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Recent Department Publications

Last update: December 20th, 2014

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Abramson, G., Trejo Soto, C. A., & Oña Bubach, L. (2011). The role of asymmetric interactions on the effect of habitat destruction in mutualistic networks. PLoS ONE, 6(6): e21028. doi: 10.1371/journal.pone.0021028
Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schöneberg, T., Carlborg, Ö., Hannon, G. J., & Pääbo, S. (2011). Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107(3), 205-214. doi: 10.1038/hdy.2011.4
Andrés, A. M. (2011). Balancing selection in the human genome. In Encyclopedia of Life Sciences. Chichester: John Wiley & Sons. doi: 10.1002/9780470015902.a0022863
Benazzi, S., Viola, B., Kullmer, O., Fiorenza, L., Harvati, K., Paul, T., Gruppioni, G., Weber, G. W., & Mallegni, F. (2011). A reassessment of the Neanderthal teeth from Taddeo cave (southern Italy). Journal of Human Evolution, 61(4), 377-387. doi: 10.1016/j.jhevol.2011.05.001
Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., McPhee, J. B., DeWitte, S. N., Meyer, M., Schmedes, S., Wood, J., Earn, D. J. D., Herring, D. A., Bauer, P., Poinar, H. N., & Krause, J. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510. doi: 10.1038/nature10549
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F. W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., & Kaessmann, H. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348. doi: 10.1038/nature10532
de Filippo, C., Barbieri, C., Whitten, M., Mpoloka, S. W., Gunnarsdóttir, E. D., Bostoen, K., Nyambe, T., Beyer, K., Schreiber, H., Knijff, P. d., Luiselli, D., Stoneking, M., & Pakendorf, B. (2011). Y-chromosomal variation in sub-saharan Africa: Insights into the history of Niger-Congo groups. Molecular Biology and Evolution, 28(3): msq312v1, pp. 1255-1269. doi: 10.1093/molbev/msq312
Delfin, F., Salvador, J. M., Calacal, G. C., Perdigon, H. B., Tabbada, K. A., Villamor, L. P., Halos, S. C., Gunnarsdóttir, E., Myles, S., Hughes, D. A., Xu, S., Jin, L., Lao, O., Kayser, M., Hurles, M. E., Stoneking, M., & Ungria, M. C. A. d. (2011). The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European Journal of Human Genetics, 19(2), 224-230. doi: 10.1038/ejhg.2010.162
Didelot, X., Bowden, R., Street, T., Golubchik, T., Spencer, C., McVean, G., Sangal, V., Anjum, M. F., Achtman, M., Falush, D., & Donelly, P. (2011). Recombination and population structure in Salmonella enterica. PLoS Genetics, 7(7): e1002191. doi: 10.1371/journal.pgen.1002191
Enard, W. (2011). FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution. Current Opinion in Neurobiology, 21(3), 415-424. doi: 10.1016/j.conb.2011.04.008
Fiorenza, L., Benazzi, S., Viola, B., Kullmer, O., & Schrenk, F. (2011). Relationship Between Cusp Size and Occlusal Wear Pattern in Neanderthal and Homo sapiens First Maxillary Molars. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 294(3), 453-461. doi: 10.1002/ar.21325
Fischer, A., Prüfer, K., Good, J. M., Halbwax, M., Wiebe, V., André, C., Atencia, R., Mugisha, L., Ptak, S. E., & Pääbo, S. (2011). Bonobos fall within the genomic variation of chimpanzees. PLoS ONE, 6(6): e21605, pp. 1-10. doi: 10.1371/journal.pone.0021605
Fu, X., Giavalisco, P., Liu, X., Catchpole, G., Fu, N., Ning, Z.-B., Guo, S., Yan, Z., Somel, M., Pääbo, S., Zeng, R., Willmitzer, L., & Khaitovich, P. (2011). Rapid metabolic evolution in human prefrontal cortex. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6181-6186. doi: 10.1073/pnas.1019164108
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Karsch-Mizrachi, I., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research, 39(Suppl. 1). doi: 10.1093/nar/gkq1173
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Mizrachi, I. K., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Database: the Journal of Biological Databases and Curation, 2011: baq027, pp. 1-6. doi: 10.1093/database/baq027
Gross, A., Tönjes, A., Kovacs, P., Veeramah, K. R., Ahnert, P., Roshyara, N. R., Gieger, C., Rueckert, I.-M., Loeffler, M., Stoneking, M., Wichmann, H.-E., Novembre, J., Stumvoll, M., & Scholz, M. (2011). Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genetics, 12: 67. doi: 10.1186/1471-2156-12-67
Grossmann, T., Johnson, M. H., Vaish, A., Hughes, D. A., Quinque, D., Stoneking, M., & Friederici, A. D. (2011). Genetic and neural dissociation of individual responses to emotional expressions in human infants. Developmental Cognitive Neuroscience, 1(1), 57-66. doi: 10.1016/j.dcn.2010.07.001
Gunnarsdóttir, E. D., Li, M., Bauchet, M., Finstermeier, K., & Stoneking, M. (2011). High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Research, 21(1), 1-11. doi: 10.1101/gr.107615.110
Gunnarsdóttir, E. D., Nandineni, M. R., Li, M., Myles, S., Gil, D., Pakendorf, B., & Stoneking, M. (2011). Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications, 2: 228. doi: 10.1038/ncomms1235
Harrison, A., Lemey, P., Hurles, M., Moyes, C., Horn, S., Pryor, J., Malani, J., Supuri, M., Masta, A., Teriboriki, B., Toatu, T., Penny, D., Rambaut, A., & Shapiro, B. (2011). Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation. Viruses, 3(2), 83-101. doi: 10.3390/v3020083
Herre, H., Hoehndorf, R., Kelso, J., Loebe, F., & Schulz, S. (2011). OBML – Ontologies in biomedicine and life sciences. Journal of Biomedical Semantics, 2(Suppl. 4): I1, pp. 1-6. doi: 10.1186/2041-1480-2-S4-I1
Horn, S., Durka, W., Wolf, R., Ermala, A., Stubbe, A., Stubbe, M., & Hofreiter, M. (2011). Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species. PLoS ONE, 6(1): e14622. doi: 10.1371/journal.pone.0014622
Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., Zeng, R., Chen, W., Pääbo, S., & Khaitovich, P. (2011). MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics, 7(10): e1002327, pp. 1-14. doi: 10.1371/journal.pgen.1002327
Jin, C., Li, J., Green, C. D., Yu, X., Tang, X., Han, D., Xian, B., Wang, D., Huang, X., Cao, X., Yan, Z., Hou, L., Liu, J., Shukeir, N., Khaitovich, P., Chen, C. D., Zhang, H., Jenuwein, T., & Han, J.-D.-J. (2011). Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell Metabolism, 14(2), 161-172. doi: 10.1016/j.cmet.2011.07.001
Ka, S., Albert, F. W., Denbow, D. M., Pääbo, S., Siegel, P. B., Andersson, L., & Hallböök, F. (2011). Differentially expressed genes in hypothalamus in relation to genomic regions under selection in two chicken lines resulting from divergent selection for high or low body weight. Neurogenetics, 12(3), 211-221. doi: 10.1007/s10048-011-0290-9
Kircher, M., Heyn, P., & Kelso, J. (2011). Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12: 382. doi: 10.1186/1471-2164-12-382
Lerner, H. R. L., Meyer, M., James, H. F., Hofreiter, M., & Fleischer, R. C. (2011). Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers. Current Biology, 21(21), 1838-1844. doi: 10.1016/j.cub.2011.09.039
Li, J., Zhang, L., Zhou, H., Stoneking, M., & Tang, K. (2011). Global patterns of genetic diversity and signals of natural selection for human ADME genes. Human Molecular Genetics, 20(3), 528-540. doi: 10.1093/hmg/ddq498
Li, M., & Chen, S.-S. (2011). The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology, 11: 3. doi: 10.1186/1471-2148-11-3
Lippold, S., Knapp, M., Kuznetsova, T., Leonard, J. A., Benecke, N., Ludwig, A., Rasmussen, M., Cooper, A., Weinstock, J., Willerslev, E., Shapiro, B., & Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2: 450, pp. 1-6. doi: 10.1038/ncomms1447
Lippold, S., Matzke, N. J., Reissmann, M., & Hofreiter, M. (2011). Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology, 11: 328. doi: 10.1186/1471-2148-11-328
Liu, Y., Han, D., Han, Y., Yan, Z., Xie, B., Li, J., Qiao, N., Hu, H., Khaitovich, P., Gao, Y., & Han, J.-D.-J. (2011). Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research, 39(4), 1408-1418. doi: 10.1093/nar/gkq956
Myles, S., Lea, R. A., Ohashi, J., Chambers, G. K., Weiss, J. G., Hardouin, E., Engelken, J., Macartney-Coxson, D. P., Eccles, D. A., Naka, I., Kimura, R., Inaoka, T., Matsumura, Y., & Stoneking, M. (2011). Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics, 12(1): 10, pp. 1-7. doi: 10.1186/1471-2350-12-10
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011). Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology, 7: 548. doi: 10.1038/msb.2011.81
Nasidze, I., & Stoneking, M. (2011). Microbiome diversity in human saliva. In F. J. d. Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 335-339). New York: Wiley.
Nasidze, I., Li, J., Schroeder, R., Creasey, J. L., Li, M., & Stoneking, M. (2011). High diversity of the saliva microbiome in Batwa pygmies. PLoS ONE, 6(8): e23352. doi: 10.1371/journal.pone.0023352
Pugach, I., Matveyev, R., Wollstein, A., Kayser, M., & Stoneking, M. (2011). Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biology, 12(2): R19, pp. 1-18. doi: 10.1186/gb-2011-12-2-r19
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A.-M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S., & Stoneking, M. (2011). Denisova admixture and the first modern human dispersals into southeast Asia and Oceania. The American Journal of Human Genetics, 89(4), 516-528. doi: 10.1016/j.ajhg.2011.09.005
Reinartz, R., Lippold, S., Lieckfeldt, D., & Ludwig, A. (2011). Population genetic analyses of Acipenser ruthenus as a prerequisite for the conservation of the uppermost Danube population. Journal of Applied Ichthyology, 27(2), 477-483. doi: 10.1111/j.1439-0426.2011.01693.x
Schönberg, A., Theunert, C., Li, M., Stoneking, M., & Nasidze, I. (2011). High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: High diversity and demographic inferences. European Journal of Human Genetics, 19(9), 988-994. doi: 10.1038/ejhg.2011.62
Stoneking, M., & Krause, J. (2011). Learning about human population history from ancient and modern genomes. Nature Reviews Genetics, 12(9), 603-614. doi: 10.1038/nrg3029
Thalmann, O., Wegmann, D., Spitzner, M., Arandjelovic, M., Guschanski, K., Leuenberger, C., Bergl, R. A., & Vigilant, L. (2011). Historical sampling reveals dramatic demographic changes in western gorilla populations. BMC Evolutionary Biology, 11: 85, pp. 1-10. doi: 10.1186/1471-2148-11-85
Yuan, Y., Chen, Y.-P.-P., Ni, S., Xu, G. A., Tang, L., Vingron, M., Somel, M., & Khaitovich, P. (2011). Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics, 12: 347. doi: 10.1186/1471-2105-12-347