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Department of Evolutionary Genetics

Publications

2014

Barbieri, C., T. Güldemann, C. Naumann, L. Gerlach, F. Berthold, H. Nakagawa, S.W. Mpoloka, M. Stoneking and B. Pakendorf: Unraveling the complex maternal history of Southern African Khoisan populations. Am. J. Phys. Anth. 153, 435-448 (2014).

Barbieri, C., M. Vicente, S. Oliveira, K. Bostoen, J. Rocha, M. Stoneking and B. Pakendorf: Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa. PLOS ONE 9:e99117 (2014).

Benazzi, S., M. Peresani, S. Talamo, Q. Fu, M.A. Mannino, M.P. Richards and J.-J. Hublin: A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy. Journal of Human Evolution 66, 89-94 (2014).

Brown, S., P.E. Savage, A.-M.-S. Ko, M. Stoneking, Y.-C. Ko, J.-H. Loo and J.A. Trejaut: Correlations in the population structure of music, genes and language. Proc. R. Soc. B 281: 20132072 (2014).

Cao, Q., X. Didelot, Z. Wu, Z. Li, L. He, Y. Li, M. Ni, Y. You, X. Lin, Z. Li, Y. Gong, M. Zheng, M. Zhang, J. Liu, W. Wang, X. Bo, D. Falush, S. Wang and J. Zhang: Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut, doi:10.1136/gutjnl-2014-307345 (2014).

Castellano, S., G. Parra, F.A. Sánchez-Quinto, F. Racimo, M. Kuhlwilm, M. Kircher, S. Sawyer, Q. Fu, A. Heinze, B. Nickel, J. Dabney, M. Siebauer, L. White, H.A. Burbano, G. Renaud, U. Stenzel, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P.Rudan, D. Brajković, Ž. Kucan, I. Gušic, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Meyer, J. Kelso, A. Andrés and S. Pääbo: Patterns of coding variation in the complete exomes of three Neandertals. PNAS 111, 6666-71 (2014).

Delfin, F.S., A.-M.-S. Ko, M. Li, E.D. Gunnarsdóttir, K.A. Tabbada, J.M. Salvador, G.C. Calacal, M.S. Sagum, F.A. Datar, S.G. Padilla, M.C.A.D. Ungria and M. Stoneking: 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: EJHG; the official journal of the European Society of Human Genetics 22, 228-37 (2014).

Duggan, A.T. and M. Stoneking: Recent developments in the genetic history of East Asia and Oceania. Current Opinion in Genetics & Development 29, 9-14 (2014).

Duggan, A.T., B. Evans, F.R. Friedlaender, J.S. Friedlaender, G. Koki, D.A. Merriwether, M. Kayser and M. Stoneking: Maternal history of Oceania from complete mtDNA genomes: Contrasting ancient diversity with recent homogenization due to the Austronesian expansion. American Journal of Human Genetics 94, 721-733 (2014).

Engelken, J., E. Carnero-Montoro, M. Pybus, G.K. Andrews, C. Lalueza-Fox, D. Comas, I. Sekler, M. de la Rasilla, A. Rosas, M. Stoneking, M.A. Valverde, R. Vicente and E. Bosch: Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PLoS Genetics 10(2): e1004128 (2014).

Fu, Q., H. Li, P. Moorjani, F. Jay, S. Slepchenko, A.A. Bondarev, P.L.F. Johnson, A. Aximu-Petri, K. Prüfer, C. de Filippo, M. Meyer, N. Zwyns, D.C. Salazar-Garcia, Y.V. Kuzmin, S.G. Keates, P.A. Kosintsev, D.I. Razhev, M.P. Richards, N.V. Peristov, M. Lachmann, K. Douka,

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T.F.G. Higham, M.. Slatkin, J.-J. Hublin, D. Reich, J. Kelso, T.B. Viola and S. Pääbo: Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445-449 (2014).

Gansauge, M.-T. and M. Meyer: Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research 24, 1543-49 (2014).

Genome of the Netherlands Consortium, The: Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics 46, 818-25 (2014).

Giuliani, C., C. Barbieri, M. Li, L. Bucci, D. Monti, G. Passarino, D. Luiselli, C. Franceschi, M. Stoneking and P. Garagnani: Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. Aging 6(5) (2014).

Gokhman, D., E. Lavi, K. Prüfer, M.F. Fraga, J.A. Riancho, J. Kelso, S. Pääbo, E. Meshorer and L. Carmel: Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344, 523-527 (2014).

He, Z., H. Bammann, D. Han, G. Xie and P. Khaitovich: Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA 20, 1103-11 (2014).

Hellenthal, G., G.B.J. Busby, G. Band, J.F. Wilson, C. Capelli, D. Falush and S. Myers: A genetic atlas of human admixture history. Science 343, 747-751 (2014).

Henne, K., J. Li, M. Stoneking. O. Kessler, H. Schilling, A. Sonanini, G. Conrads and H.-P. Horz: Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies. BMC Evolutionary Biology. In press (2014).

Heyn, P., M. Kircher, A. Dahl, J. Kelso, P. Tomancak, A.T. Kalinka and K.M. Neugebauer: The earliest transcribed zygotic genes are short, newly evolved and different across species. Cell Reports 6, 285-292 (2014).

Horn, S.: TERT-Promoter-Mutationen im familiären und sporadischen Melanom. Spitzenforschung in der Dermatologie – Innovationen und Auszeichnungen 2014, ISSN: 1861-4620, pp. 52-57 (2014).

Horn, S., S. Prost, M. Stiller, D. Makowiecki, T. Kuznetsova, N. Benecke, E. Pucher, A.K. Hufthammer, C. Schouwenburg, B. Shapiro and M. Hofreiter: Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Molecular Ecology 23, 1717-29 (2014).

Hu, H.Y., L. He and P. Khaitovich: Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes. BMC Genomics 15, 457 (2014).

Kelso, J. and K. Prüfer: Ancient humans and the origin of modern humans. Current Opinion in Genetics & Development 29, 133-138 (2014).

Key, F.M., J.C. Teixeira, C. de Filippo and A.M. Andrés:Advantageous diversity maintained by balancing selection in humans. Current Opinion in Genetics & Development 29, 45-51 (2014).

Key, F.M., B. Peter, M.Y. Dennis, E. Huerta-Sánchez, W. Tang, L. Prokunina-Olsson, R. Nielsen, A.M. Andrés: Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4). PLOS Genetics 10(10): e1004681 (2014).

Khrameeva, E.E., K.Bozek, L. He, Z. Yan, X. Jiang, Y. Wei, K. Tang, M.S. Gelfand, K. Prüfer, J. Kelso, S. Pääbo, P. Giavalisco, M. Lachmann and P. Khaitovich: Neanderthal ancestry

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drives evolution of lipid catabolism in contemporary Europeans. Nature Communications 5:3584, doi:10.1038/ncomms4584 (2014).

Ko, A.M.-C., C.-Y. Chen, Q. Fu, F. Delfin, M. Li, H.-L. Chiu, M. Stoneking and Y.-C. Ko: Early Austronesians: into and out of Taiwan. Am. J. Hum. Genet. 94, 426-36 (2014).

Lazaridis, I., N. Patterson, A. Mittnik, G. Renaud, S. Mallick, K. Kirsanow, P.H. Sudmant, J.G. Schraiber, S. Castellano, M. Lipson, B. Berger, C. Economou, R. Bollongino, Q. Fu, K. Bos, S. Nordenfelt, H. Li, C. de Filippo, K. Prüfer, S. Sawyer, C. Posth, W. Haak, F. Hallgren, E. Fornander, N. Rohland, D. Delsate, M. Francken, J.-M. Guinet, J. Wahl, G. Ayodo, H.A. Babiker, G. Baillet, E. Balanovska, O. Balanovsky, R. Barrantes, G. Bedoya, H. Ben-Ami, J. Bene, F. Berrada, C.M. Bravi, F. Brisighelli, G.B.J. Busby, F. Cali, M. Churnosov, D.E.C. Cole, D. Corach, L. Damba, G. van Driem, S. Dryomov, J.-M. Dugoujon, S.A. Fedorova, I. Gallego Romero, M. Gubina, M. Hammer, B. Henn, T. Helvig, U. Hodoglugil, A.R. Jha, S. Karachanak-Yankova, R. Khusainova, E. Khusnutdinova, R. Kittles, T. Kivisild, W. Klitz, V. Kučinskas, A. Kushniarevich, L. Laredj, S. Litvinov, T. Loukidis, R.W. Mahley, B. Melegh, E. Metspalu, J. Molina, J. Mountain, K. Näkkäläjärvi, D. Nesheva, T. Nyambo, L. Osipova, J. Parik, F. Platonov, O.L. Posukh, V. Romano, F. Rothhammer, I. Rudan, R. Ruizbakiev, H. Sahakyan, A. Sajantila, A. Salas, E.B. Starikovskaya, A. Tarekegn, D. Toncheva, S. Turdikulova, I. Uktveryte, O. Utevska, R. Vasquez, M. Villena, M. Voevoda, C. Winkler, L. Yepiskoposyan, P. Zalloua, T. Zemunik, A. Cooper, C. Capelli, M.G. Thomas, A. Ruiz-Linares, S.A. Tishkoff, L. Singh, K. Thangaraj, R. Villems, D. Comas, R. Sukernik, M. Metspalu, M. Meyer, E.E. Eichler, J. Burger, M. Slatkin, S. Pääbo, J. Kelso, D. Reich and J. Krause: Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-413 (2014).

Lee, C.-H., S.-L. Chiang, A.-M.-S. Ko, C.-H. Hua, M.-H. Tsai, S. Warnakulasuriya, S.O. Ibrahim, Sunarjo, R.B. Zain, T.-Y. Ling, C.-L. Huang, H.-Y. Lane, C.-C. Lin and Y.-C. Ko: Betel-quid dependence domains and syndrome associated with betel-quid ingredients among chewers: An Asian multi-country evidence. Addiction 109, 1194-1204 (2014).

Lindskog, C., M. Kuhlwilm, A. Davierwala, N. Fu, G. Hegde, M. Uhlén, S. Navani, S. Pääbo and F. Pontén: Analysis of candidate genes for lineage-specific expression changes in humans and primates. Journal of Proteome Reserarch 13, 3596-3606 (2014).

Lippold, S., H. Xu, A. Ko, M. Li, G. Renaud, A. Butthof, R. Schröder and M. Stoneking: Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investigative Genetics 5:13 (2014).

Macholdt, E., V. Lede, C. Barbieri, S.W. Mpoloka, H. Chen, M. Slatkin, B. Pakendorf and M. Stoneking: Tracing pastoralist migrations to southern Africa with lactase persistence alleles. Current Biology 24, 875-79 (2014).

Meyer, M., Q. Fu, A. Aximu-Petri, I. Glocke, B. Nickel, J.-L. Arsuaga, I. Martínez, A. Gracia, J.M. Bermúdez de Castro, E. Carbonell and S. Pääbo: A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403-406 (2014).

Nogueiro, I., J. Teixeira, A. Amorin, L. Gusmão, L. Alvarez: Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants. European Journal of Human Genetics, doi:10.1038/ejhg.2014.140 (2014).

O'Brien, J.D., X. Didelot, Z. Iqbal, L. Amenga-Etego, B. Ahiska and D. Falush: A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics 197, 925-37 (2014).

Oven, M.v., S. Brauer, Y. Choi, J. Ensing, W. Schiefenhövel, M. Stoneking and M. Kayser: Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the

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Massim of Papua New Guinea. European Journal of Human Genetics, doi: 10.1038/ejhg.2014.38 (2014).

Pääbo, S.: The human condition – a molecular approach. Cell 157, 216-226 (2014) (Review).

Pfefferle, D., A.J.N. Kazem, R.R. Brockhausen, A.V. Ruiz-Lambides and A. Widdig: Monkeys spontaneously discriminate their unfamiliar paternal kin under natural conditions using facial cues. Current Biology 24, 1806-10 (2014).

Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J.C. Mullikin, S.H. Vohr, R.E. Green, I. Hellmann, P.L.F. Johnson, H. Blanche, H. Cann, J.O. Kitzman, J. Shendure, E.E. Eichler, E.S. Lein, T.E. Bakken, L.V. Golovanova, V.B. Doronichev, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 43-49 (2014).

Pybus, M., G.M. Dall'Olio, P. Luisi, M. Uzkudun, A. Carreño-Torres, P. Pavlidis, H. Laayouni, J. Bertranpetit, J. Engelken: 1000 genomes selection browser 1.0: A genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Reserarch 42(D1), D903-D909 (2014).

Racimo, F., M. Kuhlwilm and M. Slatkin: A test for ancient selective sweeps and an application to candidate sites in modern humans. Molecular Biology & Evolution, doi: 10.1093/molbev/msu255 (2014).

Renaud, G., M.C. LaFave, J. Liang, T.G. Wolfsberg, S.M. Burgess: trieFinder: an efficient program for annotating digital gene expression (DGE) tags. BMC Bioinformatics, 15:329 (13 October 2014).

Renaud, G., U. Stenzel and J. Kelso: leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Research, doi: 10.1093/nar/gku699 (2014).

Romagné, F., D. Santesmasses, L. White, G.K. Sarangi, M. Mariotti, R. Hübler, A. Weihmann, G. Parra, V.N. Gladyshev, R. Guigo and S. Castellano: SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. Nucleic Acids Research 42, D437-D443 (2014).

Sankararaman, S., S. Mallick, M. Dannemann, K. Prüfer, J. Kelso, S. Pääbo, N. Patterson and D. Reich: The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354-357 (2014).

Schreiweis, C., U. Bornschein, E. Burguière, C. Kerimoglu, S. Schreiter, M. Dannemann, S. Goyal, E. Rea, C.A. French, R. Puliyadi, M. Groszer, S.E. Fisher, R. Mundry, C. Winter, W. Hevers, S. Pääbo, W. Enard and A.M. Graybiel: Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. PNAS 111, 14253-58 (2014).

Skoglund, P., B.H. Northoff, M.V. Shunkov, A.P. Derevianko, S. Pääbo, J. Krause and M. Jakobsson: Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. PNAS 111, 2229-34 (2014).

Stiller, M., M. Molak, S. Prost, G. Rabeder, G. Baryshnikov, W. Rosendahl, S. Münzel, H. Bocherens, A. Grandal-d'Anglade, B. Hilpert, M. Germonpré, O. Stasyk, R. Pinhasi, A. Tintori, N. Rohland, E. Mohandesan, S.Y. Ho, M. Hofreiter and M. Knapp: Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International 339-340, 224-231 (2014).

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The SIGMA Type 2 Diabetes Consortium: Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506, 97-101 (2014).

Tu, H.-P., A.-M.-S. Ko, S.-L. Chiang, S.-S. Lee, H.-M. Lai, C.-M. Chung, C.-M. Huang, C.-H. Lee, T.-M. Kuo, M.-J. Hsieh and Y.-C. Ko: Joint effects of alcohol consumption and ABCG2 Q141K on chronic tophaceous gout risk. Journal of Rheumatology 41, 749-758 (2014).

Weigert, A., C. Helm, M. Meyer, B. Nickel, D. Arendt, B. Hausdorf, S.R. Santos, K.M. Halanych, G. Purschke, C. Bleidorn and T.H. Struck: Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution 31, 1391-1401 (2014).

Wunderlich, S., M. Kircher, B. Vieth, A. Haase, S. Merkert, J. Beier, G. Göhring, S. Glage, A. Schambach, E.C. Curnow, S. Pääbo, U. Martin and W. Enard: Primate iPS cells as tools for evolutionary analyses. Stem cell research 12, 622-629 (2014).

Yahara, K., X. Didelot, M.A. Ansari, S.K. Sheppard and D. Falush: Efficient inference of recombination hot regions in bacterial genomes. Molecular Biology and Evolution 31, 1593-1605 (2014).

Zhao, G., S. Guo, M. Somel and P. Khaitovich: Evolution of human longevity uncoupled from caloric restriction mechanisms. PLoS One 9(1): e84117 (2014).

2013

Barbieri, C., M. Vicente, J. Rocha, S.W. Mpoloka, M. Stoneking and B. Pakendorf: Ancient substructure in early mtDNA lineages of Southern Africa. Am. J. Hum. Gen. 92, 285-292 (2013).

Barbieri, C., A. Butthoff, K. Bostoen and B. Pakendorf: Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia. EJHG 21, 430-436 (2013).

Brandariz-Fontes, C., J.A. Leonard, J. L. Vega-Pla, N. Backström, G. Lindgren, S. Lippold and C. Rico: Y-Chromosome Analysis in Retuertas Horses. PLoS One, 8(5): e64985 (2013).

Bruche, S., M. Gusset, S. Lippold, R. Barnett, K. Eulenberger, J. Junhold, C.A. Driscoll and M. Hofreiter: A genetically distinct lion (Panthera leo) population from Ethiopia. European Journal of Wildlife Research 59(2), 215-225 (2013).

Bryk, J., M. Somel, A. Lorenc and M. Teschke: Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus). Ecology and Evolution, 3(3), 558-568 (2013).

Dabney, J., M. Meyer and S. Pääbo: Ancient DNA damage. In: DNA repair, mutagenesis, and other responses to DNA damage. (Eds.) E.C. Friedberg et al. Cold Spring Harbor Perspectives in biology 5(7): a012567 (2013).

Dabney, J., M. Knapp, I. Glocke, M.-T. Gansauge, A. Weihmann, B. Nickel, C. Valdiosera, N. Garcia, S. Pääbo, J.-L. Arsuaga and M. Meyer: Complete mitochondrial genome sequence of a Middle Pleistocene cave bear recontructed from ultrashort DNA fragments. PNAS 110, 15758-63 (2013).

Donaldson-Matasci, M.C., C.T. Bergstrom and M. Lachmann: When unreliable cues are good enough. American Naturalist 182(3), 313-327 (2013).

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Duggan, A.T. and M. Stoneking: A highly unstable recent mutation in human mtDNA. The American Journal of Human Genetics 92, 279-284 (2013).

Ferreira, Z., S. Seixas, A.M. Andres, W.W. Kretzschmar, J.C. Mullikin, P.F. Cherukuri, P. Cruz, W.J. Swanson, NISC Comparative Sequencing Program, A.G. Clark, E.D. Green and B. Hurle: Reproduction and immunity-driven natural slection in the human WFDC locus. Molecular Biology and Evolution 30, 938-950 (2013).

Ferreira, Z., B. Hurle, A.M. Andrés, W.W. Kretzschmar, J.C. Mullikin, P.F. Cherukuri, P. Cruz, M.K. Gonder, A.C. Stone, S. Tishkoff, W.J. Swanson, NISC Comparative Sequencing Program, E.D. Green, A.G. Clark and S. Seixas: Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biology and Evolution 5(12), 2512-2523 (2013).

Fu, Qiaomei, M. Meyer, X. Gao, U. Stenzel, H.A. Burbano, J. Kelso and S. Pääbo: DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 110, 2223-27 (2013).

Fu, Q., A. Mittnik, P.L.F. Johnson, K. Bos, M. Lari, R. Bollongino, C. Sun, L. Giemsch, R. Schmitz, J. Burger, A.M. Ronchitelli, F. Martini, R.G. Cremonesi, J. Svoboda, P. Bauer, D. Caramelli, S. Castellano, D. Reich, S. Pääbo and J. Krause: A revised timescale for human evolution based on ancient mitochondrial genomes. Current Biology 23, 553-559 (2013).

Gansauge, M.-T. and M. Meyer: Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols 8(4), 737-748 (2013).

Good, J.M., V. Wiebe, F. Albert, H.A. Burbano, M. Kircher, R.E. Green, M. Halbwax, C. André, R. Atencia, A. Fischer and S. Pääbo: Comparative population genomics of the ejaculate in humans and the great apes. Molecular Biology and Evolution 30(4), 964-976 (2013).

Grossmann, T., A. Vaish, J. Franz, R. Schroeder, M. Stoneking and A.D. Friederici: Emotional voice processing: Investigating the role of genetic variation in the serotonin transporter across development. PLoS One 8(7): e68377 (2013).

Guschanski, K., J. Krause, S. Sawyer, L.M. Valente, S. Bailey, K. Finstermeier, R. Sabin, E. Gilissen, G. Sonet, Z.T. Nagy, G. Lenglet, F. Mayer and V. Savolainen: Next-generation museomics disentangles one of the largest primate radiations. Systematic Biology 62(4), 539-554 (2013).

Ka, S., E. Markljung, H. Ring, F.W. Albert, M. Harun-Or-Rashid, P. Wahlberg, P.M. Garcia-Roves, J.R. Zierath, D.M. Denbow, S. Pääbo, P.B. Siegel, L. Andersson and F. Hallbook: The 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 (2013).

Ko, A.-M.-S., H.-P. Tu, T.-T. Liu, J.-G. Chang, C.-Y. Yuo, S.-L. Chiang, S.-J. Chang, Y.-F. Liu, A.-M.-J. Ko, C.-H. Lee, C.-P. Lee, C.-M. Chang, S.-F. Tsai and Y.-C. Ko: ALPK1 genetic regulation and risk in relation to gout. International Journal of Epidemiology 42(2), 466-474 (2013).

Kuhlwilm, M., A. Davierwala and S. Pääbo: Identification of putative target genes of the transcription factor RUNX2. PLOS ONE 8(12) e83218 (2013).

Kunz, M., M. Dannemann and J. Kelso: High-throughput sequencing of the melanoma genome. Experimental Dermatology 22(1), 10-17 (2013).

Lachmann, M.: 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 (2013).

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Li, J., I. Nasidze, D. Quinque, M. Li, H.-P. Horz, C. Andre, R.M. Garriga, M. Halbwax, A. Fischer and M. Stoneking: The saliva microbiome of Pan and Homo. BMC Microbiology 13: 204 (2013).

Li, Z., H. Bammann, M. Li, H. Liang, Z. Yan, Y.-P.-P. Chen, M. Zhao and P. Khaitovich: Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains. RNA - A Publication of the RNA Society, 19(12), 1693-1702 (2013).

Maricic, T., V. Günther, O. Georgiev, S. Gehre, M. Ćurlin, C. Schreiweis, R. Naumann, H.A. Burbano, M. Meyer, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, S. Gajović, J. Kelso, W. Enard, W. Schaffner and S. Pääbo: A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Molecular Biology and Evolution 30(4), 844-852 (2013).

Mazin, P., J. Xio, X. Liu, Z. Yan, X. Zhang, M. Li, L. He, M. Somel, Y. Yuan, Y.-P.-P. Chen, N. Li, Y. Hu, N. Fu, Z. Ning, R. Zeng, H. Yang, W. Chen, M. Gelfand and P. Khaitovich: Widespread splicing changes in human brain development and aging. Molecular Systems Biology 9: 663 (2013).

Oña Bubach, L.: On the role of resonance in drug failure under HIV treatment interruption. Theoretical Biology & Medical Modelling, 10: 44(2013).

Pickrell, J.K., N. Patterson, P.-R. Loh, M. Lipson, B. Berger, M. Stoneking, B. Pakendorf and D. Reich: Ancient west Eurasian ancestry in southern and eastern Africa. PNAS 111, 2632-37 (2014).

Prado-Martinez, J., I. Hernando-Herraez, B. Lorente-Galdos, M. Dabad, O. Ramirez, C. Baeza-Delgado, C. Morcillo-Suarez, C. Alkan, F. Hormozdiari, E. Raineri, J. Estellé, M. Fernandez-Callejo, M. Valles, L. Ritscher, T. Schöneberg, E. de la Calle-Mustienes, S. Casillas, R. Rubio-Acero, M. Melé, J. Engelken, M. Caceres, J.L. Gomez-Skarmeta, M. Gut, J. Bertranpetit, I.G. Gut, T. Abello, E.E. Eichler, I. Mingarro, C. Lalueza-Fox, A. Navarro and T. Marques-Bonet: The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics 14: 363 (2013).

Prado-Martinez, J., P.H. Sudmant, J.M. Kidd, H. Li, J.L. Kelley, B. Lorente-Galdos, K.R. Veeramah, A.E. Woerner, T.D. O'Connor, G. Santpere, A. Cagan, C. Theunert, F. Casals, H. Laayouni, K. Munch, A. Hobolth, A.E. Halager, M. Malig, J. Hernandez-Rodriguez, I. Hernando-Herraez, K. Prüfer, M. Pybus, L. Johnstone, M. Lachmann, C. Alkan, D. Twigg, N. Petit, C. Baker, F. Hormozdiari, M. Fernandez-Callejo, M. Dabad, M.L. Wilson, L. Stevison, C. Camprubi, T. Carvalho, A. Ruiz-Herrera, L. Vives, M. Mele, T. Abello, I. Kondova, R.E. Bontrop, A. Pusey, F. Lankester, J.A. Kiyang, R.A. Bergl, E. Lonsdorf, S. Myers, M. Ventura, P. Gagneux, D. Comas, H. Siegismund, J. Blanc, L. Agueda-Calpena, M. Gut, L. Fulton, S.A. Tishkoff, J.C. Mullikin, R.K. Wilson, I.G. Gut, M.K. Gonder, O.A. Ryder, B.H. Hahn, A. Navarro, J.M. Akey, J. Bertranpetit, D. Reich, T. Mailund, M.H. Schierup, C. Hvilsom, A.M. Andrés, J.D. Wall, C.D. Bustamante, M.F. Hammer, E.E. Eichler and T. Marques-Bonet: Great ape genetic diversity and population history. Nature 499, 471-75 (2013).

Prüfer, K., K.E. Langergraber, S. Pääbo and L. Vigilant: Reply to Gibb et al.: Divergence times, generation lengths and mutation rates in great apes and humans. Letter. PNAS 110(8), e612 (2013).

Pugach, I., F.Delfin, E. Gunnarsdóttir, M. Kayser and M. Stoneking: Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 110, 1803-1808 (2013).

Pugach, I. and M. Stoneking: 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 (2013).

8

Renaud, G., M. Kircher, U. Stenzel and J. Kelso: freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics 29(9), 1208-1209 (2013).

Sheppard, S.K., X. Didelot, G. Meric, A. Torralbo, K.A. Jolley, D.J. Kelly, S.D. Bentley, M.C.J. Maiden, J. Parkhill and D. Falush: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. PNAS 110, 11923-27 (2013).

Somel, M., X. Liu and P. Khaitovich: Human brain evolution: transcripts, metabolites and their regulators. Nature Reviews Neuroscience 14(2), 112-127 (2013).

Stiller, M. and M. Hofreiter: An ancient DNA perspective on the cave bears from Peştera cu Oase, Romani. In: Life and death at the Peştera cu Oase: a setting for modern human emergence. (Eds.) E. Trinkaus, S. Constantin and J. Zilhão. Oxford University Press New York , pp. 159-167 (2013).

Stoneking, M. and K. Harvati: Early Old World migrations of Homo sapiens: human biology. In: The Encyclopedia of Global Human Migration. (Ed.) I. Ness. Blackwell Publishing Ltd., doi: 10.1002/9781444351071.wbeghm805 (2013).

Thalmann, O., B. Shapiro, P. Cui, V.J. Schuenemann, S.K. Sawyer, D.L. Greenfield, M.B. Germonpré, M.V. Sablin, F. López-Giráldez, X. Domingo-Roura, H. Napierala, H.-P. Uerpmann, D.M. Laponte, A.A. Acosta, L. Giemsch, R.W. Schmitz, B. Worthington, J.E. Buikstra, A. Druzhkova, A.S. Graphodatsky, N.D. Ovodov, N. Wahlberg, A.H. Freedman, R.M. Schweizer, K.-P. Koepfli, J.A. Leonard, M. Meyer, J. Krause, S. Pääbo, R.E. Green and R.K. Wayne: Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342, 871-874 (2013).

Viola, B. and S. Pääbo: What's new in Central Aisa? In: Basic Issues in archaeology, anthropology, and ethnography of Eurasia. Festschrift on the occasion of Anatoly Derevianko's 70th birthday. Institute of Archaeology and Ethnography SB RAS Press, Novosibirsk, pp.555-565 (2013).

Yahara, K., Y. Furuta, K. Oshima, M. Yoshida, T. Azuma, M. Hattori, I. Uchiyama and I. Kobayashi: Chromosome painting in silico in a bacterial species reveals fine population structure. Mol. Biol. Evol. 30, 1454-64 (2013).

2012

Albert, F.W. M. Somel, M. Carneiro, A. Aximu-Petri, M. Halbwax, O. Thalmann, J.A. Blanco-Aguiar, I.Z. Plyusnina, L. Trut, R. Villafuerte, N. Ferrand, S. Kaiser, P. Jensen and S. Pääbo: A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genetics 8(9), e1002962 (2012).

Ballantyne, K.N., M. van Oven, A. Ralf, M. Stoneking, R.J. Mitchell, R.A. van Oorschot and M. Kayser: MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci. Int. Genet. 6, 425-36 (2012).

Barbieri, C., M. Whitten, K. Beyer, H. Schreiber, M. Li and B. Pakendorf: Contrasting maternal and paternal histories in the linguistic context of Burkina Faso. Molecular Biololy & Evolution 29, 1213-23 (2012).

Burbano, H.A., R.E. Green, T. Maricic, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, J. Kelso, K.S. Pollard, M. Lachmann and S. Pääbo: Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS ONE 7(3) e32877 (2012).

9

Carneiro, M., F.W. Albert, J. Melo-Ferreira, N. Galtier, P. Gayral, J.A. Blanco-Aguiar, R. Villafuerte, M.W. Nachman and N. Ferrand: Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) Genome. Molecular Biology and Evolution 29(7), 1837-1849 (2012).

Carnero-Montoro, E., L. Bonet, J. Engelken, T. Bielig, M. Martínez-Florensa, F. Lozano and E. Bosch: Evolutionary and functional evidence for positive selection at the human CD5 immune receptor gene. Molecular Biology and Evolution 29(2), 811-823 (2012).

Clovis, Y.M., W. Enard, F. Marinaro, W.B. Huttner and De Pietri Tonelli, D.: Convergent repression of Foxp2 3'UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons. Development 139, 3332-42 (2012).

Dabney, J. and M. Meyer: Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques 52, 87-94 (2012).

Dannemann, M., B. Nickel, E. Lizano, H.A. Burbano and J. Kelso: Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics 13:116 (2012).

Dannemann, M., M. Lachmann, A. Lorenc: 'maskBAD' – a package to detect and remove Affymetrix probes with binding affinity differences. BMC Bioinformatics 13:56 (2012).

Dannemann, M., K. Prüfer, E. Lizano, B. Nickel, H.A. Burbano and J. Kelso: Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biology and Evolution 4(4): 552-564 (2012).

de Filippo C., K. Bostoen, M. Stoneking, B. Pakendorf: Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc. Biol. Sci. 279, 3256-63 (2012).

Delfin, F., S. Myles, Y. Choi, D. Hughes, R. Illek, M. van Oven, B. Pakendorf, M. Kayser and M. Stoneking: Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands. Molecular Biology & Evolution 29, 545-64 (2012).

Didelot, X., G. Méric, D. Falush and A.E. Darling: Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics 13, 256 (2012).

Enard, W.: Functional primate genomics – leveraging the medical potential. Journal of Molecular Medicine 90, 471-480 (2012).

Fietz, S.A., R. Lachmann, H. Brandl, M. Kircher, N. Samusik, R. Schröder, N. Lakshmanaperumal, I. Henry, J. Vogt, A. Riehn, W. Distler, R. Nitsch, W. Enard, S. Pääbo and W.B. Huttner: Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. PNAS 109, 11836-41 (2012).

Fu, Q., P. Rudan, S. Pääbo and J. Krause: Complete mitochondrial genomes reveal Neolithic expansion into Europe. PLoS ONE 7(3), e32473 (2012).

Gravlund, P., K. Aaris-Sørensen, M. Hofreiter, M. Meyer, J.P. Bollback and N. Noe-Nygaard: Ancient DNA extracted from Danish auroch (Bos primigenius): Genetic diversity and preservation. Annals of Anatomy 194, 103-111 (2012).

Gross, A., M. Hartung, K. Prufer, J. Kelso and E. Rahm: Impact of ontology evolution on functional analyses. Bioinformatics 28, 2671- 2677 (2012).

Han, Y., D. Han, Z. Yan, J.D. Boyd-Kirkup, C.D. Green, P. Khaitovich and J.-D.-J. Han: Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain. Aging Cell 11(6), 1055-1064 (2012).

10

Hartmann, S., C. Helm, B. Nickel, M. Meyer, T.H. Struck, R. Tiedemann, J. Selbig and C. Bleidorn: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS ONE 7, e29843 (2012).

Helm, C., S.H. Bernhart, C.H.z. Siederdissen, B. Nickel and C. Bleidorn: Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular Phylogenetics and Evolution 64(1), 198-203 (2012).

Hering, L, M.J. Henze, M. Kohler, A. Kelber, C. Bleidorn, M. Leschke, B. Nickel, M. Meyer, M. Kircher, P. Sunnucks and G. Mayer: Opsins in onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods. Mol. Biol. Evol. 29, 3451-8 (2012).

Hevers, W. und H. Lüddens: Pharmakologische und präklinische Grundlagen: Aminosäuren. In: Handbuch der Psychopharmakotherapie. (Eds.) G. Gründer and O. Benkert, Springer-Verlag Berlin Heidelberg, 169-184 (2012).

Hu, H.Y., L. He, K. Fominykh, Z. Yan, S. Guo, X. Zhang, M.S. Taylor, L. Tang, J. Li, J. Liu, W. Wang, H. Yu and P. Khaitovich: Evolution of the human-specific microRNA miR-941. Nature Communications 3, 1145 (2012).

Jinam, T., C. Hong, M. Phipps, M. Stoneking, M. Ameen, J. Edo, N. Saitou: Evolutionary history of continental South East Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Molecular Biology & Evolution 29, 3513-3527 (2012).

Kenny, E.E., N.J. Timpson, M. Sikora, M.C. Yee, A. Moreno-Estrada C., Eng, S. Huntsman, E.G: Burchard, M. Stoneking, C.D. Bustamante and S. Myles: Melanesian blond hair is caused by an amino acid change in TYRP1. Science 336, 554 (2012).

Khrameeva, E.E., A.A. Mironov, G.G. Fedonin, P. Khaitovich and M.S. Gelfand: Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One 7(4): e33947 (2012).

Kircher, M.: Analysis of high-throughput ancient DNA sequencing data. In: Ancient DNA: Methods and protocols, Methods in Molecular Biology, vol. 840, Springer Science+Business Media, (Eds.) B. Shapiro and M. Hofreiter, pp. 197-228 (2012).

Kircher, M., S. Sawyer, M. Meyer: Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40(1) e3 (2012).

Knapp, M., M. Stiller and M. Meyer: Generating barcoded libraries for multiplex high-throughput sequencing. In: Ancient DNA: Methods and protocols, Methods in Molecular Biology, vol. 840, Springer Science+Business Media, (Eds.) B. Shapiro and M. Hofreiter, pp. 155-170 (2012).

Langergraber, K.E., K. Prüfer, C. Rowney, C. Boesch, C. Crockford, K. Fawcett, E. Inoue, M. Inoue-Muruyama, J.C. Mitani, M.N. Muller, M.M. Robbins, G. Schubert, T. Stoinski, B. Viola, D. Watts, R.M. Wittig, R.W. Wrangham, K. Zuberbühler, S. Pääbo, and L. Vigilant: Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. PNAS 109, 15716-21 (2012).

Lawson, D.J., G. Hellenthal, S. Myers and D. Falush: Inference of population structure using dense haplotype data. PLoS Genetics 8(1), e1002453 (2012).

Lawson, D.J. and D. Falush: Population identification using genetic data. Annual Review of Genomics and Human Genetics 13, 337-361 (2012).

Lee, C.-H., A.-M.-S. Ko, C.-F. Yen, K.-S. Chu, Y.-J. Gao, S. Warnakulasuriya, Sunarjo, S.O.

11

Ibrahim, R.B. Zain, W.K. Patrick and Y.-C. Ko: Betel-quid dependence and oral potentially malignant disorders in six Asian countries. British Journal of Psychiatry 201(5), 383-391 (2012).

Li, J., V. Menard, R.L. Benish, R.J. Jurevic, C. Guillemette, M. Stoneking, P.A. Zimmerman and R.K. Mehlotra: Worldwide variation in human drug-metabolism enzyme genes CYP2B6 and UGT2B7: implications for HIV/AIDS treatment. Pharmacogenomics 13, 555-570 (2012).

Li, M., R. Schroeder, A. Ko and M. Stoneking: Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Research 40, e137 (2012).

Li, M. and M. Stoneking: A new approach for detecting low-level mutations in next-generation sequence data. Genome Biology 13:R34 (2012).

Liu, X., M. Sohmel, L. Tang, Z. Yan, X. Jiang, S. Guo, Y. Yuan, L. He, A. Oleksiak, Y. Zhang, N. Li, Y. Hu, W. Chen, Z. Qiu, S. Pääbo and P. Khaitovich: Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Research 22, 611-622 (2012).

Mailund, T., A.E. Halager, M. Westergaard, J.Y. Dutheil, K. Munch, L.N. Andersen, G. Lunter, K. Pruefer, A. Scally, A. Hobolth and M.H. Schierup: 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 (2012).

Meyer, M., M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, P.H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R.E. Green, K. Bryc, A.W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M.F. Hammer, M.V. Shunkov, A.P. Derevianko, N. Patterson, A.M. Andrés, E.E. Eichler, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222-226 (2012).

Pickrell, J.K., N. Patterson, C. Barbieri, F. Berthold, L. Gerlach, T. Güldemann, B. Kure, S.W. Mpoloka, H. Nakagawa, C. Naumann, M. Lipson, P.-R. Loh, J. Lachance, J. Mountain, C. Bustamante, B. Berger, S. Tishkoff, B. Henn, M. Stoneking, D. Reich and B. Pakendorf: The genetic prehistory of southern Africa. Nature Communications 3, 1143 (2012).

Prüfer, K., K. Munch, I. Hellmann, K. Akagi, J.R. Miller, B. Walenz, S. Koren, G. Sutton, C. Kodira, R. Winer, J.R. Knight, J.C. Mullikin, S.J. Meader, C.P. Ponting, G. Lunter, S. Higashino, A. Hobolth, J. Dutheil, E. Karakoҫ, C. Alkan, S. Sajjadian, C.R. Catacchio, M. Ventura, T. Marques-Bonet, E.E. Eichler, C. André, R. Atencia, L. Mugisha, J. Junhold, N. Patterson, M. Siebauer, J.M. Good, A. Fischer, S.E. Ptak, M. Lachmann, D.E. Symer, T. Mailund, M.H. Schierup, A.M. Andrés, J. Kelso and S. Pääbo: The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527-531 (2012).

Quillen E.E., M. Bauchet, A.W. Bigham, M.E. Delgado-Burbano, F.X. Faust, Y.C. Klimentidis, X. Mao, M. Stoneking and M.D. Shriver: OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. Hum. Genet. 131, 1073-80 (2012).

Ratikainen, I.I., L.R.H. Sødal, A.J.N. Kazem and J. Wright: Private and public information use strategies by foraging groups of wild Siberian jays. Animal Behaviour 83(5), 1243-1251 (2012).

Rost, B., T. Gaasterland, T. Lengauer, M. Linial, S. Markel, B.M. McKay, R. Schneider, P. Horton and J.F. Kelso: Paving the future: finding suitable ISMB venues. Bioinformatics 28(19), 2556-2559 (2012).

12

Sankararaman, S., N. Patterson, H. Li, S. Pääbo and D. Reich: The date of interbreeding between Neandertals and modern humans. PLoS Genetics 8(10): e1002947 (2012).

Sawyer, S., J. Krause, K. Guschanski, V. Savolainen and S. Pääbo: Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7(3) e34131 (2012).

Schmidt, M., S. Horn, K. Flieger, K. Ehlers, C. Wilhelm and R. Schnetter: 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 (2012).

Stoneking, M.: Genetic evidence concerning the origins and dispersals of modern humans. In: Causes and consequences of human migration. (Eds.) M.H. Crawford and B.C. Campbell, Cambridge University Press, pp. 11-20 (2012).

Theunert C., K. Tang, M. Lachmann, S. Hu and M. Stoneking: Inferring the history of population size change from genome-wide SNP data. Mol. Biol. Evol. 29, 3653-3667 (2012).

Weng, K., H. Hu, A.G. Xu, P. Khaitovich and M. Somel: 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 (2012).

White, L. and S. Castellano: Evolutionary basis for the use of selenocysteine. (Invited book chapter). In: Selenium: Its molecular biology and role in human health. (Eds.) D.L. Hatfield et al., Springer Science+Business Media, LLC, doi: 10.1007/978-1-4614-1025-6_7, 85-93 (2012).

Xu, S., I. Pugach, M. Stoneking, M. Kayser, L. Jin and The HUGO Pan-Asian SNP Consortium: Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. PNAS 109, 4574-79 (2012).

Xu, S. and M. Stoneking: Reply to Denham and Donohue: Asian-Papuan genetic admixture is in excellent agreement with Austronesian dispersal in eastern Indonesia. PNAS 109(39): E2578 (2012).

Yuan, Y., Y.-P.-P. Chen, J. Boyd-Kirkup, P. Khaitovich and M. Somel: Accelerated aging-related transcriptome changes in the female prefrontal cortex. Aging Cell 11(5), 894-901 (2012).

2011

Abramson, G., C.A. Trejo Soto, L. Oña: 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 (2011).

Albert, F.W., E. Hodges, J.D. Jensen, F. Besnier, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, J.M. Good, R.E. Green, H. Burbano, I.Z. Plyusnina, L. Trut, L. Andersson, T. Schöneberg, Ö. Carlborg, G.J. Hannon and S. Pääbo: Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity 107, 205-214 (2011).

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Andrés, A.M.: Balancing selection in the human genome (Advanced article). In: Encyclopedia of Life Sciences, John Wiley & Sons, Ltd., Chichester. http://www.els.net, doi: 10.1002/9780470015902.a0022863 (2011).

Benazzi, S., B. Viola, O. Kullmer, L. Fiorenza, K. Harvati, T. Paul, G. Gruppioni, G.W. Weber and F. Mallegni:A reassessment of the Neanderthal teeth from Taddeo cave (southern Italy). Journal of Human Evolution 61, 377-387 (2011).

Bocherens H., M. Stiller, K.A. Hobson, M. Pacher, G. Rabeder, J.A. Burns, T. Tütken and M. Hofreiter: Niche partitioning between two sympatric genetically distinct cave bears (Ursus spelaeus and Ursus ingressus) and brown bear (Ursus arctos) from Austria: Isotopic evidence from fossil bones. Quaternary International 245, 238-248 (2011).

Bos, K.I., V.J. Schuenemann, G.B. Golding, H.A. Burbano, N. Waglechner, B.K. Coombes, J.B. McPhee, S.N. DeWitte, M. Meyer, S. Schmedes, J. Wood, D.J.D. Earn, D.A. Herring, P. Bauer, H.N. Poinar and J. Krause: A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510 (2011).

Brawand, D., M. Soumillon, A. Necsulea, P. Julien, G. Csárdi, P. Harrigan, M. Weier, A. Liechti, A. Aximu-Petri, M. Kircher, F.W. Albert, U. Zeller, P. Khaitovich, F. Grützner, S. Bergmann, R. Nielsen, S. Pääbo and H. Kaessmann: The evolution of gene expression levels in mammalian organs. Nature 478, 343-348 (2011).

de Filippo, C., C. Barbieri, M. Whitten, S.W. Mpoloka, E.D. Gunnarsdottir, K. Bostoen, T. Nyambe, K. Beyer, H. Schreiber, P. de Knijff, D. Luiselli, M. Stoneking and B. Pakendorf: Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups. Molecular Biology and Evolution 28, 1255-1269 (2011).

Delfin, F., J.M. Salvador, G.C. Calacal, H.B. Perdigon, K.A. Tabbada, L.P. Villamor, S.C. Halos, El Gunnarsdóttir, S. Myles, D.A. Hughes, S. Xu, L. Jin, O. Lao, M. Kayser, M.E. Hurles, M. Stoneking and M.C.A. De Ungria: 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, 224-230 (2011).

Didelot, X., R. Bowden, T. Street, T. Golubchik, C. Spencer, G. McVean, V. Sangal, M.F. Anjum, M. Achtman, D. Falush and P. Donnelly: Recombination and population structure in Salmonella enterica. PLoS Genetics 7(7), e1002191 (2011).

Enard, W.: FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution. Current Opinion in Neurobiology 21, 415-424 (2011).

Fiorenza, L, S. Benazzi, B. Viola, O. Kullmer and F. Schrenk: Relationship between cusp size and occlusal wear pattern in Neanderthal and Homo sapiens first maxillary molars. The Anatomical Record 294, 453-461 (2011).

Fischer, A., K. Prüfer, J.M. Good, M. Halbwax, V. Wiebe, C. André, R. Atencia, L. Mugisha, S.E. Ptak and S. Pääbo: Bonobos fall within the genomic variation of chimpanzees. PLoS ONE 6(6), e21605 (2011).

Fu, X., P. Giavalisco, X. Liu, G. Catchpole, N. Fu, Z.B. Ning, S. Guo, Z. Yan, M. Somel, S. Pääbo, R. Zeng, L. Willmitzer and P. Khaitovich: Rapid metabolic evolution in human prefrontal cortex. Proc. Natl. Acad. Sci. USA 108, 6181-86 (2011).

Gaudet, P, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T.K. Attwood, A. Bateman, J.A. Blake, C.J. Bult, J.M. Cherry, R.L. Chisholm, G. Cochrane, C.E. Cook, J.T. Eppig, M.Y. Galperin, R. Gentleman, C.A. Goble, T. Gojobori, J.M. Hancock, D.G. Howe, T. Imanishi, J. Kelso, D. Landsman, S.E. Lewis, I.K. Mizrachi, S. Orchard, B.F. Ouellette, S. Ranganathan, L. Richardson, P. Rocca-Serra, P.N. Schofield, D. Smedley, C. Southan, T.W. Tan, T.

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Tatusova, P.L. Whetzel, O. White, C. Yamasaki, BioDBCore Working Group: Towards BioDBcore: a community-definded information specification for biological databases. Database baq027, doi:10.1093/database/baq027 (2011).

Gaudet, P, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T.K. Attwood, A. Bateman, J.A. Blake, C.J. Bult, J.M. Cherry, R.L. Chisholm, G. Cochrane, C.E. Cook, J.T. Eppig, M.Y. Galperin, R. Gentleman, C.A. Goble, T. Gojobori, J.M. Hancock, D.G. Howe, T. Imanishi, J. Kelso, D. Landsman, S.E. Lewis, I.K. Mizrachi, S. Orchard, B.F. Ouellette, S. Ranganathan, L. Richardson, P. Rocca-Serra, P.N. Schofield, D. Smedley, C. Southan, T.W. Tan, T. Tatusova, P.L. Whetzel, O. White, C. Yamasaki, BioDBCore Working Group: Towards BioDBcore: a community-definded information specification for biological databases. Nucleic Acids Research 39, D7-D10, doi:10.1093/nar/gkq1173 (2011).

Gralle, M. and S. Pääbo: A comprehensive functional analysis of ancestral human signal peptides. Molecular Biology and Evolution 28, 25-28 (2011).

Gross, A., A. Tönjes, P. Kovacs, K.R. Veeramah, P. Ahnert, N.R. Roshyara, C. Gieger, I. Rueckert, M. Loeffler, M. Stoneking, H. Wichmann, J. Novembre, M. Stumvoll and M. Scholz: Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genetics 12:67 (2011).

Grossman, T., M.H. Johnson, A. Vaish, D.A. Hughes, D. Quinque, M. Stoneking and A.D. Friederici: Genetic and neural dissociation of individual responses to emotional expressions in human infants. Developmental Cognitive Neuroscience 1, 57-66 (2011).

Gunnarsdóttir, E.D., M. Li, M. Bauchet, K. Finstermeier and M. Stoneking. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Research 21, 1-11 (2011).

Gunnarsdóttir, E.D., M.R. Nandineni, M. Li, S. Myles, D. Gil, B. Pakendorf and M. Stoneking: Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications 2:228 (2011).

Herre, H., R. Hoehndorf, J. Kelso, F. Loebe and S. Schulz: OBML – Ontologies in biomedicine and life sciences. Journal of Biokmedical Semantics 2 (Suppl 4):I1 (2011).

Hu, H.Y., S. Guo, J. Xi, Z. Yan, N. Fu, X. Zhang, C. Menzel, H. Liang, H. Yang, M. Zhao, R. Zeng, W. Chen, S. Pääbo and P. Khaitovich: MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics 7(10):e1002327 (2011).

Jin, C., J. Li, C.D. Green, X. Yu, X. Tang, D. Han, B. Xian, D. Wang, X. Huang, X. Cao, Z. Yan, L. Hou, J. Liu, N. Shukeir, P. Khaitovich, C.D. Chen, H. Zhang, T. Jenuwein and J.-D.-J. Han: Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway. Cell Metabolism 14(2), 161-172 (2011).

Jordan, S., J. Krause, A. Prager, M. Mitrovic, S. Jonjic, U.H. Koszinowski and B. Adler: 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 (2011).

Ka, S., F.W. Albert, D.M. Denbow, S. Pääbo, P.B. Siegel, L. Andersson and F. Hallböök: 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, 211-21 (2011).

Kircher, M., P. Heyn and J. Kelso: Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12:382 (2011).

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Lerner, H.R.L., M. Meyer, H.F. James, M. Hofreiter and R.C. Fleischer: Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeydreepers. Current Biology 8, 1838-44 (2011).

Li, J., L. Zhang, H. Zhou, M. Stoneking and K. Tang: Global patterns of genetic diversity and signals of natural selection for human drug metabolizing enzyme and transporter genes. Human Molecular Genetics 20, 528-540 (2011).

Li, M. and S. Chen: The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology 11:3 (2011).

Liebscher, I., U. Müller, D. Teupser, E. Engemaier, K.M.Y. Engel, L. Ritscher, D. Thor, K. Sangkuhl, A. Ricken, A. Wurm, D. Piehler, S. Schmutzler, H. Fuhrmann, F.W. Albert, A. Reichenbach, J. Thiery, T. Schöneberg and A. Schulz: Altered immune response in mice deficient for the G protein-coupled receptor GPR34. Journal of Biological Chemistry 286, 2101-10 (2011).

Lippold, S., M. Knapp, T. Kuznetsova, J.A. Leonard, N. Benecke, A. Ludwig, M. Rasmussen, A. Cooper, J. Weinstock, E. Willerslev, B. Shapiro and M. Hofreiter: Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications 2, 450 (2011).

Lippold, S., N.J. Matzke, M. Reissmann and M. Hofreiter. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology 11:328 (2011).

Liu, Y., D. Han, Y. Han, Z. Yan, B. Xie, J. Li, N. Qiao, H. Hu, P. Khaitovich, Y. Gao and J.-D.-J. Han: 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 (2011).

Münzel, S.C., M. Stiller, M. Hofreiter, A. Mittnik, N.J. Conard and H. Bocherens: Pleistocene bears in the Swabian Jura (Germany): Genetic replacement, ecological displacement, extinctions and survival. Quaternary International 245, 225-237 (2011).

Myles, S., R.A. Lea, J. Ohashi, G.K. Chambers, J.G. Weiss, E. Hardouin, J. Engelken, D.P. Macartney-Coxson, D.A. Eccles, I. Naka, R. Kimura, T.A.Inaoka, Y. Matsumura and M. Stoneking: Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics 12:10 (2011).

Nagaraj, N., J.R. Wisniewski, T. Geiger, J. Cox, M. Kircher, J. Kelso, S. Pääbo and M. Mann: Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology 7, 548, doi:10.1038/msb.2011.81 (2011).

Nasidze, I. and M. Stoneking: Microbiome diversity in human saliva. Chapter 33 in: F.J. de Bruijn (Ed.): Handbook of molecular microbial ecology, Volume II. John Wiley & Sons, Inc., 335-339 (2011).

Nasidze, I., J. Li, R. Schroeder, J.L. Creasey, M. Li and M. Stoneking: High diversity of the saliva microbiome in Batwa Pygmies. PLoS ONE 6(8) e23352 (2011).

Oña, L. and M. Lachmann: Ant aggression and evolutionary stability in plant-ant and plant-pollinator mutualistic interactions. Journal of Evolutonary Biology 24, 617-629 (2011).

Oota, H. and M. Stoneking: Effects of human migration on genome diversity in East Asia. In: Racial Representations in Asia, T. Yasuko (ed.), Kyoto University Press, Kyoto, pp. 173-187 (2011).

Pugach, I., R. Matveyev, A. Wollstein, M. Kayser and M. Stoneking: Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biology 12, R19

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(2011).

Rabeder, G., M. Hofreiter and M. Stiller: Chronological and systematic position of cave bear fauna from Ajdovska jama near Krško (Slovenia). In: Ajdovska jama: Palaeontology, zoology and archaeology of Ajdovska jama near Krsko in Slovenia. (Eds.) M. Pacher, V. Pohar and G. Rabeder. Verlag der österreichischen Akademie der Wissenschaften Wien, pp. 79-86 (2011).

Ranganathan, S., C. Schönbach, J. Kelso, B. Rost, S. Nathan and T.W. Tan: 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 (2011).

Reich, D., N. Patterson, M. Kircher, F. Delfin, M.R. Nandineni, I. Pugach, A.M. Ko, Y. Ko, T.A. Jinam, M.E. Phipps, N. Saitou, A. Wollstein, M. Kayser, S. Pääbo and M. Stoneking: Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics 89, 516-528 (2011).

Reimers-Kipping, S., W. Hevers, S. Pääbo, W. Enard: Humanized Foxp2 specifically affects cortico-basal ganglia circuits. Neuroscience 175, 75-84 (2011).

Schönbach, C., T.W. Tan, J. Kelso, B. Rost, S. Nathan and S. Ranganathan: InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics 12 (Suppl 3):S1 (2011).

Schönberg, A., C. Theunert, M. Li, M. Stoneking and I. Nasidze: 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, 988-994 (2011).

Somel, M., X. Liu, L. Tang, Z. Yan, H. Hu, S. Guo, X. Jiang, X. Zhang, G. Xu, G. Xie, N. Li, Y. Hu, W. Chen, S. Pääbo and P. Khaitovich: MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol. 9(12): e1001214 (2011).

Stewart, J.R., S. Aspinall, M. Beech, P. Fenberg, P. Hellyer, N. Larkin, S.W. Lokier, F.G. Marx, M. Meyer, R. Miller, P.S. Rainbow, J.D. Taylor, J.E. Whittaker, K. Al-Mehsin, C.J. Strohmenger: 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, 3675-90 (2011).

Stoneking, M. and J. Krause: Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 12, 603-614 (2011).

Viola, B., S.V. Markin, A. Zeuin, M.V. Shunkov and A.P. Derevianko: Late Pleistocene hominins from the Altai mountains, Russia. In: Characteristic features of the Middle to Upper Paleolithic transition in Eurasia. (Eds.) A.P. Derevianko and M.V. Shunkov. Institute of Archaeology and Ethnography SB RAS Press, Novosibirsk, pp. 207-213 (2011).

Yan, Z., H.Y. Hu, X. Jiang, V. Maierhofer, E. Neb, L. He, Y. Hu, H. Hu, N. Li, W. Chen and P. Khaitovich: Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Research 39(15), 6596-6607 (2011).

Yuan, Y., Y.-P.-P. Chen, S. Ni, G.A. Xu, L. Tang, M. Vingron, M. Somel and P. Khaitovich: Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics 12: 347 (2011).

2010

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Addis, L., A.D. Friederici, S.A. Kotz, B. Sabisch, J. Barry, N. Richter, A.A. Ludwig, R. Rübsamen, F.W. Albert, S. Pääbo, D.F. Newbury and A.P. Monaco: A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3. Genes, Brain and Behavior 9, 545-61 (2010).

Athanasiadis, G., E. Esteban, M. Gaya-Vidal, J.M. Dugoujon, N. Moschonas, H. Chaabani, N. Bissar-Tadmouri, N. Harich, M. Stoneking and P. Moral: Different evolutionary histories of coagulation factor VII gene in human populations? Annals of Human Genetics 74, 34-45 (2010).

Athanasiadis, G., E. Gonzalez-Perez, E. Esteban, J.M. Dugoujon, M. Stoneking and P. Moral: The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions. BMC Evolutionary Biology 10, 84 (2010).

Briggs, A.W., U. Stenzel, M. Meyer, J. Krause, M. Kircher and S. Pääbo: Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Research 38 (6), e87 (2010).

Burbano, H.A., E. Hodges, R.E. Green, A.W. Briggs, J. Krause, M. Meyer, J.M. Good, T. Maricic, P.L.F. Johnson, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, F.W. Albert, M. de la Rasilla, J. Fortea, A. Rosas, M. Lachmann, G.J. Hannon and S. Pääbo: Targeted investigaton of the Neandertal genome by array-based sequence capture. Science 328, 723-725 (2010).

de Filippo, C., P. Heyn, L. Barham, M. Stoneking and B. Pakendorf: Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia. American Journal of Physical Anthropology 141, 382-394 (2010).

Donaldson-Matasci, M.C., C.T. Bergstrom and M. Lachmann: The fitness value of information. Oikos 119, 219-230 (2010).

Giger, T., P. Khaitovich, M. Somel, A. Lorenc, E. Lizano, L. Harris, M. Ryan, M. Lan, M. Wayland, S. Bahn and S. Pääbo: Evolution of neuronal and endothelial transcriptomes in primates. Genome Biology and Evolution 2, 284-292 (2010).

Good, J.M., T. Giger, M.D. Dean, and M.W. Nachman: Widespread over-expression of the X chromosome in sterile F1 hybrid mice. PLoS Genetics 6, e1001148 (2010).

Gralle, M., I. Schäfer, P. Seibel and S. Pääbo: A functional test of Neandertal and modern human mitochondrial targeting sequences. Biochem. Biophys. Res. Comm. 402, 747-749 (2010).

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H.-Y. Fritz, N.F. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, K. Prüfer, M. Meyer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Höber, B. Höffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, C. Verna, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R.W. Schmitz, P.L.F. Johnson, E.E. Eichler, D. Falush, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich and S. Pääbo: A draft sequence of the Neandertal genome. Science 328, 710-722 (2010).

Heyn, P., U. Stenzel, A.W. Briggs, M. Kircher, M. Hofreiter and M. Meyer: Road blocks on paleogenomes – polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Research 38, e161, doi:10.1093/nar/gkq572 (2010).

Hoehndorf, R., A.-C. Ngonga Ngomo and J. Kelso: Applying the functional abnormality ontology pattern to anatomical functions. Journal of Biomedical Semantics, 1:4 (2010).

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Hoehndorf, R., A.-C. Ngonga Ngomo, M. Dannemann and J. Kelso: Statistical tests for associations between two directed acyclic graphs. PLoS ONE 5 (6), e10996 (2010).

Hoehndorf, R., A. Oellrich, M. Dumontier, J. Kelso, D. Rebholz-Schuhmann and H. Herre: Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics 11, 441 (2010).

Kelso, J., R. Hoehndorf and K. Prüfer: Ontologies in biology. In: Theory and Applications of Ontologies. Second Volume. Ontology: The Information-science Stance. (Eds) M. Healey, A. Kameas and R. Poli, Springer-Verlag, 347-371 (2010).

Kircher, M. and J. Kelso: High-throughput DNA sequencing – concepts and limitations. Bioessays 32, 524-536 (2010).

Krause, J., A.W. Briggs, M. Kircher, T. Maricic, N. Zwyns, A. Derevianko and S. Pääbo: A complete mtDNA genome of an early modern human from Kostenki, Russia. Current Biology 20, 231-236 (2010).

Krause, J., Q. Fu, J.M. Good, B. Viola, M.V. Shunkov, A.P. Derevianko and S. Pääbo: The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894-897 (2010).

Li, M., A. Schönberg, M. Schaefer, R. Schroeder, I. Nasidze and M. Stoneking: Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. The American Journal of Human Genetics 87, 237-249 (2010).

Maricic, T., M. Whitten and S. Pääbo: Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5 (11), e14004 (2010).

Meyer, M., and M. Kircher: Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols doi:10.1101/pdb.prot5448 (2010).

Prüfer, K., U. Stenzel, M. Hofreiter, S. Pääbo, J. Kelso, R.E. Green: Computational challenges in the analysis of ancient DNA. Genome Biology 11, R47 (2010).

Pulvers, J.N., J. Bryk, J.L. Fish, M. Wilsch-Bräuninger, Y. Arai, D. Schreier, R. Naumann, J. Helppi, B. Habermann, J. Vogt, R. Nitsch, A. Tóth, W. Enard, S. Pääbo and W.B. Huttner: Mutations in mouse Aspm (abnormal spindle-like microcephaly associated) cause not only microcephaly but also major defects in the germline. PNAS 107, 16595-16600 (2010).

Reich, D., R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L.F. Johnson, T. Maricic, J.M. Good, T. Marques-Bonet, C. Alkan, Q. Fu, S. Mallick, H. Li, M. Meyer, E.E. Eichler, M. Stoneking, M. Richards, S. Talamo, M.V. Shunkov, A.P. Derevianko, J.-J. Hublin, J. Kelso, M. Slatkin and S. Pääbo: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053-60 (2010).

Somel, M., S. Guo, N. Fu, Z. Yan, H.Y. Hu, Y. Xu, Y. Yuan, Z. Ning, Y. Hu, C. Menzel, H. Hu, M. Lachmann, R. Zeng, W. Chen and P. Khaitovich: MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Research 20, 1207-1218 (2010).

Stäubert, C., I. Böselt, J. Bohnekamp, H. Römpler, W. Enard, and T. Schöneberg: Structural and functional evolution of the trace amine-associated receptors TAAR3, TAAR4 and TAAR5 in primates. PLoS One 5 (6), e11133 (2010).

Stoneking, M. and F. Delfin: The human genetic history of East Asia: Weaving a complex Tapestry. Current Biology 20, R188-193 (2010).

Wollstein, A., O. Lao, C. Becker, S. Brauer, R.J. Trent, P. Nürnberg, M. Stoneking and M.

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Kayser: Demographic history of Oceania inferred from genome-wide data. Current Biology 20, 1983-1992 (2010).

Xu, A.G., L. He, Z. Li, Y. Xu, M. Li, X. Fu, Z. Yan, Y. Yuan, C. Menzel, N. Li, M. Somel, H. Hu, W. Chen, S. Pääbo and P. Khaitovich: Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-seq. PLoS Computational Biology 6, e1000843 (2010).

2009

Albert, F.W., Ö. Carlborg, I. Plyusnina, F. Besnier, D. Hedwig, S. Lautenschläger, D. Lorenz, J. McIntosh, C. Neumann, H. Richter, C. Zeising, R. Kozhemyakina, O. Shchepina, J. Kratzsch, L. Trut, D. Teupser, J. Thiery, T. Schöneberg, L. Andersson and S. Pääbo: Genetic architecture of tameness in a rat model of animal domestication. Genetics 182, 541-554 (2009).

Balaresque, P., E.J. Parkin, L. Roewer, D.R. Carvalho-Silva, R.J. Mitchell, R.A.H. van Oorschot, J. Henke, M. Stoneking, I. Nasidze, J. Wetton, P. de Knijff, C. Tyler- Smith and M.A. Jobling: Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications. International Journal of Legal Medicine 123, 15-23 (2009).

Briggs, A., J.M. Good, R.E. Green, J. Krause, T. Maricic, U. Stenzel, C. Lalueza-Fox, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, R. Schmitz, V.B. Doronichev, L.V.Golovanova, M. de la Rasilla, J. Fortea, A. Rosas and S. Pääbo: Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325, 318-321 (2009).

Briggs, A.W., J.M. Good R.E., Green, J. Krause, T. Maricic, U. Stenzel and S. Pääbo: Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources. JoVE. 31. http://www.jove.com/index/details.stp?id=1573, doi: 10.3791/1573 (2009).

Dannemann, M., A. Lorenc, I. Hellmann, P. Khaitovich and M. Lachmann: The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 25, 2772-79 (2009).

Enard, W.: The phenotype in high dimensions. Book review: Evolutionary Genomics and Proteomics by M. Pagel and A. Pomiankowski. Trends in Ecology and Evolution 24, 70-71 (2009).

Enard, W., S. Gehre, K. Hammerschmidt, S.M. Hölter, T. Blass, M. Somel, M.K. Brückner, C. Schreiweis, C. Winter, R. Sohr, L. Becker, V. Wiebe, B. Nickel, T. Giger, U. Müller, M. Groszer, T. Adler, A. Aguilar, I. Bolle, J. Calzada-Wack, C. Dalke, N. Ehrhardt, J. Favor, H. Fuchs, V. Gailus-Durner, W. Hans, G. Hölzlwimmer, A. Javaheri, S. Kalaydjiev, M. Kallnik, E. Kling, S. Kunder, I. Moßbrugger, B. Naton, I. Racz, B. Rathkolb, J. Rozman, A. Schrewe, D. Busch, J. Graw, B. Ivandic, M. Klingenspor, T. Klopstock, M. Ollert, L. Quintanilla-Martinez, H. Schulz, E. Wolf, W. Wurst, A. Zimmer, S.E. Fisher, R. Morgenstern, T. Arendt, M. Hrabé de Angelis, J. Fischer, J. Schwarz and S. Pääbo: A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 137, 961-71 (2009).

Green, R.E., A.W. Briggs, J. Krause, K. Prüfer, H.A. Burbano, M. Siebauer, M. Lachmann and S. Pääbo: The Neandertal genome and ancient DNA authenticity. EMBO Journal 28, 2494-2502 (2009).

Halbwax, M., C.K. Mahamba, A.-M. Ngalula and C. André: Placental retention in a bonobo (Pan paniscus). Journal of Medical Primatology 38, 171-174 (2009).

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Herráez, D.L., M. Bauchet, K. Tang, C. Theunert, I. Pugach, J. Li, M.R. Nandineni, A. Gross, M. Scholz and M. Stoneking: Genetic variation and recent positive selection in worldwide human populations: Evidence from nearly 1 million SNPs. Plos One 4 (11), e7888 (2009).

Hillmer, A.M., J. Freudenberg, S. Myles, S. Herms, K. Tang, D.A. Hughes, F.F. Brockschmidt, Y. Ruan, M. Stoneking and M.M. Nöthen: Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Human Genetics 126, 255-264 (2009).

Hoehndorf, R., J. Kelso and H. Herre: The ontology of biological sequences. BMC Bioinformatics 10, 377 (2009).

Hoehndorf, R., J. Bacher, M. Backhaus, S.E. Gregorio, Jr., F. Loebe, K. Prüfer, A. Uciteli, J. Visagie, H. Herre and J. Kelso: BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics 10, S5 (2009).

Hughes, D.A., A. Hinney, H. Brumm, A.-K. Wermter, H. Biebermann, J. Hebebrand and M. Stoneking: Increased constraints on MC4R during primate and human evolution. Human Genetics 124, 633-647 (2009).

Hughes, D.A., M. Jastroch, M. Stoneking and M. Klingenspor: Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis. BMC Evolutionary Biology 9, 4 (2009).

Kircher, M., U. Stenzel and J. Kelso: Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology 10, R83 (2009).

Landsman, D., R. Gentleman, J. Kelso and B.F. Francis Ouellette: DATABASE: A new forum for biological databases and curation. Database bap002, doi:10.1093/database/bap002 (2009).

Maricic, T. and S. Pääbo: Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques 46, 51-57 (2009).

McIntyre, M.H., E. Herrmann, V. Wobber, M. Halbwax, C. Mohamba, N. de Sousa, R. Atencia, D. Cox and B. Hare: Bonobos have more human-like second-to-fourth finger length ratio (2D:4D) than chimpanzees: a hypothesized indication of lower prenatal androgens. Journal of Human Evolution 56, 361-365 (2009).

Mona, S., K.E. Grunz, S. Brauer, B. Pakendorf, L. Castri, H. Sudoyo, S. Marzuki, R.H. Barnes, J. Schmidtke, M. Stoneking and M. Kayser: Genetic admixture history of eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis. Molecular Biology and Evolution 26, 1865-1877 (2009).

Moreno-Estrada, A., K. Tang, M. Sikora, T. Marquès-Bonet, F. Casals, A. Navarro, F. Calafell, J. Bertranpetit, M. Stoneking and E. Bosch: Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populations. Molecular Biology and Evolution 26, 2285-2297 (2009).

Myles, S., M. Stoneking and N. Timpson: An assessment of the portability of ancestry informative markers between human populations. BMC Medical Genomics 2, 45 (2009).

Nasidze, I., D. Quinque, M. Rahmani, S. Ali Alemohamad, P. Asadova, O. Zhukova and M. Stoneking: MtDNA and Y-chromosome variation in the Talysh of Iran and Azerbaijan. American Journal of Physical Anthropology 138, 82-89 (2009).

Nasidze, I, J. Li, D. Quinque, K. Tang and M. Stoneking: Global diversity in the human salivary microbiome. Genome Research 19, 636-643 (2009).

21

Nasidze, I., D. Quinque, J. Li, M. Li, K. Tang and M. Stoneking: Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Analytical Biochemistry 391, 64-68 (2009).

Ptak, S., W. Enard, V. Wiebe, I. Hellmann, J. Krause, M. Lachmann and S. Pääbo: Linkage disequlibrium extends across putative selected sites in FOXP2. Mol. Biol. Evol. 26, 2181-84 (2009).

Roewer, L., S. Willuweit, M. Stoneking and I. Nasidze: A Y-STR database of Iranian and Azerbaijanian minority populations. Forensic Science International: Genetics 4, e53-e55 (2009).

Ryan, A.W., D. Hughes, K. Tang, D. Kelleher, T. Ryan, R. McManus and M. Stoneking: Natural selection and the molecular basis of electrophoretic variation at the coagulation F13B locus. European Journal of Human Genetics 17, 219-227 (2009).

Somel, M., H. Franz, Z. Yan, A. Lorenc, S. Guo, T. Giger, J. Kelso, B. Nickel, M. Dannemann, S. Bahn, M.J. Webster, C.S. Weickert, M. Lachmann, S. Pääbo and P. Khaitovich: Transcriptional neoteny in the human brain. PNAS 106, 5743-48 (2009).

Stiller, M., M. Knapp, U. Stenzel, M. Hofreiter and M. Meyer: Direct multiplex sequencing (DMPS) - a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Research 19, 1843-1848 (2009).

Stoneking, M.: Humans as second orangutans: sense or nonsense? BioEssays 31, 1010-1012 (2009).

Weickert, C.S., M. Elashoff, A.B. Richards, D. Sinclair, S. Bahn, S. Pääbo, P. Khaitovich and M.J. Webster: Transcriptome analysis of male-female differences in prefrontal cortical development. Molecular Psychiatry 14, 558-561 (2009).

2008

Albert, F.W.: Uncovering the genetic basis for tameness – a research strategy. Vestnik VOGiS 12, 19-23 (2008).

Albert, F.W., O. Shchepina, C. Winter, H. Römpler, D. Teupser, R. Palme, U. Ceglarek, J. Kratzsch, R. Sohr, L.N. Trut, J. Thiery, R. Morgenstern, I.Z. Plyusnina, T. Schoeneberg and S. Pääbo: Phenotypic differences in behavior, physiology and neurochemistry between rats selected for tameness and for defensive aggression towards humans. Hormones and Behavior 53, 413-421 (2008).

Balaresque, P., G.R. Bowden, E.J. Parkin, G.A. Omran, E. Heyer, L. Quintana-Murci, L. Roewer, M. Stoneking, I. Nasidze, D.R. Carvalho-Silva, C. Tyler-Smith, P. de Knijff and M.A. Jobling: Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis. Human Mutation 29, 1171-80 (2008).

Bergstrom, C.T., B. Kerr and M. Lachmann: Building trust by wasting time. In: Moral Markets: The Critical Role of Values in the Economy. (Ed.) P.J. Zak, Princeton University Press, 142-156 (2008).

Bryk, J., E. Hardouin, I. Pugach, D. Hughes, R. Strotmann, M. Stoneking and S. Myles: Positive selection in East Asians for an EDAR allele that enhances NF-κB activation. PLoS One 3 (5), e2209 (2008).

22

Chaix, R., M. Somel, D.P. Kreil, P. Khaitovich and G.A. Lunter: Evolution of primate gene expression: Drift and corrective sweeps? Genetics 180, 1379-89 (2008).

Donaldson-Matasci, M.C., M. Lachmann and C.T. Bergstrom: Phenotypic diversity as an adaptation to environmental uncertainty. Evolutionary Ecology Research 10, 493-515 (2008).

Farkas, L.M., C. Haffner, T. Giger, P. Khaitovich, K. Nowick, C. Birchmeier, S. Pääbo and W.B. Huttner: Insulinoma-associated 1 has a panneurogenic role and promotes the generation and expansion of basal progenitors in the developing mouse neocortex. Neuron 60, 40-55 (2008).

Fechner, A., D. Quinque, S. Rychkov, I. Morozowa, O. Naumova, Y. Schneider, S. Willuweit, O. Zhukova, L. Roewer, M. Stoneking, and I. Nasidze: Boundaries and clines in the west Eurasian Y-chromosome landscape: insights from the European part of Russia. American Journal of Physical Anthropology 137, 41-47 (2008).

Giger, T., L. Excoffier, U. Amstutz, P.J.R. Day, A. Champigneulle, M.M. Hansen, J. Kelso and C.R. Largiader: Population transcriptomics of life-history variation in the genus Salmo. Molecular Ecology 17, 3095-3108 (2008).

Green, R.E., A.-S. Malaspinas, J. Krause, A.W. Briggs, P.L.F. Johnson, C. Uhler, M. Meyer, J.M. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H.A. Burbano, M. Ronan, J.M. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin and S. Pääbo: A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416-426 (2008).

Groszer, M., D.A. Keays, R.M.J. Deacon, J.P. de Bono, S. Prasad-Mulcare, S. Gaub, M.G. Baum, C.A. French, J. Nicod, J.A. Coventry, W. Enard, M. Fray, S.D.M. Brown, P.M. Nolan, S. Pääbo, K.M. Channon, R.M. Costa, J. Eilers, G. Ehret, J.N.P. Rawlins and S.E. Fisher: Impaired synaptic plasticity and motor learning in mice with a point mutation implicated in human speech deficits. Current Biology 18, 354-362 (2008).

Güldemann, T. and M. Stoneking: A historical appraisal of clicks: a linguistic and genetic population perspective. Annual Review of Anthropology 37, 93-109 (2008).

López Herráez, D. and M. Stoneking: High fractions of exogenous DNA in human buccal samples reduce the quality of large-scale genotyping. Analytical Biochemistry 383, 329-331 (2008).

Hoehndorf, R., F. Loebe, R. Poli, H. Herre and J. Kelso: GFO-Bio: A biological core ontology. Applied Ontology 3, 219-227 (2008).

Hublin, J.-J., S. Pääbo et al.: Suggested guidelines for invasive sampling of hominid remains. Journal of Human Evolution 55, 756-757 (2008).

Hughes, D.A., K. Tang, R. Strotmann, T. Schöneberg, J. Prenen, B. Nilius and M. Stoneking: Parallel selection on TRPV6 in human populations. PLoS ONE 3 (2), e1686 (2008).

Kayser, M., O. Lao, K. Saar, S. Brauer, X. Wang, P. Nürenberg, R.J. Trent and M. Stoneking: Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. American Journal of Human Genetics 82, 194-198 (2008).

Kayser, M., O. Lao and M. Stoneking: Reply to Hedrick. American Journal of Human Genetics 83, 140-142 (2008).

Kayser, M., Y. Choi, M. van Oven, S. Mona, S. Brauer, D. Suarkia, W. Schiefenhövel and M. Stoneking: The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia. Molecular Biology and Evolution 25, 1362-1374 (2008).

23

Khaitovich, P., H.E. Lockstone, M.T. Wayland, T.M. Tsang, S.D. Jayatilaka, A.J. Guo, J. Zhou, M. Somel, L.W. Harris, E. Holmes, S. Pääbo and S. Bahn: Metabolic changes in schizophrenia and human brain evolution. Genome Biology 9, R124 (2008).

Kircher, M., C. Bock and M. Paulsen: Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlkl/Gtl2 imprinting region. BMC Genomics 9, 346, doi: 10.1186/1471-2164-9-346 (2008).

Klingenspor, M., T. Fromme, D.A. Hughes, L. Manzke, E. Polymeropoulos, T. Riemann, M. Trzcionka, V. Hirschberg and M. Jastroch: An ancient look at UCP1. Biochimica et Biophysica Acta 1777, 637-641 (2008).

Krause, J., T. Unger, A. Noçon, A.-S. Malaspinas, S.-O. Kolokotronis, M. Stiller, L. Soibelzon, H. Spriggs, P.H. Dear, A.W. Briggs, S.C.E. Bray, S.J. O’Brien, G. Rabeder, P. Matheus, A. Cooper, M. Slatkin, S. Pääbo and M. Hofreiter: Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology 8: 220, doi:10.1186/1471-2148-8-220 (2008).

Lalueza-Fox, C., E. Gigli, M de la Rasilla, J. F. Bertranpetit and J. Krause: Genetic characterization of the ABO blood group in Neandertals. BMC Evolutionary Biology 8, 342, doi:10.1186/1471-2148-8-342 (2008).

Mehlotra, R.K., G. Mattera, M.J. Bockarie, J.D. Maguire, J.K. Baird, Y.D. Sharma, M. Alifrangis, G. Dorsey, P.J. Rosenthal, D.J. Fryauff, J.W. Kazura, M. Stoneking and P.A. Zimmerman: Discordant patterns of genetic variation at two chloroquine resistance loci in worldwide populations of the malaria parasite Plasmodium falciparum. Antimicrobial Agents and Chemotherapy 52, 2212-22 (2008).

Meyer, M., U. Stenzel and M. Hofreiter: Parallel tagged sequencing on the 454 platform. Nature Protocols 3, 267-278 (2008).

Meyer, M., A. W. Briggs, T. Maricic, B. Höber, B. Höffner, J. Krause, A. Weihmann, , S. Pääbo and M. Hofreiter: From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Research doi:10.1093/nar/gkm1095, 36, e5 (2008).

Myles, S., K. Tang, M. Somel, R.E. Green, J. Kelso and M. Stoneking: Identification and analysis of genomic regions with large between-population differentiation in humans. Annals Human Genetics 72, 99-110 (2008).

Myles S., D. Davison, J. Barrett, M. Stoneking and N. Timpson: Worldwide population differentiation at disease-associated SNPs. BMC Medical Genomics 1, 22 (2008).

Nasidze, I., D. Quinque, M. Rahmani, S.A. Alemohamad and M. Stoneking: Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran. Annals Human Genetics 72, 241-252 (2008).

Pruefer, K., U. Stenzel, M. Dannemann, R.E. Green, M. Lachmann and J. Kelso: PatMaN: rapid alignment of short sequences to large databases. Bioinformatics 24, 1530-32 (2008).

Roewer, L., S. Willuweit, C. Krüger, M. Nagy, S. Rychkov, I. Morozowa, O. Naumova, Y. Schneider, O. Zhukova, M. Stoneking and I Nasidze: Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations. International Journal of Legal Medicine 122, 219-233 (2008).

Somel, M., H. Creely, H. Franz, U. Mueller, M. Lachmann, P. Khaitovich and S. Pääbo: Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS ONE 3 (1), e1504 (2008).

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Stoneking, M.: Mitochondrial genome: evolution. In: Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, http://www.els.net/ [DOI: 10.1002/9780470015902.a0005074.pub2] (2008).

Stoneking, M.: Human origins: the molecular perspective. EMBO Reports 9, S46-S50 (2008).

2007

Briggs, A.W., U. Stenzel, P.L.F. Johnson, R.E. Green, J. Kelso, K. Prüfer, M. Meyer, J. Krause, M.T. Ronan, M. Lachmann and S. Pääbo: Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616-21 (2007).

Chen, H., R.E. Green, S. Pääbo and M. Slatkin: The joint allele-frequency spectrum in closely related species. Genetics 177, 387-398 (2007).

Clark, V.J., S.E. Ptak, I. Tiemann, Y. Qian, G. Coop, A.C. Stone, M. Przeworski, N. Arnheim and A. Di Rienzo: Combining sperm typing and linkage disequlibrium analyses reveals differences in selective pressures or recombination rates across human populations. Genetics 175, 795-804 (2007).

Cordaux, R., D. Srikanta, J. Lee, M. Stoneking, and M.A. Batzer: In search of polymorphic Alu insertions with restricted geographic distributions. Genomics 90, 154-158 (2007).

d'Abbadie, M., M. Hofreiter, A. Vaisman, D. Loakes, D. Gasparutto, J. Cadet, R. Woodgate, S. Pääbo and P. Holliger: Molecular breeding of polymerases for amplification of ancient DNA. Nature Biotechnology 25, 939-43 (2007).

DaRe, J.T., R.K. Mehlotra, P. Michon, I. Mueller, J. Reeder, Y.D. Sharma, M. Stoneking, and P.A. Zimmerman: Microsatellite polymorphism within pfcrt provides evidence of continuing evolution of chloroquine-resistant alleles in Papua New Guinea. Malaria Journal 6, 34 (2007).

Donaldson, M.C., M. Lachmann and C.T. Bergstrom: The evolution of functionally referential meaning in a structured world. Journal of Theoretical Biology. 246, 225-233 (2007).

Francks, S. Maegawa, J. Lauren, B.S. Abrahams, A. Velayos-Baeza, S.E. Medland, S. Colella, M. Groszer, E.Z. McAuley, T.M. Caffrey, T. Timmusk, P. Pruunsild, I. Koppel, P.A. Lind, N. Matsumoto-Itaba, J. Nicod, L. Xiong, R. Joober, W. Enard, B. Krinsky, E. Nanba, A.J. Richardson, B.P. Riley, N.G. Martin, S.M. Strittmatter, H.-J. Möller, D. Rujescu, D. St. Clair, P. Muglia, J.L. Roos, S.E. Fisher, R. Wade-Martins, G.A. Rouleau, J.F. Stein, M. Karayiorgou, D.H. Geschwind, J. Ragoussis, K.S. Kendler, M.S. Airaksinen, M. Oshimura, L.W. DeLisi and A.P. Monaco: LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Molecular Psychiatry 12, 1129-39 (2007).

Fu, N., I. Drinnenberg, J. Kelso, J.R. Wu, S. Pääbo, R. Zeng and P. Khaitovich: Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE 2 (2), e216 (2007).

Hoehndorf, R., F. Loebe, J. Kelso and H. Herre: Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics 8, 377 (2007).

25

Hofreiter, M., S. Münzel, N.J. Conard, J. Pollack, M. Slatkin, G. Weiss and S. Pääbo: Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene. Current Biology 17, R122-23 (2007).

Khaitovich, P.: Brain expression-is it all in our SNPs? Molecular Systems Biology 3, 155 (2007).

Krause, J., L. Orlando, D. Serre, B. Viola, K. Prüfer, M.P. Richards, J.-J. Hublin, C. Hänni, A.P. Derevianko and S. Pääbo: Neanderthals in central Asia and Siberia. Nature 449, 902-904 (2007).

Krause, J., C. Lalueza-Fox, L. Orlando, W. Enard, R.E. Green, H.A. Burbano, J.-J. Hublin, J. Bertranpetit, C. Hänni, J. Fortea, M. de la Rasilla, A. Rosas and S. Pääbo: The derived FOXP2 variant of modern humans was shared with Neandertals. Current Biology 17, 1908-12 (2007).

Kuch, M., D.R. Gröcke, M.C. Knyf, T.M.P. Gilbert, B. Younghusband, T. Young, I. Marshall, M. Stoneking and H. Poinar: A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA. American Journal of Physical Anthropology 132, 594-604 (2007).

Lalueza-Fox, C., H. Römpler, D. Caramelli, C. Stäubert, G. Catalano, D. Hughes, N. Rohland, E. Pilli, L. Longo, S. Condemi, M. de la Rasilia, J. Fortea, A. Rosas, M. Stoneking, T. Schöneberg, J. Bertranpetit and M. Hofreiter: A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318, 1453-55 (2007).

Lizano, E., J. Schuster, M. Müller, J. Kelso and M. Mörl: A splice variant of the human CCA adding enzyme with modified activity. J. Mol. Biol 366, 1258-65 (2007).

Meyer, M., U. Stenzel, S. Myles, K. Prüfer and M. Hofreiter: Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research 35, e97 (2007).

Myles, S., E. Hradetzky, J. Engelken, O. Lao, P. Nürnberg, R. J. Trent, X. Wang, M. Kayser and M. Stoneking: Identification of a candidate genetic variant for the high prevalence of type II diabetes in Polynesians. European Journal of Human Genetics 15, 584-589 (2007).

Myles, S., M. Somel, K. Tang, J. Kelso and M. Stoneking: Identifying genes underlying skin pigmentation differences among human populations. Human Genetics 120, 613-621 (2007).

Myles, S., D. Hughes and M. Stoneking: Detecting local selection in human populations: In: Recent Advances in Molecular Biology and Evolution: Applications to Biological Anthropology. (Eds.) C. Santos and M. Lima, Research Signpost, Kerala, 66-81 (2007).

Nasidze, I., D. Quinque, I. Udina, S. Kunizheva, and M. Stoneking: The Gagauz, a linguistic enclave, are not a genetic isolate. Annals Human Genetics 71, 379-389 (2007).

Pakendorf, B., I.N. Novgorodov, V.L. Osakovskij, and M. Stoneking: Mating patterns amongst Siberian reindeer herders: inferences from mtDNA and Y-chromosomal analyses. American Journal of Physical Anthropology 133, 1013-1027 (2007).

Prüfer, K., B. Muetzel, H. Do, G. Weiss, P. Khaitovich, E. Rahm, S. Pääbo, M. Lachmann and W. Enard: FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8, 41 (2007).

Rhesus Macaque Genome Sequencing and Analysis Consortium: Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234 (2007).

26

Roewer, L., C. Krüger, S. Willuweit, M. Nagy, H. Rodig, L. Kokshunova, T. Rothämel, S. Kravchenko, M.A. Jobling, M. Stoneking and I. Nasidze: Y-chromosomal STR haplotypes in Kalmyk population samples. Forensic Science International 173, 204-209 (2007).

Rootsi, S., L.A. Zhivotovsky, M. Baldovic, M. Kayser, I.A. Kutuev, R. Khusainova, M.A. Bermisheva, M. Gubina, S. Fedorova, A.M. Ilumäe, E.K. Khusnutdinova, L.P. Osipova, M. Stoneking, V. Ferak, J. Parik, T. Kivisild, P.A. Underhill and R. Villems: A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. European Journal of Human Genetics 15, 204-211 (2007).

Stoneking, M. and I. Nasidze: Reply to Parson. Annals Human Genetics 71, 279-280 (2007).

Stoneking, M. and M. Kayser: Genealogical markers: mtDNA and the Y-chromosome. In: Genetic Variation: A Laboratory Manual. (Eds.) M.P. Weiner, S.B. Gabriel, J.C. Stephens, Cold Spring Harbor Laboratory Press, New York, 421-436 (2007).

Tang, K., K.R. Thornton and M. Stoneking: A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology 5, e171 (2007).

Thalmann, O., A. Fischer, F. Lankester, S. Pääbo and L. Vigilant: The complex evolutionary history of gorillas: Insights from genomic data. Mol. Biol. Evol. 24, 146-158 (2007).

Timpson, N., J. Heron, G.D. Smith and W. Enard: Comment on papers by Evans et al. and Mekel-Bobrov at al. on evidence for positive selection of MCPH1 and ASPM. Science 317, 1036a (2007).

Weber, M., I. Hellmann, M.B. Stadler, L. Ramos, S. Pääbo, M. Rebhan and D. Schübeler: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics 39, 457-466 (2007).

2006

Burek, P., R. Hoehndorf, F. Loebe, J. Visagie, H. Herre and J. Kelso: A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics 22, e66-e73 (2006).

Creely, H., and P. Khaitovich: Human brain evolution. In: Progress in Brain Research, (Eds.) Hemby & Bahn, 295-309 (2006).

Fischer, A., J. Pollack, O. Thalmann, B. Nickel and S. Pääbo: Demographic history and genetic differentiation in apes. Current Biology 16, 1133-38 (2006).

Fish, J.L., Y. Kosodo, W. Enard, S. Pääbo and W.B. Huttner: Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells. PNAS 103, 10438-43 (2006).

Goidts, V., L. Armengol, W. Schempp, J. Conroy, N. Nowak, S. Muller, D.N. Cooper, X. Estivill, W. Enard, J.M. Szamalek et al.: Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet 119, 185-198 (2006).

Green, R.E., J. Krause, S.E. Ptak, A.W. Briggs, M.T. Ronan, J.F. Simons, L. Du, M. Egholm, J.M. Rothberg, M. Paunovic and S. Pääbo: Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330-36 (2006).

27

Hammer, M.F., T. M. Karafet, H. Park, K. Omoto, S. Harihara, M. Stoneking and S. Horai: Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. Journal of Human Genetics 51, 47-58 (2006).

Hoehndorf, R., K. Prüfer, M. Backhaus, H. Herre, J. Kelso, F. Loebe and J. Visagie: A proposal for a gene functions wiki. In: OTM workshops 2006 (Eds.) R. Meersman, Z. Tari, P. Herrero et al., Springer-Verlag, 669-678 (2006).

Hublin, J.-J. and S. Pääbo: Neandertals. Current Biology 16, R113-14 (2006).

Jaenicke-Després, V. and B.D. Smith: Ancient DNA and the integration of archaeological and genetic approaches to the study of maize domestication. In: Histories of maize. Academic Press, 83-95 (2006).

Kayser, M., S. Brauer, R. Cordaux, A. Casto, O. Lao, L.A. Zhivotovsky, C. Moyse-Faurie, R.B. Rutledge, W. Schiefenhoevel, D. Gil, A.A. Lin, P.A. Underhill, P.J. Oefner, R.J. Trent and M. Stoneking: Melanesian and Asian Origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Molecular Biology and Evolution 23, 2234-44 (2006).

Khaitovich, P., K. Tang, H. Franz, J. Kelso, I. Hellmann, W. Enard, M. Lachmann and S. Pääbo: Positive selection on gene expression in the human brain. Current Biology 16, R356-58 (2006).

Khaitovich, P., W. Enard, M. Lachmann and S. Pääbo: Evolution of primate gene expression. Nature Reviews Genetics 7, 693-702 (2006).

Khaitovich, P., J. Kelso, H. Franz, J. Visagie, T. Giger, S. Joerchel, E. Petzold, R.E. Green, M. Lachmann and S. Pääbo: Functionality of intergenic transcription: An evolutionary comparison. PLoS Genetics 2, 1590-1598 (2006).

Krause, J., P.H. Dear, J. Pollack, M. Slatkin, H. Spriggs, I. Barnes, A. Lister, I. Ebersberger, S. Pääbo and M. Hofreiter: Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439, 724-727 (2006).

Lalueza-Fox, C., J. Krause, D. Caramelli, G. Catalano, L. Milani, M.L. Sampietro, F. Calafell, C. Martinez-Maza, M. Bastir, A. Garcia-Tabernero, M. de la Rasilla, J. Fortea, S. Pääbo, J. Bertranpetit and A. Rosas: Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European Neandertals. Curr. Biol. 16, R629-30 (2006).

Lizano, E. and M. Mörl: tRNA. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. (Eds.) D. Ganten, K. Ruckpaul, 1920-24 (2006).

Nasidze I. and M. Stoneking: Mother tongue: Concomitant replacement of language and mtDNA in South Caspian populations of Iran. In: The Evolution of Language. (Eds.) A. Cangelosi, A.D.M. Smith and K. Smith, World Scientific Co. Pte. Ltd., New Jersey, 432-433 (2006).

Nasidze, I., D. Quinque, M. Rahmani, S.A. Alemohamad and M. Stoneking: Concomitant replacement of language and mtDNA in South Caspian populations of Iran. Current Biology 16, 668-673 (2006).

Noonan, J.P., G. Coop, S. Kudaravalli, D. Smith, J. Krause, J. Alessi, F. Chen, D. Platt, S. Pääbo, J.K. Pritchard and E.M. Rubin: Sequencing and analysis of Neanderthal genomic DNA. Science 314, 1113-18 (2006).

Pakendorf, B., I.N. Novgorodov, V.L. Osakovskij, A.P. Danilova, A.P. Protod'jakonov and M. Stoneking: Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts. Human Genetics 120, 334-353 (2006).

28

Prabhakar, S., J.P. Noonan, S. Pääbo and E.M. Rubin: Accelerated evolution of conserved noncoding sequences in humans. Science 314, 786 (2006).

Quinque, D., R. Kittler, M. Kayser, M. Stoneking and I. Nasidze: Evaluation of saliva as a source of human DNA for population and association studies. Analytical Biochemistry 353, 272-277 (2006).

Römpler, H., P.H. Dear, J. Krause, M. Meyer, N. Rohland, T. Schöneberg, H. Spriggs, M. Stiller and M. Hofreiter: Multiplex amplification of ancient DNA. Nature Protocols 1, 720-728 (2006).

Serre, D. and S. Pääbo: The fate of European Neanderthals: results and perspectives from ancient DNA analyses. In: Neanderthals revisited. (Eds.) K. Harvati and T. Harrison, Springer, Dordrecht, The Netherlands, 211-219 (2006).

Serre, D., R.W. Schmitz and S. Pääbo: Genetic analyses of the Neanderthals from the Feldhofer Caves. In: Rheinische Ausgrabungen, Band 58: Neanderthal 1856-2006. (Ed.) R.W. Schmitz, Verlag Philipp von Zabern, Mainz am Rhein, 329-333 (2006).

Serre, D., A. Langaney, M. Chech, M. Teschler-Nicola, M. Paunovic, P. Mennecier, M. Hofreiter, G. Possnert and S. Pääbo: No evidence of Neanderthal mtDNA contribution to early modern humans. In: Early modern humans and the Moravian Gate. (Ed.) M. Teschler-Nicola, Springer Verlag, Wien, 491-504 (2006).

Somel, M., P. Khaitovich, S. Bahn, S. Pääbo and M. Lachmann: Gene expression becomes heterogeneous with age. Current Biology 16, R359-60 (2006).

Stiller, M., R.E. Green, M. Ronan, J.F. Simons, L. Du, W. He, M. Egholm, J. Rothberg, S.G. Keats, N.D. Ovodov, E.E. Antipina, G.F. Baryshnikov, Y.V. Kuzmin, A.A. Vasilevski, G.E. Wuenschell, J. Termini, M. Hofreiter, V. Jaenicke-Després and S. Pääbo: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. PNAS 103, 13578-84 (2006).

Stoneking, M.: Genetic evidence for our recent African ancestry. In: The Prehistory of Africa. (Ed.) H. Soodyall, Jonathan Ball Publishers, Johannesburg, South Africa, 24-36 (2006).

Stoneking, M.: Investigating the health of our ancestors: insights from the evolutionary genetic consequences of prehistoric diseases. In: Integrative approaches to human health and evolution. (Eds.) T.G. Bromage, A. Vidal, E. Aguirre and A. Perez-Ochoa, Elsevier B. V., Amsterdam, 106-114 (2006).

Stoneking, M. and I. Nasidze: The patient is not dead yet: premature autopsy of an mtDNA data set. Annals Human Genetics 70, 327-331 (2006).

Stroud, J.C., Y. Wu, D.L. Bates, A. Han, K. Nowick, S. Pääbo, H. Tong and L. Chen: Structure of the forhead domain of FOXP2 bound to DNA. Structure 14, 159-166 (2006).

Tiffin, N., J.F. Kelso, A.R. Powell, H. Pan, V.B. Bajic and W.A. Hide: Integration of text- and data-mining using ontologies successfully identifies disease gene candidates. IMIA Yearbook of Medical Informatics (2006).

2005

Beauval, C., B. Maureille, F. Lacrampe-Cuyaubère, D. Serre, D. Peressinotto, J.-G. Bordes, D. Cochard, I. Couchoud, D. Dubrasquet, V. Laroulandie, A. Lenoble, J.-B. Mallye, S. Pasty,

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J. Primault, N. Rohland, S. Pääbo and E. Trinkaus: A late Neandertal femur from Les Rochers-de-Villeneuve, France. PNAS 102, 7085-7090 (2005).

Bull, J.J., L.A. Meyers and M. Lachmann: Quasispecies made simple. PLoS Computational Biology 1, e61 (2005).

Carninci, P., et. al. FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group): The transcriptional landscape of the mammalian genome. Science 309: 1559-63 (2005).

Cheng, Z., M. Ventura, X. She, P. Khaitovich, T. Graves, K. Osoegawa, D. Church, P. DeJong, R.K. Wilson, S. Pääbo, M. Rocchi and E.E. Eichler: A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437, 88-93 (2005).

The Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).

Ebersberger, I. and M. Meyer: A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern. Molecular Biology and Evolution 22, 1240-1245 (2005).

Enard, W.: Mensch und Schimpanse. Ein genetischer Vergleich. In: Urmensch und Wissenschaften. Festschrift Dieter Groh zum 70sten Geburtstag. (Eds.) B. Kleeberg, F. Crivellari and T. Walter, Darmstadt, Wissenschaftliche Buchgesellschaft, 125-136 (2005).

Fischer, A., Y. Gilad, O. Man and S. Pääbo: Evolution of bitter taste receptors in humans and apes. Molecular Biology and Evolution 22, 432-436 (2005).

Franz, H., C. Ullmann, A. Becker, M. Ryan, S. Bahn, T. Arendt, M. Simon, S. Pääbo and P. Khaitovich: Systematic analysis of gene expression in human brains before and after death. Genome Biology 6, R112 (doi:10.1186/gb-2005-6-13-r112) (2005).

Fraser, H.B., P. Khaitovich, J.B. Plotkin, S. Pääbo and M.B. Eisen: Aging and gene expression in the primate brain. PLoS Biology 3, e274, 1653-1661 (2005).

Gilbert, M.T.P., H.-J. Bandelt, M. Hofreiter and I. Barnes: Assessing ancient DNA studies. Trends in Ecology and Evolution 20, 541-544 (2005).

Hamilton, G., M. Stoneking and L. Excoffier: Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proceedings of the National Academy of Sciences USA 102, 7476-7480 (2005).

Heissig, F., J. Krause, J. Bryk, P. Khaitovich, W. Enard and S. Pääbo: Functional analysis of human and chimpanzee promoters. Genome Biology 6, R57 (2005).

Hellmann, I., K. Prüfer, H. Ji, M.C. Zody, S. Pääbo and S.E. Ptak: Why do human diversity levels vary at a megabase scale? Genome Research 15, 1222-1231 (2005).

Hofreiter, M.: Evolutionsgeschichte alpiner Höhlenbären aus molekulargenetischer Sicht. Mitt. Komm. Quartärforsch. Österr. Akad. Wiss. 14, 67-72 (2005).

Hofreiter, M.: Ancient DNA typing, book review. Homo – Journal of comparative human biology, 55, 298-300 (2005).

M. Hofreiter and L. Vigilant: Ancient DNA: Phylogenetic Applications. In: Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK (2005).

Iyengar, A., V.N. Babu, S. Hedges, A. Venkataraman, N. MacLean and P.A. Morin: Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus). Molecular Ecology 14, 2281-2297 (2005).

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Khaitovich, P., S. Pääbo and G. Weiss: Toward a neutral evolutionary model of gene expression. Genetics 170, 929-939 (2005).

Khaitovich, P., I. Hellmann, W. Enard, K. Nowick, M. Leinweber, H. Franz, G. Weiss, M. Lachmann and S. Pääbo: Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309, 1850-1854 (2005).

Laan, M., V. Wiebe, E. Khusnutdinova, M. Remm and S. Pääbo: X-chromosome as a marker for population history: linkage disequlibrium and haplotype study in Eurasian populations. Eur. J. Hum. Genet. 13, 452-462 (2005).

Leonard, J.A., N. Rohland, S. Glaberman, R. C. Fleischer, A. Caccone and M. Hofreiter: A rapid loss of stripes: the evolutionary history of the extinct quagga. RSBL 1, 291-295 (2005).

Mehlotra, R.K., G. Mattera, K. Bhatia, J.C. Reeder, M. Stoneking and P.A. Zimmerman: Insight into the early spread of chloroquine resistant Plasmodium falciparum in Papua New Guinea. Journal of Infectious Diseases 192, 2174-2179 (2005).

Meyers, L.A., F.D. Ancel and M. Lachmann: Evolution of Genetic Potential. PLoS Computational Biology 1, e32, 236-243 (2005).

Mikkelsen, T., L. Hillier, E. Eichler, M. Zody, D. Jaffe, S. Yang, W. Enard, I. Hellmann, K. Lindblad-Toh, T. Altheide et al.: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).

Mörl, M., E. Lizano, D.K. Willkomm and R.K. Hartmann: Production of RNAs with homogeneous 5’- and 3’-ends. Handbook of RNA Biochemistry. (Eds.) R.K. Hartmann, A. Bindereif, A. Schön and E. Westhof, Wiley-VCH 22-35 (2005).

Nasidze, I., D. Quinque, I. Dupanloup, R. Cordaux, L. Kokshunova and M. Stoneking: Genetic evidence for the Mongolian ancestry of Kalmyks. American Journal of Physical Anthropology. 128, 846-954 (2005).

Nasidze I., D. Quinque, M. Ozturk, N. Bendukidze and M. Stoneking: MtDNA and Y-chromosome variation in Kurdish groups. Annals of Human Genetics 69, 401-412 (2005).

Noonan, J.P., M. Hofreiter, D. Smith, J.R. Priest, N. Rohland, G. Rabeder, J. Krause, J.C. Detter, S. Pääbo and E.M. Rubin: Genomic Sequencing of Pleistocene cave bears. Science 309, 597-600 (2005).

Oota, H., B. Pakendorf, G. Weiss, A.v. Haeseler, S. Pookajorn, W. Settheetham-Ishida, D. Tiwawech, T. Ishida and M. Stoneking: Recent Origin and Cultural Reversion of a hunter-gatherer group. PLoS Biology 3, e71, 536-542 (2005).

Pääbo, S.: Was ist Forschung? In: Entwurfsatlas Forschungs- und Technologiebau. (Eds.) H. Braun and D. Grömling), Birkhäuser, Basel-Berlin-Boston, 10f (2005).

Pakendorf, B. and M. Stoneking: Mitochondrial DNA and human evolution. Annual Review of Genomics and Human Genetics 6:165-183 (2005).

Ptak, S.E., D.A. Hinds, K. Köhler, B. Nickel, N. Patil, D.G. Ballinger, M. Przeworski, K.A. Frazer and S. Pääbo: Fine-scale recombination patterns differ between chimpanzees and humans. Nature Genetics 37, 429-434 (2005).

Rabeder, G., M. Hofreiter and E.M. Wild: Die Bären der Brieglersberghöhle. Die Höhle 56, 36-43 (2005).

Rohland, N., J.L. Pollack, D. Nagel, C. Beauval, J. Airvaux, S. Pääbo and M. Hofreiter: The population history of extant and extinct hyenas. Mol. Biol. Evol. 22, 2435-43 (2005).

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Römpler, H., A. Schulz, C. Pitra, G. Coop, M. Przeworski, S. Pääbo and T. Schöneberg: The rise and fall of the chemoattractant receptor GPR33. J Biol Chem. 280, 31068-31075 (2005).

Schuster, J., H. Betat and M. Mörl: Is yeast on its way to evolving tRNA editing? EMBO Report 6, 367-372 (2005).

Smith, S. and P.A. Morin: Optimal storage conditions for highly dilute DNA samples: A role for trehalose as a preserving agent. J. Forensic Sci. 50, 1101-1108 (2005).

Stoneking, M.: Gene, Geographie und Sprache. In: Gene, Sprachen und ihre Evolution. (Ed.) G. Hauska, Unversitätsverlag Regensburg GmbH, Regensburg, Germany, 133-140 (2005).

Tanino, M., M.A. Debily, T. Tamura, T. Hishiki, O. Ogasawara, K. Murakawa, S. Kawamoto, K. Itoh, S. Watanabe, S.J. de Souza, S. Imbeaud, E. Graudens, E. Eveno, P. Hilton, Y. Sudo, J. Kelso, K. Ikeo, T. Imanishi, T. Gojobori, C. Auffray, W. Hide and K. Okubo: The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res. 1; 33(Database Issue), D567-D572. (2005).

Tiffin, N., J.F. Kelso, A.R. Powell, H. Pan, V.B. Bajic and W.A. Hide: Integration of text- and data-mining using ontologies successfully identifies disease gene candidates. Nucleic Acids Research 33, 1544-52 (2005).

Thalmann, O., D. Serre, M. Hofreiter, D. Lukas, J. Eriksson and L. Vigilant: New insights into gorilla population history derived from molecular fossils in gorilla evolution. Molecular Ecology, 14, 179-188 (2005).

Woods, C.G., J. Bond and W. Enard: Autosomal recessive primary microcephaly (MCPH): A review of clinical, molecular and evolutionary findings. American Journal of Human Genetics 76, 717-728 (2005).

Yohn, C.T., Z. Jiang, S.D. McGrath, K.E. Hayden, P. Khaitovich, M.E. Johnson, M.Y. Eichler, J.D. McPherson, S. Zhao, S. Pääbo and E.E. Eichler: Lineage-specific expansions of retroviral insertions within the genomes of African great-apes but not humans and orangutans. PLoS Biology 3, 577-587 (2005).

2004

Aitken, N., S. Smith, C. Schwarz and P.A. Morin: Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach. Molecular Ecology 13, 1423-1431 (2004).

Bergstrom, C. and M. Lachmann: Shannon Information and Biological Fitness. Proceedings of the IEEE information theory workshop (2004).

Betat, H., C. Rammelt, G. Martin and M. Mörl: Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities. Molecular Cell 15, 389-398 (2004).

Cordaux, R., R. Aunger, G. Bentley, I. Nasidze, S. M. Sirajuddin and M. Stoneking: Independent origins of Indian caste and tribal paternal lineages. Current Biology 14, 231-235 (2004).

Cordaux, R., G. Bentley, R. Aunger, S. M. Sirajuddin and M. Stoneking: Y-STR haplotypes from eight south Indian groups based on five loci. J. Forensic Science 49, 847-848 (2004).

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Cordaux, R., E. Deepa, H. Vishwanathan and M. Stoneking: Genetic evidence for the demic diffusion of agriculture to India. Science 304, 1125 (2004).

Cordaux, R., G. Weiss, N. Saha and M. Stoneking: The northeast Indian passageway: a barrier or corridor for human migrations? Molecular Biology & Evolution 21, 1525-1533 (2004).

Enard, W. and S. Pääbo: Comparative primate genomics. Annual Review of Genomics and Human Genetics 5, 351-78 (2004).

Enard, W., A. Fassbender, F. Model, P. Adorján, S. Pääbo and A. Olek: Differences in DNA methylation patterns between humans and chimpanzees. Current Biology 14, R148-149 (2004).

Erler, A., M. Stoneking and M. Kayser: Development of Y-chromosomal microsatellite markers for non-human primates. Molecular Ecology 13, 2921-2930 (2004).

Fischer, A., V. Wiebe, S. Pääbo and M. Przeworski: Evidence for a complex demographic history of chimpanzees. Molecular Biology & Evolution 21, 799-808 (2004).

Gilad, Y., V. Wiebe, M. Przeworski, D. Lancet and S. Pääbo: Loss of Olfactory Recepter Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates. PLoS Biology 2, 120-125 (2004). Authorship retracted (see PLoS Biol 5(6): e148 doi:10.1371/journal.pbio.0050148).

Hartmann, R.K., M. Mörl and M. Sprinzl: The tRNA world. RNA 10, 344-349 (2004).

Hofreiter, M. and M. Pacher: Using ancient DNA to elucidate raw material origin of bone points from Potocka Zijalka (Slovenia): preliminary results. Mitt. Komm. Quartärforsch. Österr. Akad. Wiss. 13, 201-210 (2004).

Hofreiter, M., G. Rabeder, V. Jaenicke-Després, G. Withalm, D. Nagel, M. Paunovic, G. Jambrĕsić and S. Pääbo: Evidence for reproductive isolation between cave bear populations. Current Biology 14, 40-43 (2004).

Hofreiter, M., D. Serre, N. Rohland, G. Rabeder, D. Nagel, N. Conard, S. Münzel and S. Pääbo: Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences of the USA 101, 12963-12968 (2004).

Hofreiter, M., O. Loreille, D. Ferriola, T.J. Parsons: Ongoing Controversy over Romanov Remains. Letter. Science 306, 407-408 (2004).

Hughes, D. A., R. Cordaux and M. Stoneking: Quick guide: humans. Current Biology 14, R367-R369 (2004).

Imanishi, T. et al.: Integrative annotation of 21,037 human genes validated by full-length cDNA clones. Public Library of Science: Biology 2, e162 (2004).

Iyengar, A., C.A. Stockwell, D. Layfield and P.A: Morin: Characterization of microsatellite markers in a threatened species, the White Sands pupfish (Cyprinodon tularosa). Molecular Ecology Notes 4, 191-193 (2004).

Kasperavičiūtė, D., V. Kučinskas and M. Stoneking: Y chromosome and mitochondrial DNA variation in Lithuanians. Annals Human Genetics 68, 438-452 (2004).

Kayser, M., R. Kittler, A. Erler, M. Hedman, A. C. Lee, A. Mohyuddin, S. Q. Mehdi, Z. Rosser, M. Stoneking, M. A. Jobling, A. Sajantila and C. Tyler-Smith: A comprehensive survey of human Y-chromosome microsatellites. American Journal of Human Genetics 74, 1183-1197 (2004).

Kelso, J.: EST resources, clone sets, and databases. Invited Chapter in: Encyclopedia of Genomics, Proteomics and Bioinformatics. Dunn, M., Jorde, L., Little, P., Subramaniam, S.

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(eds). John Wiley & Sons Ltd. Chichester, UK. Selected for advance online pre-publication (http://www.wiley.com//legacy/wileychi/ggpb/) 2004. Print publication 2005.

Khaitovich, P., B. Mützel, X. She, M. Lachmann, I. Hellmann, J. Dietzsch, S. Steigele, H.-H. Do, G. Weiss, W. Enard, F. Heissig, T. Arendt, K. Nieselt-Struwe, E.E. Eichler and S. Pääbo: Regional patterns of gene expression in human and chimpanzee brains. Genome Research 14, 1462-1473 (2004).

Khaitovich, P., G. Weiss, M. Lachmann, I. Hellmann, W. Enard, B. Muetzel, U. Wirkner, W. Ansorge and S. Pääbo: A neutral model of transcriptome evolution. PLoS Biology 2, 682-689 (2004).

Lachmann, M. and C.T. Bergstrom: The disadvantage of combinatorial communication. Proceedings of the Royal Society of London - Series B: Biological Sciences. 271, 2337-43 (2004).

Lachmann, M., M.E.J. Newman and C. Moore: The physical limits of communication or Why any sufficiently advanced technology is indistinguishable from noise. American Journal of Physics. 72, 1290-1293 (2004).

Levinger, L., I. Oestreich, C. Florentz and M. Mörl: A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3’-end processing and CCA addition. Journal of Molecular Biology 337, 535-544 (2004).

Levinger, L., M. Mörl and C. Florentz: tRNA 3'end metabolism and human mitochondrial disease. Nucleic Acids Research 32, 5430-5441 (2004).

Matheus, P., J. Burns, J. Weinstock and M. Hofreiter: Pleistocene brown bears in the mid-continent of North America. Science 306, 1150 (2004).

Morin, P.A. and T.L. Goldberg: Determination of genealogical relationships from genetic data: a review of methods and applications. In: Kinship and Behavior in Primates. (Ed.) B. Chapais & C.M. Berman), New York, Oxford Univ. Press, 15-45 (2004).

Morin, P.A., Luikart, G., Wayne, R.K. and the SNP workshop group: SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution 19, 208-216 (2004).

Nasidze, I., E. Y. S. Ling, D. Quinque, I. Dupanloup, R. Cordaux, S. Rychkov, O. Naumova, O. Zhukova, N. Sarraf-Zadegan, G. A. Naderi, S. Asgary, S. Sardas, D. D. Farhud, T. Sarkisian, C. Asadov, A. Kerimov and M. Stoneking: Mitochondrial DNA and Y-chromosome variation in the Caucasus. Annals of Human Genetics 68, 205-221 (2004).

Nasidze, I., D. Quinque, I. Dupanloup, S. Rychkov, O. Naumova, O. Zhukova and M. Stoneking: Genetic evidence concerning the origins of South and North Ossetians. Annals of Human Genetics 68, 588-599 (2004).

Nembaware, V., K.H. Wolfe, F. Bettoni, J. Kelso and C. Seoighe: Allele-specific transcript isoforms in human. FEBS Letters 577: 233-38 (2004).

Pääbo, S.: Ancient DNA. In: DNA - Changing Science and Society. (Ed.) T. Krude, Cambridge University Press, Cambridge, 68-87 (2004).

Pääbo, S., H. Poinar, S. Serre, V. Jaenicke-Després, J. Hebler, N. Rohland, M. Kuch, J. Krause, L. Vigilant and M. Hofreiter: Genetic analyses from ancient DNA. Annual Review of Genetics, 38, 645-79 (2004).

Ptak, S.E., A.D. Roeder, M. Stephens, Y. Gilad, S. Pääbo and M. Przeworski: Absence of the TAP2 human recombination hospot in chimpanzees. PLoS Biology 2, 849-855 (2004).

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Ptak, S.E., K. Voelpel and M. Przeworski: Insights into recombination from patterns of linkage disequilibrium in humans. Genetics 167, 187-197 (2004).

Rabeder, G. and M. Hofreiter: Der neue Stammbaum der Höhlenbären. Die Höhle 55, 58-77 (2004).

Rabeder, G., M. Hofreiter, D. Nagel and G. Withalm: New taxa of alpine cave bears (Ursidae, Carnivora). Cahiers scientifiques / Hors série no. 2, 49-67 (2004).

Rabeder, G., M. Hofreiter, M. Pacher and G. Withalm: The systematic position of cave bears from Potocka Zijalka. Mitt. Komm. Quartärforsch. Österr. Akad. Wiss. 13, 197-200 (2004).

Roeder, A.D., F.I. Archer, H.N. Poinar and P.A. Morin: A novel method for collection and preservation of faeces for genetic studies. Molecular Ecology Notes 4, 761-764 (2004).

Rohland, N., H. Siedel and M. Hofreiter: Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. Biotechniques 36, 814-821 (2004).

Schuster, J. and M. Mörl: Mitochondrial tRNA Editing. Topics in Current Genetics 8, 81-96 (2004).

Serre, D., M. Hofreiter and S. Pääbo: Mutations induced by ancient DNA extracts? Letter. Molecular Biology and Evolution 21, 1463-1467 (2004).

Serre, D. and S. Pääbo: Evidence for gradients of human genetic diversity within and among continents. Genome Research: 14, 1679-1685 (2004).

Serre, D., A. Langaney, M. Chech, M. Teschler-Nicola, M. Paunovic, P. Mennecier, M. Hofreiter, G. Possnert and S. Pääbo: No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biology 2, 313-317 (2004).

Smith, S., N. Aitken, C. Schwarz and P.A. Morin: Characterization of 15 single nucleotide polymorphism markers for chimpanzees (Pan troglodytes). Molecular Ecology Notes 4, 348-351 (2004).

Thalmann, O., J. Hebler, H.N. Poinar, S. Pääbo and L. Vigilant: Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Molecular Ecology 13, 321-335 (2004).

The International Chimpanzee Chromosome 22 Consortium: Watanabe, H., A. Fujiyama, M. Hattori, T.D. Taylor, A. Toyoda, Y. Kuroki, H. Noguchi, A. BenKahla, H. Lehrach, R. Sudbrak, M. Kube, S. Taenzer, P. Galgoczy, M. Platzer, M. Scharfe, G. Nordsiek, H. Blöcker, I. Hellmann, P. Khaitovich, S. Pääbo, R. Reinhardt, H.-J. Zheng, X.-L. Zhang, G.-F. Zhu, B.-F. Wang, G. Fu, S.-X. Ren, G.-P. Zhao, Z. Chen, Y.-S. Lee, J.-E. Cheong, S.-H. Choi, K.-M. Wu, T.-T. Liu, K.-J. Hsiao, S.-F. Tsai, C.-G. Kim, S. Oota, T. Kitano, Y. Kohara, N. Saitou, H.-S. Park, S.-Y. Wang, M.-L. Yaspo and Y. Sakaki: DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429, 382-388 (2004).

Vishwanathan, H., E. Deepa, R. Cordaux, M. Stoneking, M. V. Usha Rani and P. P. Majumder: Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers. Annals Human Genetics 68, 128-138 (2004).

2003

Augustin, M.A., A.S. Reichert, H. Betat, R. Huber, M. Mörl and C. Steegborn: Crystal structure of the human CCA-adding enzyme: insights into template-independent

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polymerization. Journal of Molecular Biology 328, 985-994 (2003).

Betat, H., and M. Mörl: tRNA Import in Mitochondrien. Biospektrum 1, 33-35 (2003).

Cordaux, R. and M. Stoneking: South Asia, the Andamanese and the genetic evidence for an "early" human dispersal out of Africa. American Journal of Human Genetics 72, 1586-1590 (2003).

Cordaux, R., N. Saha, G.R. Bentley, R. Aunger, S.M. Sirajuddin and M. Stoneking: Mitochondrial DNA analysis reveals diverse histories of tribal populations of India. European Journal of Human Genetics 11, 253-264 (2003).

Gilad, Y., Bustamente, C.D. Lancet and S. Pääbo: Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am. J. Hum. Genet. 73, 489-501 (2003).

Gilad, Y., Man, O., Pääbo, S and D. Lancet: Human specific loss of olfactory receptor genes. Proc. Natl. Acad. Sci. USA 100, 3324-3327 (2003).

Hellmann, I., Ebersberger, I., Ptak, S., Pääbo, S. and M. Przeworski: A neutral explanation for the correlation between diversity levels and recombination rates in humans. American Journal of Human Genetics 72, 1527-35 (2003).

Hellmann, I., S. Zöllner, W. Enard, I. Ebersberger, B. Nickel and S. Pääbo: Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Research 13, 831-837 (2003).

Hofreiter, M., J.I. Mead, P. Martin and H.N. Poinar: Molecular Caving. Current Biology 13, R693-95, R1-4 (2003).

Hofreiter, M. and L. Vigilant: Ancient human DNA: phylogenetic applications. In: Encyclopedia of the Human Genome. (Ed.) D. Cooper, Nature Publishing Group, London (2003).

Hofreiter, M., H. Siedel, W.V. Neer and L. Vigilant: Mitochondrial DNA sequence from an enigmatic gorilla population (Gorilla gorilla uellensis). American Journal of Physical Anthropology 121, 361-368 (2003).

Hofreiter, M., J.L. Betancourt, A.P. Sbriller, V. Markgraf and H.G. McDonald: Phylogeny, diet, and habitat of an extinct ground sloth from Cuchillo Curá, Neuquén Province, southwest Argentina. Quaternary Research 59, 364-378 (2003).

Jaenicke-Després, V., E. Buckler, B.D. Smith, M.T.P. Gilbert, A. Cooper, J. Doebley and S. Pääbo: Early allelic selection in maize as revealed by ancient DNA. Science 302, 1206-1208 (2003).

Kaessmann, H.: Human and chimpanzee nucleotide diversity. In: Nature Encyclopedia of the Human Genome. (Ed.) D. Cooper, Nature Publishing Group, London (2003).

Kayser, M.: The human Y chromosome – introduction into genetics and applications. Forensic Science Review 15(2), 77-89 (2003).

Kayser M., S. Brauer and M. Stoneking: A genome scan to detect candidate regions influenced by local natural selection in human populations. Molecular Biology and Evolution, 20(6), 893-900 (2003).

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Kayser, M., S. Brauer, G. Weiss, P.A. Underhill, L. Roewer, W. Schiefenhövel and M. Stoneking: Melanesian origin of Polynesian Y chromosomes. Current Biology 10, 1237-1246 (2000).

Koller, D.L., M.J. Econs, P.A. Morin, J.C. Christian, S.L. Hui, P. Parry, M.E. Curran, L.A. Rodriguez, P.M. Conneally, G. Joslyn, M. Peacock, C.C. Johnston and T. Foroud: Genome screen for QTLs contributing to normal variation in bone mineral density and osteoporosis. Journal of Clinical Endocrinology and Metabolism 85, 3116-3120 (2000).

Krings, M., C. Capelli, F. Tschentscher, H. Geisert, S. Meyer, A. von Haeseler, K. Grossschmidt, G. Possnert, M. Paunovic and S. Pääbo: A view of Neandertal genetic diversity. Nature Genetics 26, 144-146 (2000).

Kumar, S., P.W. Hedrick, T. Dowling, and M. Stoneking: Questioning evidence for recombination in human mitochondrial DNA. Science 288, 1931a (2000).

Kumar, S.S., I. Nasidze, S.R. Walimbe and M. Stoneking: Discouraging prospects for ancient DNA from India. American Journal of Physical Anthropology 113, 129-133 (2000).

Mack, S.J., T.L. Bugawan, P.V. Moonsamy, J.A. Erlich, E.A. Trachtenberg, Y.K. Paik, A.B. Begovich, N. Saha, H P. Beck, M. Stoneking and H.A. Erlich: Evolution of Pacific/Asian populations inferred from HLA class II allele frequency distributions. Tissue Antigens 55, 383-400 (2000).

Morin, P.A.: Genetic Resources: Opportunities and perspectives for the new century. Conservation Genetics 1, 271-275 (2000; published in May 2001).

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Morin, P.A.: Preservation of DNA from endangered species (letter). Science 289, 725-726 (2000).

Motz, M., S. Pääbo and C. Kilger: Improved cycle sequencing of GC-rich templates by a combination of nucleotide analogs. BioTechniques 29, 268-270 (2000).

Pääbo, S.: Gene, Sprache und die Besiedelung des europäischen Nordens Europas –Zum Ursprung von Populationen aus molekulargenetischer Sicht. In: Wie enstehen neue Qualitäten in komplexen Systemen? (Ed.) Max-Planck-Gesellschaft. Vandenhoeck & Ruprecht, Göttingen, 49-56 (2000).

Pääbo, S.: Of bears, conservation genetics, and the value of time travel (Commentary). Proceedings of the National Academy of Sciences, USA 97, 1320-1321 (2000).

Poinar, H.N. and G. Eglinton: Preservation of endangered species DNA. Science 289, 725 (2000).

Reichert, A.S. and M. Mörl: Repair of tRNAs in metazoan mitochondria. Nucleic Acids Research 28, 2043-2048 (2000).

Roewer, L., M. Kayser, K. Anslinger, C. Augustin, A. Caglia, D. Corach, S. Füredi, G. Geserick, L. Henke, M. Hidding, H.J. Kärgel, P. de Knijff, R. Lessing, V. Pascali, W. Parson, M. Prinz, B. Rolf, P. Schneider , R. Szibor, J. Teifel-Geding, M. Krawczak: Caucasian Y-STR haplotype reference database for forensic application. In: Progress in Forensic Genetics, Vol. 8. (Eds.) G.F. Sensabaugh, P.J. Lincoln and B. Olaisen. Elsevier Science B.V., Amsterdam, 613-615 (2000).

Roewer, L., M. Kayser, P. de Knijff, K. Anslinger, D. Corach, S. Füredi, G. Geserick, L. Henke, M. Hidding, H.J. Kärgel, R. Lessig, M. Nagy, V.L. Pascali, W. Parson, B. Rolf, C. Schmitt, R. Szibor, J. Teifel-Greding and M. Krawczak: A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males. Forensic Science International 114, 31-43 (2000).

Rogers, J., M.C. Mahaney, S.M. Witte, S. Nair, D. Newman, S. Wedel, L.A. Rodriguez, K.S. Rice, S.H. Slifer, A. Perelygin, M. Slifer, P. Palladino-Negro, T. Newman, K. Chambers, G. Joslyn, P. Parry and P.A. Morin: A genetic linkage map of the baboon (papio hamadryas) genome based on human microsatellite polymorphisms. Genomics 67, 237-247 (2000).

Rosser, Z.H., T. Zerjal, M.E. Hurles, M. Adojaan, D. Alavantic, A. Amorim, W. Amos, M. Armenteros, E. Arroyo, G. Barbujani, L. Beckamnn, J. Bertranpetit, E. Bosch, D.G. Bradley, G. Brede, G.C. Cooper, H.B.S.M. Corte-Real, P. de Knijff, R. Decorte, Y.E. Dubrova, O. Evgrafov, A. Gilissen, S. Glisic, M. Gölge, E.W. Hill, A. Jeziorowska, L. Kalaydjieva, M. Kayser, S.A. Kravchenco, J. Lavinha, L.A. Livshits, S. Maria, K. McElreavy, T.A. Meitinger, B. Melegh, R.J. Mitchell, J. Nicholson, S. Norby, A. Noveletto, A. Pandya, J. Parik, P.C. Patsalis, L. Pereira, B. Peterlin, G. Pielberg, M.J. Prata, C. Previdere, K. Rajczy, L. Roewer, S. Rootsi, D.C. Rubinsztein, J. Saillard, F.R. Santos, M. Shlumukova, G. Stefanescu, B.C. Sykes, A. Tolun, R. Villems, C. Tyler-Smith and M.A. Jobling: Y-chromosomal diversity within Europe is clinal and influenced primarily by geography, rather than by language. American Journal of Human Genetics 67, 1526-1543 (2000).

Saas J., K. Ziegelbauer, A. von Haeseler, B. Fast and M. Boshart: A developmentally regulated aconitase related to iron-regulatory protein 1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei. Journal of Biological Chemistry 275, 2745-2755 (2000).

Santos, F.R., A. Pandya, M. Kayser, R.J. Mitchell, A. Liu, L. Singh, G. Destro-Bisol, A. Novelletto, R. Qamar, S.Q. Mehdi, R. Adhikari, P. de Knijff and C. Tyler-Smith: A

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polymorphic L1 retroposon insertion in the centromere of the human Y chromosome. Human Molecular Genetics 9, 421-430 (2000).

Sheen, F., S.T. Sherry, G.M. Risch, M. Robichaux, I. Nasidze, M. Stoneking, M.A. Batzer and G.D. Swergold: Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Research 10, 1496-1508 (2000).

Stoneking, M: DNA and recent human evolution. In: The Origin of Humankind. (Eds.) M. Aloisi, B. Battaglia, E. Carafoli and G.A. Danieli, IOS Press, Amsterdam, 7 (2000).

Stoneking, M: Hypervariable sites in the mtDNA control region are mutational hotspots. American Journal of Human Genetics 67, 1029-1032 (2000).

Szibor R., M. Kayser and L. Roewer: Identification of the human Y-chromosomal microsatellite locus DYS19 from degraded DNA. American Journal of Forensic Medicine and Pathology 21 (3), 252-254 (2000).

Tishkoff, S.A., A.J. Pakstis, M. Stoneking, J.R. Kidd, G. Destro-Bisol, A. Sajantila, A.S. Deinard, G. Sirugo, T. Jenkins, K.K. Kidd and A.G. Clark: Short tandem-repeat polymorphism/Alu haplotype variation at the PLAT locus: implications for modern human origins. American Journal of Human Genetics 67, 901-925 (2000).

von Haeseler, A.: Maximum likelihood tree reconstruction. Zoology-Analysis of Complex Systems 102, 101-110 (2000).

Weiss, G: Maximum likelihood estimation of genetic diversity. In: Archaeogenetics: DNA and the population prehistory of Europe. (Eds.) C. Renfrew and K. Boyle. McDonald Institute Monographs, University of Cambridge, 279-283 (2000).

Zöllner, S. and A. von Haeseler: A coalescent approach to study linkage disequilibrium between between SNPs. American Journal of Human Genetics 66, 615-628 (2000).

1999

Baake, E. and A. von Haeseler: Distance measures in terms of substitution processes. Theor. Pop. Biol. 55, 116-175 (1999).

Bugawan, T.L., S.J. Mack, M. Stoneking, M. Saha, H.P. Beck and H.A. Erlich: HLA class I allele distributions in six Pacific/Asian populations: evidence of selection at the HLA-A locus. Tissue Antigens 53, 311-319 (1999).

Burckhardt, F., A. von Haeseler and S. Meyer: HvrBase: Compilation of mtDNA control region sequences from primates. Nucl. Acids Res. 27, 138-142 (1999).

Deininger, P.L., S.T. Sherry, G. Risch, C. Donaldson, M.B. Robichaux, H. Soodyall, T. Jenkins, F. Sheen, G. Swergold, M. Stoneking and M.A. Batzer: Interspersed repeat insertion polymorphisms for studies of human molecular anthropology. In: Genomic Diversity: Applications in Human Population Genetics. (Eds.) S.S. Papiha, R. Deka and R. Chakraborty, Plenum Press, New York, NY, 201-212 (1999).

Fujino, T., N. Nararatnam, A. Jamuz, A. von Haeseler and J. Scott: C to U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica. Nucl. Acids Res. 27, 2662-2671 (1999).

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Greenwood, A.D., C. Capelli, G. Possnert and S. Pääbo: Nuclear DNA sequences from Pleistocene megafauna. Mol. Biol. Evol. 16, 1466-1473 (1999).

Greenwood, A.D and S. Pääbo: Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants. Mol. Ecol. 8, 133-137 (1999).

Hofreiter, M.: Möglichkeiten und Grenzen der Analyse archäologischer DNA. In: Beiträge zur Archäozoologie und Prähistorischen Anthropologie, Band II. (Eds.) M. Kokabi and E. May, Verlagsbüro Wais and Partner, Stuttgart (1999).

Kaessmann, H., F. Heißig, A. von Haeseler and S. Pääbo: DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genetics 22, 78-81 (1999).

Kaessmann, H., V. Wiebe and S. Pääbo: Extensive nuclear DNA sequence diversity among chimpanzees. Science 286, 1159-1162 (1999).

Krings, M., H. Geisert, R.W. Schmitz, H. Krainitzki and S. Pääbo: DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. USA 96, 5581-5585 (1999).

Krings, M., A.-H. Salem, K. Bauer, H. Geisert, A.K. Malek, L. Chaix, C. Simon, D. Welsby, A. Di Rienzo, G. Utermann, A. Sajantila, S. Pääbo and M. Stoneking: mtDNA analysis of Nile River Valley populations: a genetic corridor or a barrier to migration? Am. J. Hum. Genet. 64, 1166-1176 (1999).

Meyer, S., G. Weiss and A. von Haeseler: Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152, 1103-1110.

Nasidze, I. and M. Stoneking: Construction of larger-size sequencing templates from degraded DNA. BioTechniques 27, 480-488 (1999).

Pääbo, S.: Human Evolution. Trends Genet. 15(12), M13-M16 (1999).

Pääbo, S.: Neolithic genetic engineering (News and Views). Nature 398, 194-195 (1999).

Poinar, H.N. and B.A. Stankiewicz: Protein preservation and DNA retrieval from ancient tissues. Proc. Natl. Acad. Sci. USA 96, 8426-8431 (1999).

Redd, A.J. and M. Stoneking: Peopling of Sahul: mitochondrial DNA variation in Australian aboriginal and Papua New Guinean populations. American Journal of Human Genetics 65, 808-828 (1999).

Schöniger, M. and A. von Haeseler: Toward Assigning Helical Regions in ribosomal RNA and testing the appropriateness of evolutionary models. J. Mol. Evol. 49, 691-698 (1999).

Stone, A.C. and M. Stoneking: Analysis of ancient DNA from a prehistoric Amerindian cemetery. Philosophical Transactions of the Royal Society of London B 354,153-159 (1999).

Szabo, Z., S.A. Levi-Minzi, A M. Christiano, C. Struminger, M. Stoneking, M.A. Batzer, and C.D. Boyd: Sequential loss of two neighboring exons of the tropoelastin gene during primate evolution. Journal of Molecular Evolution 49, 664-671 (1999).

Vigilant, L. and S. Pääbo: A chimpanzee millenium. Biol. Chem. 380, 1353-1354 (1999).

Von Haeseler, A.: Model based phylogenetic inference. Bolyai Society Mathematical Studies 7, 307-321 (1999).

Von Haeseler, A.: Der Zufall in der Biologie - Molekulare Evolutionstheorie. Nova Acta Leopoldina NF 79, 79-90 (1999).

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Yokobori, S.-I., T. Ueda, G. Feldmaier-Fuchs, S. Pääbo, R. Ueshima, A. Kondow, K. Nishikawa and K. Watanabe: Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, urochordata). Genetics 153, 1851-1862 (1999).

1998

Allen, M., A.-S. Engström, S. Meyer, O. Handt, T. Saldeen, A. von Haeseler, S. Pääbo and U. Gyllensten: Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J. For. Sci. 43(3), 453-464 (1998).

Cao, Y., A. Janke, P.J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Pääbo and M. Hasegawa: Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47, 307-322 (1998).

Castresana, J., G. Feldmaier-Fuchs and S. Pääbo: Codon reassignment and amino acid composition in hemichordate mitochondria. Proc. Natl. Acad. Sci. USA 95, 3703-3707 (1998).

Castresana, J., G. Feldmaier-Fuchs, S.-I. Yokobori, N. Satoh and S. Pääbo: The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 150(3), 1115-1123 (1998).

Gravlund, P., M. Meldgaard, S. Pääbo and P. Arctander: Polyphyletic origin of the small-bodied, high-arctic subspecies of tundra reindeer (Rangifer tarandus). Mol. Phylogenet. Evol. 10, 151-159 (1998).

Handt, O., S. Meyer and A. von Haeseler: Compilation of human mitochondrial control region sequences. Nucl. Acids Res. 26, 126-129 (1998).

Jazin, E., H. Soodyall, P. Jalonen, E. Lindholm, M. Stoneking and U. Gyllensten: Mitochondrial mutation rate revisited: hot spots and polymorphism. Nature Genetics 18, 109-110 (1998).

Laan, M. and S. Pääbo: Mapping genes by drift-generated linkage disequilibrium. Am. J. Hum. Genet. 63, 654-656 (1998).

Melton, T., S. Clifford, J. Martinson, M. Batzer and M. Stoneking: Genetic evidence for the proto-Austronesian homeland in Asia: mitochondrial and nuclear DNA variation in Taiwanese aboriginal tribes. American Journal of Human Genetics 63, 1807-1823 (1998).

Novick, G.E., C.C. Novick, J. Yunis, E. Yunis, P.A. Mayolo, W.D. Scheer, P.L. Deininger, M. Stoneking, D.S. York, M.A. Batzer and R.J. Herrera: Polymorphic Alu insertions and the Asian origin of native American populations. Human Biology 70, 23-39 (1998).

Poinar, H.N., M. Hofreiter, W.G. Spaulding, P.S. Martin, B.A. Stankiewicz, H. Bland, R.P. Evershed, G. Possnert and S. Pääbo: Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281, 402-406 (1998).

Reichert, A., U. Rothbauer and M. Mörl: Processing and Editing of Overlapping tRNAs in Human Mitochondria. J. Biol. Chem. 273, 31977-31984 (1998).

Stone, A.C. and M. Stoneking: MtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. American Journal of Human Genetics 62, 1153-1170 (1998).

Stoneking, M.: Women on the move. Nature Genetics 20, 219-220 (1998).

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Terwilliger, J.D., S. Zöllner, M. Laan and S. Pääbo: Mapping genes through the use of linkeage disequilibrium generated by genetic drift. Human Heredity 48, 138-154 (1998).

Uyenoyama, M.K. and A. von Haeseler (Eds.): Proceedings of the Trinational Workshop on Molecular Evolution. Duke University Publication Group, Durham, N.C. (1998).

Von Haeseler, A. and M. Schöniger: Evolution of DNA and amino acid sequences with dependent sites. J. Comp. Biol. 5, 149-163 (1998).

Weiss, G. and A. von Haeseler: Inference of population history using likelihood ratio statistic. Genetics 149, 1539-1546 (1998).

Zietkiewicz, E., V. Yotova, M. Jarnik, M. Korab-Laskowska, K.K. Kidd, D. Modiano, R. Scozzari, M. Stoneking, S. Tishkoff, M. Batzer and D. Labuda: Genetic structure of the ancestral population of modern humans. Journal of Molecular Evolution 47, 146-155 (1998).

1997

Batzer, M.A., S.T. Sherry, P.L. Deininger and M. Stoneking: Alu repeats and human evolution: a critique (response). Journal of Molecular Evolution 45, 7-8 (1997).

Benes, V., C. Kilger, H. Voss, S. Pääbo and W. Ansorge: Direct primer walking on P1 plasmid DNA. BioTechniques 23, 99-100 (1997).

Börner, G.V., S.-I. Yokobori, M. Mörl, M. Dörner and S. Pääbo: RNA editing in metazoan mitochondria: Staying fit without sex. FEBS Lett. 409, 320-324 (1997).

Cooper, A., H.N. Poinar, S. Pääbo, J. Radovcic, A. Debenath, M. Caparros, C. Barroso-Riuz, J. Bertranpetit, C. Nielsen-Marsh, R.E.M. Hedges and B. Sykes: Neandertal genetics. Science 277, 1021-1025 (1997).

Kilger, C. and S. Pääbo: Direct DNA sequence determination from total genomic DNA. Nucleic Acids Res. 25, 2032-2034 (1997).

Kilger, C. and S. Pääbo: Direct exponential amplification and sequencing (DEXAS) of genomic DNA. Biol. Chem. 378, 99-105 (1997).

Kilger, C., M. Krings, H. Poinar and S. Pääbo: "Colony sequencing": Direct sequencing of plasmid DNA from bacterial colonies. BioTechniques 22, 412-414 (1997).

Krings, M., A. Stone, R.W. Schmitz, H. Krainitzki, M. Stoneking and S. Pääbo: Neandertal DNA sequences and the origin of modern humans. Cell 90, 19-30 (1997).

Laan, M. and S. Pääbo: Demographic history and linkage disequilibrium in human populations. Nature Genetics 17, 435-438 (1997).

Melton, T., C. Ginther, G. Sensabaugh, H. Soodyall and M. Stoneking: Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations. Journal of Forensic Sciences 42, 582-592 (1997).

Melton, T., M. Wilson, M. Batzer and M. Stoneking: Extent of heterogeneity in mitochondrial DNA of European populations. Journal of Forensic Sciences 42, 437-446 (1997).

Petri, B., S. Pääbo, A. von Haeseler and D. Tautz: Paternity assessment and population subdivision in a natural population of the larger mouse-eared bat (Myotis myotis). Molecular Ecology 6, 235-242 (1997).

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Redd, A.J., S.L. Clifford and M. Stoneking: Multiplex DNA typing of short-tandem-repeat loci on the Y chromosome. Biological Chemistry 378, 923-927 (1997).

Sherry, S.T., H.C. Harpending, M.A. Batzer and M. Stoneking: Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics 147, 1977-1982 (1997).

Soodyall, H., T. Jenkins, A. Mukherjee, E. Du Toit, D.F. Roberts and M. Stoneking: The founding mitochondrial DNA lineages of Tristan da Cunha islanders. American Journal of Physical Anthropology 104, 157-166 (1997).

Stoneking, M.: Recent African origin of human mitochondrial DNA: review of the evidence and current status of the hypothesis. In: Progress in Population Genetics and Human Evolution. (Eds.) P. Donnelly and S. Tavaré, Springer-Verlag, New York, 1-13 (1997).

Stoneking, M.: The human genome project and molecular anthropology. Genome Research 7, 87-91 (1997).

Stoneking, M., J.J. Fontius, S.L. Clifford, H. Soodyall, S. Arcot, N. Saha, T. Jenkins, M.A. Tahir, P.L. Deininger and M.A. Batzer: Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Research 7, 1061-1071 (1997).

Strimmer, K. and A. von Haeseler: Likelihood mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proceedings of the National Academy of Sciences of the USA 94, 6815-6819 (1997).

Strimmer, K., N. Goldman and A. von Haeseler: Bayesian Probabilities and Quartet Puzzling. Molecular Biological Evolution 14, 210-211 (1997).

Vingron, M. and A. von Haeseler: Towards integration of multiple alignment and phylogenetic tree construction. Journal of Comparative Biology 4, 23-34 (1997).

Weiss, G. and A. von Haeseler: A coalescent approach to the polymerase chain reaction. Nucleic Acids Research 25, 3082-3087 (1997).

Weiss, G., A. Henking and A. von Haeseler: Distribution of pairwise differences in growing populations. In: Progress in Population Genetics and Human Evolution. (Eds.) P. Donnelly and S. Tavaré, Springer-Verlag, New York. IMA Volumes in Mathematics and its Applications 87, 81-95 (1997).

Yokobori, S.-I. and S. Pääbo: Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr. J. Mol. Biol. 265, 95-99 (1997).

Zietkiewicz, E., V. Yotova, M. Jarnik, M. Korab-Laskowska, K.K. Kidd, D. Modiano, R. Scozzari, M. Stoneking, S. Tishkoff, M. Batzer and D. Labuda: Nuclear DNA diversity in worldwide distributed human populations. Gene 205, 161-171 (1997).

Zulman-Rossi, J., M.A. Batzer, M. Stoneking, O. Delattre and G. Thomas: Inter-ethnic polymorphism of EWS intron 6: genome plasticity mediated by Alu retroposition and recombination. Human Genetics 99, 357-363 (1997).