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, doi: 10.1093/molbev/msr291 First published online: November 29, 2011.

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. In press.

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. Accepted.

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).

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, 103-11 (2012).

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).

Hevers, W. und H. Lüddens: Pharmakologische und präklinische Grundlagen: Aminosäuren. In: Handbuch der Psychopharmakotherapie. (Eds.) G. Gründer and O. Benkert, Springer-Verlag Berlin Heidelberg, 170-182 (2012).

Kircher, M.: Analysis of high-throughput ancient DNA sequencing data. In: Ancient DNA: Methods and protocols. (Eds.) B. Shapiro and M. Hofreiter, Methods in Molecular Biology, 840, 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. (Eds.) B. Shapiro and M. Hofreiter, Methods in Molecular Biology, 840, 155-170 (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).

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. doi:10.1101/gr.127324.111 (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).

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).

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).

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, doi: 10.1093/molbev/msq312 (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).

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. 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).

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).

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).

Kircher, M., S. Sawyer, M. Meyer: Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research, doi:10.1093/nar/gkr771 (2011).

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).

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).

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).

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: Denosiva 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).

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).

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

2010

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).

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 doi: 10.1093/molbev/msq312 (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).

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, Mingkun, 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, e1404 (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).

Reimers-Kipping, S., W. Hevers, S. Pääbo, W. Enard: Humanized Foxp2 specifically affects cortico-basal ganglia circuits. Neuroscience. doi: 10.1016/j.neuroscience.2010.11.042 (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: MircoRNA, 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. 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).

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, 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).

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, e2209 (2008).

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).

Herráez, D.L. 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, doi:10.1016/j.jhevol.2008.04.010 (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, 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).

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).

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).