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Recent Department Publications

Last update: December 22nd, 2014

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2014

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
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
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
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2013

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
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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
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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
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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
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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
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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
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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

2012

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
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2011

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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
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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
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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
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Kircher, M. (2011). Understanding and improving high-throughput sequencing data production and analysis. PhD Thesis, Univ., Leipzig.
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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
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