impact of ontology evolution on functional analyses. Bioinformatics, 28(20), 2671-2677. doi: 10.1093/bioinformatics/bts498
Han, Y., Han, D., Yan, Z., Boyd-Kirkup, J. D., Green, C. D., Khaitovich, P., & Han, J.-D.-J. (2012). Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain. Aging Cell, 11(6), 1055-1064. doi: 10.1111/acel.12007
Hartmann, S., Helm, C., Nickel, B., Meyer, M., Struck, T. H., Tiedemann, R., Selbig, J., & Bleidorn, C. (2012). Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS One, 7(1): e29843. doi: 10.1371/journal.pone.0029843
Helm, C., Bernhart, S. H., Siederdissen, C. H. z., Nickel, B., & Bleidorn, C. (2012). Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular Phylogenetics and Evolution, 64(1), 198-203. doi: 10.1016/j.ympev.2012.03.017
Hering, L., Henze, M. J., Kohler, M., Kelber, A., Bleidorn, C., Leschke, M., Nickel, B., Meyer, M., Kircher, M., Sunnucks, P., & Mayer, G. (2012). Opsins in Onychophora (Velvet Worms) Suggest a Single Origin and Subsequent Diversification of Visual Pigments in Arthropods. Molecular Biology and Evolution, 29(11), 3451-3458. doi: 10.1093/molbev/mss148
Hevers, W., & Lüddens, H. (2012). Pharmakologische und präklinische Grundlagen: Aminosäuren. In Handbuch der Psychopharmakotherapie (2. Aufl., pp. 169-184). Berlin [u.a.]: Springer. doi: 10.1007/978-3-642-19844-1_17
Horn, S. (2012). Case study: enrichment of ancient mitochondrial DNA by hybridization capture. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 189-195). New York: Humana Press. doi: 10.1007/978-1-61779-516-9_22
Horn, S. (2012). Target Enrichment via DNA Hybridization Capture. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 177-188). New York: Humana Press. doi: 10.1007/978-1-61779-516-9_21
Hu, H. Y., He, L., Fominykh, K., Yan, Z., Guo, S., Zhang, X., Taylor, M. S., Tang, L., Li, J., Liu, J., Wang, W., Yu, H., & Khaitovich, P. (2012). Evolution of the human-specific microRNA miR-941. Nature Communications, 3: 1145. doi: 10.1038/ncomms2146
Jinam, T. A., Hong, L.-C., Phipps, M. E., Stoneking, M., Ameen, M., Edo, J., HUGO Pan-Asian SNP Consortium, & Saitou, N. (2012). Evolutionary history of continental South East Asians: "Early Train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Molecular Biology and Evolution, 29(11), 3513-3527. doi: 10.1093/molbev/mss169
Kenny, E. E., Timpson, N. J., Sikora, M., Yee, M.-C., Moreno-Estrada, A., Eng, C., Huntsman, S., Burchard, E. G., Stoneking, M., Bustamante, C. D., & Myles, S. (2012). Melanesian blond hair is caused by an amino acid change in TYRP1. Science, 336(6081), 554-554. doi: 10.1126/science.1217849
Khrameeva, E. E., Mironov, A. A., Fedonin, G. G., Khaitovich, P., & Gelfand, M. S. (2012). Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One, 7(4): e33947. doi: 10.1371/journal.pone.0033947
Kircher, M. (2012). Analysis of high-throughput ancient DNA sequencing data. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 197-228). New York: Humana Press. doi: 10.1007/978-1-61779-516-9_23
Kircher, M., Sawyer, S., & Meyer, M. (2012). Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research, 40(1): e3. doi: 10.1093/nar/gkr771
Knapp, M., Stiller, M., & Meyer, M. (2012). Generating barcoded libraries for multiplex high-throughput sequencing. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 155-170). New York: Humana Press. doi: 10.1007/978-1-61779-516-9_19
Langergraber, K., Pruefer, K., Rowney, C., Boesch, C., Crockford, C., Fawcett, K., Inoue, E., Inoue-Muruyama, M., Mitani, J. C., Muller, M. N., Robbins, M. M., Schubert, G., Stoinski, T. S., Viola, B., Watts, D., Wittig, R., Wrangham, R. W., Zuberbühler, K., Pääbo, S., & Vigilant, L. (2012). Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proceedings of the National Academy of Sciences of the United States of America, 109(39), 15716-15721. doi: 10.1073/pnas.1211740109
Lawson, D. J., & Falush, D. (2012). Population identification using genetic data. Annual Review of Genomics and Human Genetics, 13, 337-361. doi: 10.1146/annurev-genom-082410-101510
Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012). Inference of Population Structure using Dense Haplotype Data. PLoS Genetics, 8(1): e1002453. doi: 10.1371/journal.pgen.1002453
Lee, C.-H., Ko, A.-M.-S., Yen, C.-F., Chu, K.-S., Gao, Y.-J., Warnakulasuriya, S., Sunarjo,.-., Ibrahim, S. O., Zain, R. B., Patrick, W. K., & Ko, Y.-C. (2012). Betel-quid dependence and oral potentially malignant disorders in six Asian countries. British Journal of Psychiatry, 201(5), 383-391. doi: 10.1192/bjp.bp.111.107961
Li, J., Menard, V., Benish, R. L., Jurevic, R. J., Guillemette, C., Stoneking, M., Zimmerman, P. A., & Mehlotra, R. K. (2012). Worldwide variation in human drug-metabolism enzyme genes CYP2B6 and UGT2B7: implications for HIV/AIDS treatment. Pharmacogenomics, 13(5), 555-570. doi: 10.2217/pgs.11.160
Li, M., & Stoneking, M. (2012). A new approach for detecting low-level mutations in next-generation sequence data. Genome Biology, 13(5): R34. doi: 10.1186/gb-2012-13-5-r34
Li, M., Schröder, R., Ko, A.-M.-S., & Stoneking, M. (2012). Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Research, 40(18): e137. doi: 10.1093/nar/gks499
Liu, X., Somel, M., Tang, L., Yan, Z., Jiang, X., Guo, S., Yuan, Y., He, L., Oleksiak, A., Zhang, Y., Li, N., Hu, Y., Chen, W., Qiu, Z., Pääbo, S., & Khaitovich, P. (2012). Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Research, 22(4), 611-622. doi: 10.1101/gr.127324.111
Mailund, T., Halager, A. E., Westergaard, M., Dutheil, J. Y., Munch, K., Andersen, L. N., Lunter, G., Pruefer, K., Scally, A., Hobolth, A., & Schierup, M. H. (2012). A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. PLoS Genetics, 8(12): e1003125. doi: 10.1371/journal.pgen.1003125
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., Filippo, C. d., Sudmant, P. H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R. E., Bryc, K., Briggs, A. W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M. F., Shunkov, M. V., Derevianko, A. P., Patterson, N., Andrés, A. M., Eichler, E. E., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), 222-226. doi: 10.1126/science.1224344
Pickrell, J. K., Patterson, N., Berthold, F., Barbieri, C., Gerlach, L., Gueldemann, T., Kure, B., Mpoloka, S. W., Nakagawa, H., Naumann, C., Lipson, M., Loh, P.-R., Lachance, J., Mountain, J., Bustamante, C. D., Berger, B., Tishkoff, S. A., Henn, B. M., Stoneking, M., Reich, D., & Pakendorf, B. (2012). The genetic prehistory of southern Africa. Nature Communications, 3: 1143. doi: 10.1038/ncomms2140
Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E., Alkan, C., Sajjadian, S., Catacchio, C. R., Ventura, M., Marques-Bonet, T., Eichler, E. E., André, C., Atencia, R., Mugisha, L., Junhold, J., Patterson, N., Siebauer, M., Good, J. M., Fischer, A., Ptak, S. E., Lachmann, M., Symer, D. E., Mailund, T., Schierup, M. H., Andrés, A. M., Kelso, J., & Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-531. doi: 10.1038/nature11128
Quillen, E. E., Bauchet, M., Bigham, A. W., Delgado-Burbano, M. E., Faust, F. X., Klimentidis, Y. C., Mao, X., Stoneking, M., & Shriver, M. D. (2012). OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. Human Genetics, 131(7), 1073-1080. doi: 10.1007/s00439-011-1135-1
Ratikainen, I. I., Sødal, L. R. H., Kazem, A., & Wright, J. (2012). Private and public information use strategies by foraging groups of wild Siberian jays. Animal Behaviour, 83(5), 1243-1251. doi: 10.1016/j.anbehav.2012.02.016
Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., McKay, B. M., Schneider, R., Horton, P., & Kelso, J. F. (2012). Paving the future: finding suitable ISMB venues. Bioinformatics, 28(19), 2556-2559. doi: 10.1093/bioinformatics/bts420
Sankararaman, S., Patterson, N., Li, H., Pääbo, S., & Reich, D. (2012). The date of interbreeding between Neandertals and modern humans. PLoS Genetics, 8(10): e1002947. doi: doi:10.1371/journal.pgen.1002947
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012). Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One, 7(3): e34131. doi: 10.1371/journal.pone.0034131
Schmidt, M., Horn, S., Flieger, K., Ehlers, K., Wilhelm, C., & Schnetter, R. (2012). Synchroma pusillum sp. nov. and other New Algal Isolates with Chloroplast Complexes Confirm the Synchromophyceae (Ochrophyta) as a Widely Distributed Group of Amoeboid Algae. Protist, 163(4), 544-559. doi: 10.1016/j.protis.2011.11.009
Stoneking, M. (2012). Genetic evidence concerning the origins and dispersals of modern humans. In M. H. Crawford, & B. C. Campbell (Eds.), Causes and Consequences of Human Migration: An Evolutionary Perspective (pp. 11-20). Cambridge: Cambridge Univ. Pr.
Theunert, C., Tang, K., Lachmann, M., Hu, S., & Stoneking, M. (2012). Inferring the history of population size change from genome-wide SNP data. Molecular Biology and Evolution, 29(2), 3653-3667. doi: 10.1093/molbev/mss175
Weng, K., Hu, H., Xu, G. A., Khaitovich, P., & Somel, M. (2012). Mechanisms of Dietary Response in Mice and Primates: A Role for EGR1 in Regulating the Reaction to Human-Specific Nutritional Content. PLoS One, 7(8): e43915. doi: 10.1371/journal.pone.0043915
White, L., & Castellano, S. (2012). Evolutionary Basis for the Use of Selenocysteine. In D. L. Hatfield, M. J. Berry, & V. N. Gladyshev (Eds.), Selenium: Its Molecular Biology and Role in Human Health (3, pp. 85-93). New York: Springer. doi: 10.1007/978-1-4614-1025-6_7
Xu, S., & Stoneking, M. (2012). Reply to Denham and Donohue: Asian-Papuan genetic admixture is in excellent agreement with Austronesian dispersal in eastern Indonesia. Proceedings of the National Academy of Sciences of the United States of America, 109(39): E2578. doi: 10.1073/pnas.1210177109
Xu, S., Pugach, I., Stoneking, M., Kayser, M., Jina, L., & The HUGO Pan-Asian SNP Consortium (2012). Genetic dating indicates that the Asian–Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proceedings of the National Academy of Sciences of the United States of America, 109(12), 4574-4579. doi: 10.1073/pnas.1118892109
Yuan, Y., Chen, Y.-P.-P., Boyd-Kirkup, J., Khaitovich, P., & Somel, M. (2012). Accelerated aging-related transcriptome changes in the female prefrontal cortex. Aging Cell, 11(5), 894-901. doi: 10.1111/j.1474-9726.2012.00859.x


Abramson, G., Trejo Soto, C. A., & Oña Bubach, L. (2011). The role of asymmetric interactions on the effect of habitat destruction in mutualistic networks. PLoS ONE, 6(6): e21028. doi: 10.1371/journal.pone.0021028
Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schöneberg, T., Carlborg, Ö., Hannon, G. J., & Pääbo, S. (2011). Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107(3), 205-214. doi: 10.1038/hdy.2011.4
Andrés, A. M. (2011). Balancing selection in the human genome. In Encyclopedia of Life Sciences. Chichester: John Wiley & Sons. doi: 10.1002/9780470015902.a0022863
Benazzi, S., Viola, B., Kullmer, O., Fiorenza, L., Harvati, K., Paul, T., Gruppioni, G., Weber, G. W., & Mallegni, F. (2011). A reassessment of the Neanderthal teeth from Taddeo cave (southern Italy). Journal of Human Evolution, 61(4), 377-387. doi: 10.1016/j.jhevol.2011.05.001
Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., McPhee, J. B., DeWitte, S. N., Meyer, M., Schmedes, S., Wood, J., Earn, D. J. D., Herring, D. A., Bauer, P., Poinar, H. N., & Krause, J. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510. doi: 10.1038/nature10549
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F. W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., & Kaessmann, H. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348. doi: 10.1038/nature10532
de Filippo, C., Barbieri, C., Whitten, M., Mpoloka, S. W., Gunnarsdóttir, E. D., Bostoen, K., Nyambe, T., Beyer, K., Schreiber, H., Knijff, P. d., Luiselli, D., Stoneking, M., & Pakendorf, B. (2011). Y-chromosomal variation in sub-saharan Africa: Insights into the history of Niger-Congo groups. Molecular Biology and Evolution, 28(3): msq312v1, pp. 1255-1269. doi: 10.1093/molbev/msq312
Delfin, F., Salvador, J. M., Calacal, G. C., Perdigon, H. B., Tabbada, K. A., Villamor, L. P., Halos, S. C., Gunnarsdóttir, E., Myles, S., Hughes, D. A., Xu, S., Jin, L., Lao, O., Kayser, M., Hurles, M. E., Stoneking, M., & Ungria, M. C. A. d. (2011). The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European Journal of Human Genetics, 19(2), 224-230. doi: 10.1038/ejhg.2010.162
Didelot, X., Bowden, R., Street, T., Golubchik, T., Spencer, C., McVean, G., Sangal, V., Anjum, M. F., Achtman, M., Falush, D., & Donelly, P. (2011). Recombination and population structure in Salmonella enterica. PLoS Genetics, 7(7): e1002191. doi: 10.1371/journal.pgen.1002191
Döppes, D., Rabeder, G., & Stiller, M. (2011). Was the Middle Würmian in the High Alps warmer than today? Quaternary International, 245(2), 193-200. doi: 10.1016/j.quaint.2011.07.029
Enard, W. (2011). FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution. Current Opinion in Neurobiology, 21(3), 415-424. doi: 10.1016/j.conb.2011.04.008
Fiorenza, L., Benazzi, S., Viola, B., Kullmer, O., & Schrenk, F. (2011). Relationship Between Cusp Size and Occlusal Wear Pattern in Neanderthal and Homo sapiens First Maxillary Molars. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 294(3), 453-461. doi: 10.1002/ar.21325
Fischer, A., Prüfer, K., Good, J. M., Halbwax, M., Wiebe, V., André, C., Atencia, R., Mugisha, L., Ptak, S. E., & Pääbo, S. (2011). Bonobos fall within the genomic variation of chimpanzees. PLoS ONE, 6(6): e21605, pp. 1-10. doi: 10.1371/journal.pone.0021605
Fu, X., Giavalisco, P., Liu, X., Catchpole, G., Fu, N., Ning, Z.-B., Guo, S., Yan, Z., Somel, M., Pääbo, S., Zeng, R., Willmitzer, L., & Khaitovich, P. (2011). Rapid metabolic evolution in human prefrontal cortex. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6181-6186. doi: 10.1073/pnas.1019164108
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Karsch-Mizrachi, I., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research, 39(Suppl. 1). doi: 10.1093/nar/gkq1173
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Mizrachi, I. K., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Database: the Journal of Biological Databases and Curation, 2011: baq027, pp. 1-6. doi: 10.1093/database/baq027
Gralle, M., & Pääbo, S. (2011). A Comprehensive Functional Analysis of Ancestral Human Signal Peptides. Molecular Biology and Evolution, 28(1), 25-28. doi: 10.1093/molbev/msq223
Gross, A., Tönjes, A., Kovacs, P., Veeramah, K. R., Ahnert, P., Roshyara, N. R., Gieger, C., Rueckert, I.-M., Loeffler, M., Stoneking, M., Wichmann, H.-E., Novembre, J., Stumvoll, M., & Scholz, M. (2011). Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genetics, 12: 67. doi: 10.1186/1471-2156-12-67
Grossmann, T., Johnson, M. H., Vaish, A., Hughes, D. A., Quinque, D., Stoneking, M., & Friederici, A. D. (2011). Genetic and neural dissociation of individual responses to emotional expressions in human infants. Developmental Cognitive Neuroscience, 1(1), 57-66. doi: 10.1016/j.dcn.2010.07.001
Gunnarsdóttir, E. D., Li, M., Bauchet, M., Finstermeier, K., & Stoneking, M. (2011). High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Research, 21(1), 1-11. doi: 10.1101/gr.107615.110
Gunnarsdóttir, E. D., Nandineni, M. R., Li, M., Myles, S., Gil, D., Pakendorf, B., & Stoneking, M. (2011). Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications, 2: 228. doi: 10.1038/ncomms1235
Harrison, A., Lemey, P., Hurles, M., Moyes, C., Horn, S., Pryor, J., Malani, J., Supuri, M., Masta, A., Teriboriki, B., Toatu, T., Penny, D., Rambaut, A., & Shapiro, B. (2011). Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation. Viruses, 3(2), 83-101. doi: 10.3390/v3020083
Herre, H., Hoehndorf, R., Kelso, J., Loebe, F., & Schulz, S. (2011). OBML – Ontologies in biomedicine and life sciences. Journal of Biomedical Semantics, 2(Suppl. 4): I1, pp. 1-6. doi: 10.1186/2041-1480-2-S4-I1
Horn, S., Durka, W., Wolf, R., Ermala, A., Stubbe, A., Stubbe, M., & Hofreiter, M. (2011). Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species. PLoS ONE, 6(1): e14622. doi: 10.1371/journal.pone.0014622
Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., Zeng, R., Chen, W., Pääbo, S., & Khaitovich, P. (2011). MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics, 7(10): e1002327, pp. 1-14. doi: 10.1371/journal.pgen.1002327
Jin, C., Li, J., Green, C. D., Yu, X., Tang, X., Han, D., Xian, B., Wang, D., Huang, X., Cao, X., Yan, Z., Hou, L., Liu, J., Shukeir, N., Khaitovich, P., Chen, C. D., Zhang, H., Jenuwein, T., & Han, J.-D.-J. (2011). Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell Metabolism, 14(2), 161-172. doi: 10.1016/j.cmet.2011.07.001
Jordan, S., Krause, J., Prager, A., Mitrovic, M., Jonjic, S., Koszinowski, U. H., & Adler, B. (2011). Virus Progeny of Murine Cytomegalovirus Bacterial Artificial Chromosome pSM3fr Show Reduced Growth in Salivary Glands due to a Fixed Mutation of MCK-2. Journal of Virology, 85(19), 10346-10353. doi: 10.1128/JVI.00545-11
Ka, S., Albert, F. W., Denbow, D. M., Pääbo, S., Siegel, P. B., Andersson, L., & Hallböök, F. (2011). Differentially expressed genes in hypothalamus in relation to genomic regions under selection in two chicken lines resulting from divergent selection for high or low body weight. Neurogenetics, 12(3), 211-221. doi: 10.1007/s10048-011-0290-9
Kircher, M. (2011). Understanding and improving high-throughput sequencing data production and analysis. PhD Thesis, Univ., Leipzig.
Kircher, M., Heyn, P., & Kelso, J. (2011). Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12: 382. doi: 10.1186/1471-2164-12-382
Lerner, H. R. L., Meyer, M., James, H. F., Hofreiter, M., & Fleischer, R. C. (2011). Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers. Current Biology, 21(21), 1838-1844. doi: 10.1016/j.cub.2011.09.039
Li, J., Zhang, L., Zhou, H., Stoneking, M., & Tang, K. (2011). Global patterns of genetic diversity and signals of natural selection for human ADME genes. Human Molecular Genetics, 20(3), 528-540. doi: 10.1093/hmg/ddq498
Li, M., & Chen, S.-S. (2011). The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology, 11: 3. doi: 10.1186/1471-2148-11-3
Liebscher, I., Müller, U., Teupser, D., Engemaier, E., Engel, K. M. Y., Ritscher, L., Thor, D., Sangkuhl, K., Ricken, A., Wurm, A., Piehler, D., Schmutzler, S., Fuhrmann, H., Albert, F. W., Reichenbach, A., Thiery, J., Schöneberg, T., & Schulz, A. (2011). Altered Immune Response in Mice Deficient for the G Protein-coupled Receptor GPR34. The Journal of Biological Chemistry, 286(3), 2101-2110. doi: 10.1074/jbc.M110.196659
Lippold, S., Knapp, M., Kuznetsova, T., Leonard, J. A., Benecke, N., Ludwig, A., Rasmussen, M., Cooper, A., Weinstock, J., Willerslev, E., Shapiro, B., & Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2: 450, pp. 1-6. doi: 10.1038/ncomms1447
Lippold, S., Matzke, N. J., Reissmann, M., & Hofreiter, M. (2011). Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology, 11: 328. doi: 10.1186/1471-2148-11-328
Liu, Y., Han, D., Han, Y., Yan, Z., Xie, B., Li, J., Qiao, N., Hu, H., Khaitovich, P., Gao, Y., & Han, J.-D.-J. (2011). Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research, 39(4), 1408-1418. doi: 10.1093/nar/gkq956
Myles, S., Lea, R. A., Ohashi, J., Chambers, G. K., Weiss, J. G., Hardouin, E., Engelken, J., Macartney-Coxson, D. P., Eccles, D. A., Naka, I., Kimura, R., Inaoka, T., Matsumura, Y., & Stoneking, M. (2011). Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics, 12(1): 10, pp. 1-7. doi: 10.1186/1471-2350-12-10
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011). Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology, 7: 548. doi: 10.1038/msb.2011.81
Nasidze, I., & Stoneking, M. (2011). Microbiome diversity in human saliva. In F. J. d. Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 335-339). New York: Wiley.
Nasidze, I., Li, J., Schroeder, R., Creasey, J. L., Li, M., & Stoneking, M. (2011). High diversity of the saliva microbiome in Batwa pygmies. PLoS ONE, 6(8): e23352. doi: 10.1371/journal.pone.0023352
Niebuhr, O., Clayards, M., Meunier, C., & Lancia, L. (2011). On place assimilation in sibilant sequences: Comparing French and English. Journal of Phonetics, 39(3), 429-451. doi: 10.1016/j.wocn.2011.04.003
Oña, L., & Lachmann, M. (2011). Ant aggression and evolutionary stability in plant–ant and plant–pollinator mutualistic interactions. Journal of Evolutionary Biology, 24(3), 617-629. doi: 10.1111/j.1420-9101.2010.02200.x
Oota, H., & Stoneking, M. (2011). Effect of human migration on genome diversity in East Asia. In Y. Takezawa (Ed.), Racial representations in Asia (pp. 173-187). Kyoto: Kyoto Univ. Press.
Pugach, I., Matveyev, R., Wollstein, A., Kayser, M., & Stoneking, M. (2011). Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biology, 12(2): R19, pp. 1-18. doi: 10.1186/gb-2011-12-2-r19
Ranganathan, S., Schönbach, C., Kelso, J. F., Rost, B., Nathan, S., & Tan, T. W. (2011). Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinformatics, 12(Suppl. 13): S1. doi: 10.1186/1471-2105-12-S13-S1
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A.-M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S., & Stoneking, M. (2011). Denisova admixture and the first modern human dispersals into southeast Asia and Oceania. The American Journal of Human Genetics, 89(4), 516-528. doi: 10.1016/j.ajhg.2011.09.005
Reimers-Kipping, S., Hevers, W., Pääbo, S., & Enard, W. (2011). Humanized Foxp2 specifically affects cortico-basal ganglia circuits. Neuroscience, 175, 75-84. doi: 10.1016/j.neuroscience.2010.11.042
Reinartz, R., Lippold, S., Lieckfeldt, D., & Ludwig, A. (2011). Population genetic analyses of Acipenser ruthenus as a prerequisite for the conservation of the uppermost Danube population. Journal of Applied Ichthyology, 27(2), 477-483. doi: 10.1111/j.1439-0426.2011.01693.x
Schönbach, C., Tan, T. W., Kelso, J. F., Rost, B., Nathan, S., & Ranganathan, S. (2011). InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics, 12(Suppl. 3): S1. doi: 10.1186/1471-2164-12-S3-S1
Schönberg, A., Theunert, C., Li, M., Stoneking, M., & Nasidze, I. (2011). High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: High diversity and demographic inferences. European Journal of Human Genetics, 19(9), 988-994. doi: 10.1038/ejhg.2011.62
Somel, M., Liu, X., Tang, L., Yan, Z., Hu, H., Guo, S., Jiang, X., Zhang, X., Xu, G., Xie, G., Li, N., Hu, Y., Chen, W., Pääbo, S., & Khaitovich, P. (2011). MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates. PLoS Biology, 9(12): e1001214. doi: 10.1371/journal.pbio.1001214
Stewart, J. R., Aspinall, S., Beech, M., Fenberg, P., Hellyer, P., Larkin, N., Lokier, S. W., Marx, F. G., Meyer, M., Miller, R., Rainbow, P. S., Taylor, J. D., Whittaker, J. E., Al-Mehsin, K., & Strohmenger, C. J. (2011). Biotically constrained palaeoenvironmental conditions of a mid-Holocene intertidal lagoon on the southern shore of the Arabian Gulf: evidence associated with a whale skeleton at Musaffah, Abu Dhabi, UAE. Quaternary Science Reviews, 30(25-26), 3675-3690. doi: 10.1016/j.quascirev.2011.09.004
Stoneking, M., & Krause, J. (2011). Learning about human population history from ancient and modern genomes. Nature Reviews Genetics, 12(9), 603-614. doi: 10.1038/nrg3029
Thalmann, O., Wegmann, D., Spitzner, M., Arandjelovic, M., Guschanski, K., Leuenberger, C., Bergl, R. A., & Vigilant, L. (2011). Historical sampling reveals dramatic demographic changes in western gorilla populations. BMC Evolutionary Biology, 11: 85, pp. 1-10. doi: 10.1186/1471-2148-11-85
Viola, B., Markin, S. V., Zenin, A., Shunkov, V., & Derevianko, A. V. (2011). Late Pleistocene hominins from the Altai Mountains, Russia. In Verchnij paleolit v Afrike i Evrazii i formirovanie čeloveka sovremennogo anatomičeskogo tipa: meždunarodnyj simpozium "Osobennosti perechoda k verchnemu paleolitu v Evrazii: kulʹturnaja dinamika i razvitie roda Nomo" (Denisova peščera, Altaj, 4-10 ijulja 2011 g.) = The Upper paleolithic in Africa and Eurasia and the origin of anatomically modern Humans: International Symposium "Features of the Upper Paleolithic Transition in Eurasia: Cultural dynamics and the Evolution of the Genus Homo" (Denisova Cave, the Altai, 4-10 July, 2011) (pp. 207-213). Novosibirsk: Izdatelʹstvo Instituta archeologii i ėtnografii SO RAN.
Yan, Z., Hu, H. Y., Jiang, X., Maierhofer, V., Neb, E., He, L., Hu, Y., Hu, H., Li, N., Chen, W., & Khaitovich, P. (2011). Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Research, 39(15), 6596-6607. doi: 10.1093/nar/gkr298
Yuan, Y., Chen, Y.-P.-P., Ni, S., Xu, G. A., Tang, L., Vingron, M., Somel, M., & Khaitovich, P. (2011). Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics, 12: 347. doi: 10.1186/1471-2105-12-347