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Recent Department Publications

Last update: September 10, 2014

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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., 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).

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).

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).

Gansauge, M.-T. and M. Meyer: Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research, doi: 10.1101/gr.174201.114 (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., 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).

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).

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 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).

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 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).

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).

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).

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, in press (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).

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).


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).

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).

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).

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, 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).

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).

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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).

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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).

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Dannemann, M., M. Lachmann, A. Lorenc: 'maskBAD' – a package to detect and remove Affymetrix probes with binding affinity differences. BMC Bioinformatics 13:56, doi: 10.1186/1471-2105-13-56 (2012).

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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).

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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).

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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. 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).

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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).

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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. doi:10.1371/journal.pgen.1002947 (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).

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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).

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Xu, Shuhua, 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).

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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).

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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).

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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).

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 (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).

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