Anthropology and Human Genetics

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Comparative Genomics & Evolution of Molecular Circuitries

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Kliesmete, Z., Wange, L. E.,Vieth, B., Esgleas, M., Radmer, J., Hülsmann, M., Geuder, J., Richter, D., Ohnuki, M., M. Götz, I. Hellmann and W. Enard, TRNP1 sequence, function and regulation co-evolve with cortical folding in mammals. bioRxiv, 2021: 2021.02.05.429919.

Parekh, S., B. Vieth, C. Ziegenhain, W. Enard, and I. Hellmann, Strategies for quantitative RNA-seq analyses among closely related species. bioRxiv, 2018: p. 297408.


Janjic, A., Wange, L.E., Bagnoli, J.W., Geuder, J., Nguyen, P., Richter, D., Vieth, B., Vick, B., Jeremias, I., Ziegenhain, C., Hellmann, I. and Enard. W. (2022). Prime-seq, efficient and powerful bulk RNA-sequencing. Genome Biology 23, 88. doi:


Bottcher, A., Buttner, M., Tritschler, S., Sterr, M., Aliluev, A., Oppenlander, L., Burtscher, I., Sass, S., Irmler, M., Beckers, J., Ziegenhain, C., Enard, W., Schamberger, A.C., Verhamme, F.M., Eickelberg, O., Theis, F.J., and Lickert, H. (2021). Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. Nature cell biology 23, 23-31.

Kempf, J., Knelles, K., Hersbach, B.A., Petrik, D., Riedemann, T., Bednarova, V., Janjic, A., Simon-Ebert, T., Enard, W., Smialowski, P., Gotz, M., and Masserdotti, G. (2021). Heterogeneity of neurons reprogrammed from spinal cord astrocytes by the proneural factors Ascl1 and Neurogenin2. Cell Rep 36, 109571.

Porquier, A., Tisserant, C., Salinas, F., Glassl, C., Wange, L., Enard, W., Hauser, A., Hahn, M., and Weiberg, A. (2021). Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea. Genome Biol 22, 225.

Takahashi, K., M. Nakamura, C. Okubo, Z. Kliesmete, M. Ohnuki, M. Narita, A. Watanabe, M. Ueda, Y. Takashima, I.  Hellmann, S. Yamanaka, The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency. PLoS Genet. 2021. 17(5): e1009587.

Kälin R.E., L. Cai, Y. Li, D. Zhao, H. Zhang, J. Cheng, W. Zhang, Y. Wu, K. Eisenhut, P. Janssen, L. Schmitt, W. Enard, F. Michels, C. Flüh, M. Hou, S.V. Kirchleitner, S. Siller, M. Schiemann, I. Andrä, E. Montanez, C. Giachino, V. Taylor, M. Synowitz, J.C. Tonn, L. von Baumgarten, C. Schulz, I. Hellmann, and R. Glass, TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression. Cell Syst. 2021 Feb 9:S2405-4712(21)00036-3.

Geuder, J., L.E. Wange, A. Janjic, J. Radmer, P. Janssen, J.W. Bagnoli, S. Müller, A. Kaul, M. Ohnuki and W. Enard, A non-invasive method to generate induced pluripotent stem cells from primate urine. Scientific Reports 11, 2021. Article number: 3516.


Shami A., D. Atzler, L.A. Bosmans, H. Winkels, S. Meiler, M. Lacy, C. van Tiel, R. Ta Megens, K. Nitz, J. Baardman, P. Kusters, T. Seijkens, C. Buerger, A. Janjic, C. Riccardi, A. Edsfeldt, C. Monaco, M. Daemen, M.P.J. de Winther, J. Nilsson, C. Weber, N. Gerdes, I. Gonçalves, E. Lutgens, Glucocorticoid-induced tumour necrosis factor receptor family-related protein (GITR) drives atherosclerosis in mice and is associated with an unstable plaque phenotype and cerebrovascular events in humans. Eur Heart J. 2020. 41(31): p. 2938-2948.

Alterauge, D., J.W. Bagnoli, F. Dahlstrom, B.M. Bradford, N.A. Mabbott, T. Buch, W. Enard, and D. Baumjohann, Continued Bcl6 Expression Prevents the Transdifferentiation of Established Tfh Cells into Th1 Cells during Acute Viral Infection. Cell Rep, 2020. 33(1): p. 108232.

Kober-Hasslacher, M., H. Oh-Strauss, D. Kumar, V. Soberon, C. Diehl, M. Lech, T. Engleitner, E. Katab, V. Fernandez-Saiz, G. Piontek, H. Li, B. Menze, C. Ziegenhain, W. Enard, R. Rad, J.P. Bottcher, H.J. Anders, M. Rudelius, and M. Schmidt-Supprian, c-Rel gain in B cells drives germinal center reactions and autoantibody production. J Clin Invest, 2020.

Kozak, E.L., S. Palit, J.R. Miranda-Rodriguez, A. Janjic, A. Bottcher, H. Lickert, W. Enard, F.J. Theis, and H. Lopez-Schier, Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2. Curr Biol, 2020. 30(6): p. 1142-1151 e6.

Mereu, E., A. Lafzi, C. Moutinho, C. Ziegenhain, D.J. McCarthy, A. Alvarez-Varela, E. Batlle, Sagar, D. Grun, J.K. Lau, S.C. Boutet, C. Sanada, A. Ooi, R.C. Jones, K. Kaihara, C. Brampton, Y. Talaga, Y. Sasagawa, K. Tanaka, T. Hayashi, C. Braeuning, C. Fischer, S. Sauer, T. Trefzer, C. Conrad, X. Adiconis, L.T. Nguyen, A. Regev, J.Z. Levin, S. Parekh, A. Janjic, L.E. Wange, J.W. Bagnoli, W. Enard, M. Gut, R. Sandberg, I. Nikaido, I. Gut, O. Stegle, and H. Heyn, Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nat Biotechnol, 2020. 38(6): p. 747-755.

Garrett, L., Y.J. Chang, K.M. Niedermeier, T. Heermann, W. Enard, H. Fuchs, V. Gailus-Durner, M.H. Angelis, W.B. Huttner, W. Wurst, and S.M. Holter, A truncating Aspm allele leads to a complex cognitive phenotype and region-specific reductions in parvalbuminergic neurons. Transl Psychiatry, 2020. 10(1): p. 66.

Ebinger, S., C. Zeller, M. Carlet, D. Senft, J.W. Bagnoli, W.H. Liu, M. Rothenberg-Thurley, W. Enard, K.H. Metzeler, T. Herold, K. Spiekermann, B. Vick, and I. Jeremias, Plasticity in growth behavior of patients' acute myeloid leukemia stem cells growing in mice. Haematologica, 2020.

LaClair, K.D., Q. Zhou, M. Michaelsen, B. Wefers, M.S. Brill, A. Janjic, B. Rathkolb, D. Farny, M. Cygan, M.H. de Angelis, W. Wurst, M. Neumann, W. Enard, T. Misgeld, T. Arzberger, and D. Edbauer, Congenic expression of poly-GA but not poly-PR in mice triggers selective neuron loss and interferon responses found in C9orf72 ALS. Acta Neuropathol, 2020. 140(2): p. 121-142.

Redondo Monte, E., A. Wilding, G. Leubolt, P. Kerbs, J.W. Bagnoli, L. Hartmann, W. Hiddemann, L. Chen-Wichmann, S. Krebs, H. Blum, M. Cusan, B. Vick, I. Jeremias, W. Enard, S. Theurich, C. Wichmann, and P.A. Greif, ZBTB7A prevents RUNX1-RUNX1T1-dependent clonal expansion of human hematopoietic stem and progenitor cells. Oncogene, 2020. 39(15): p. 3195-3205.



Vieth, B., S. Parekh, C. Ziegenhain, W. Enard, and I. Hellmann, A systematic evaluation of single cell RNA-seq analysis pipelines. Nat Commun, 2019. 10(1): p. 4667. 10.1038/s41467-019-12266-7.

Wang, S., A.H. Crevenna, I. Ugur, A. Marion, I. Antes, U. Kazmaier, M. Hoyer, D.C. Lamb, F. Gegenfurtner, Z. Kliesmete, C. Ziegenhain, W. Enard, A. Vollmar, and S. Zahler, Actin stabilizing compounds show specific biological effects due to their binding mode. Sci Rep, 2019. 9(1): p. 9731.

Wang, S., F.A. Gegenfurtner, A.H. Crevenna, C. Ziegenhain, Z. Kliesmete, W. Enard, R. Muller, A.M. Vollmar, S. Schneider, and S. Zahler, Chivosazole A Modulates Protein-Protein Interactions of Actin. J Nat Prod, 2019.

Schreiweis, C., T. Irinopoulou, B. Vieth, L. Laddada, F. Oury, E. Burguiere, W. Enard, and M. Groszer, Mice carrying a humanized Foxp2 knock-in allele show region-specific shifts of striatal Foxp2
expression levels. Cortex, 2019.

Gunz, P., A.K. Tilot, K. Wittfeld, A. Teumer, C.Y. Shapland, T.G.M. van Erp, M. Dannemann, B. Vernot, S. Neubauer, T. Guadalupe, G. Fernandez, H.G. Brunner, W. Enard, J. Fallon, N. Hosten, U. Volker, A. Profico, F. Di Vincenzo, G. Manzi, J. Kelso, B. St Pourcain, J.J. Hublin, B. Franke, S. Paabo, F. Macciardi, H.J. Grabe, and S.E. Fisher, Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity. Curr Biol, 2019. 29(1): p. 120-127 e5.

Bagnoli, J.W., L.E. Wange, A. Janjic, and W. Enard, Studying Cancer Heterogeneity by Single-Cell RNA Sequencing. Methods Mol Biol, 2019. 1956: p. 305-319.


Medvedeva, V.P., M.A. Rieger, B. Vieth, C. Mombereau, C. Ziegenhain, T. Ghosh, A. Cressant, W. Enard, S. Granon, J.D. Dougherty, and M. Groszer, Altered social behavior in mice carrying a cortical Foxp2 deletion. Hum Mol Genet, 2018.

Gegenfurtner, F.A., Zisis, T., Danaf, N.A., Schrimpf, W., Kliesmete, Z., Ziegenhain, C., Enard, W., Kazmaier, U., Lamb, D.C., Vollmar, A.M., Zahler, S. 2018. Transcriptional efects of actin‐binding compounds: the cytoplasm sets the tone. Cel. Mol. Life Sci. doi:10.1007/s00018-018-2919-4

W. Bagnoli, J.W., Ziegenhain, C., Janjic, A., Wange, L.E., Vieth, B., Parekh, S., Geuder, J., Hellmann I. & Enard W. 2018. Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nat. Communications. 9. doi:10.1038/s41467-018-05347-6

Nakai, R., Ohnuki, M., Kuroki, K., Ito, H., Hirai, H., Kitajima, R., Fujimoto, T., Nakagawa, M., Enard, W., & Imamura, M. 2018. Derivation of induced pluripotent stem cells in Japanese macaque (Macaca fuscata). Nat. Sci. Rep. 8.

Gegenfurtner, F.A., Jahn, B., Wagner, H., Ziegenhain, C., Enard, W., Geistlinger, L., ..., Zahler, S. 2018. Micropatterning as a tool to identify regulatory triggers and kinetics of actin-mediated endothelial mechanosensing. J. Cell Sci. 131.

Parekh, S., Ziegenhain, C., Vieth, B., Enard, W. & Hellmann, I. 2018. zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs. Gigascience. doi:10.1093/gigascience/giy059

Ziegenhain, C., Vieth, B., Parekh, S., Hellmann, I. & Enard, W. 2018. Quantitative single-cell transcriptomics. Brief. Funct. Genomics. doi:10.1093/bfgp/ely009

Mueller, S., Engleitner, T., Maresch, R., Zukowska, M., Lange, S., Kaltenbacher, T., … , Enard, W., Schmid, R.M., Yang, F., Unger, K., Schneider, G., Varela, I., Bradley, A., Saur, D.,  Rad, R. 2018. Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes. Nature, 554(7690), 62–68.


Regev, A., Teichmann, S., Lander, E., Amit, I., Benoist, C., Birney, E., ..., Enard, W., Human Cell Atlas Meeting Participants, et al. 2017. Science Forum: The Human Cell Atlas. eLife 6 (December).

Garz, A., Wolf, S., Grath, S., Gaidzik, V., Habringer, S., Vick, B., Rudelius, M., Ziegenhain, C., Herold, S., Weickert, M., Smets, M., Peschel, C., Oostendorp, R., Bultmann, S., Jeremias, I., Thiede, C., Döhner, K., Keller, U., Götze, K. 2017. Azacitidine Combined with the Selective FLT3 Kinase Inhibitor Crenolanib Disrupts Stromal Protection and Inhibits Expansion of Residual Leukemia-Initiating Cells in FLT3 -ITD AML with Concurrent Epigenetic Mutations. Oncotarget.

Krendl, C., Shaposhnikov, D., Rishko, V., Ori, C., Ziegenhain, C., Sass, S., Simon, L., ..., Enard, W., Theis, F., Drukker, M. 2017. GATA2/3-TFAP2A/C Transcription Factor Network Couples Human Pluripotent Stem Cell Differentiation to Trophectoderm with Repression of Pluripotency. Proceedings of the National Academy of Sciences of the United States of America 114 (45):E9579–88.

Vieth, B., Ziegenhain, C., Parekh, S., Enard, W., Hellmann, I. (2017) powsimR: Power analysis for bulk and single cell RNA-seq experiments. Bioinformatics 33 (21):3486-3488.

Witzel, M., Petersheim, D., Fan, Y., Bahrami, E., Racek, T., Rohlfs, M., Puchałka, J., ...,  Ziegenhain, C., Enard, W., ..., Klein, C. 2017. Chromatin-Remodeling Factor SMARCD2 Regulates Transcriptional Networks Controlling Differentiation of Neutrophil Granulocytes. Nature Genetics 49 (5):742–52.

Ziegenhain, C., Vieth, B., Parekh, S., Reinius, B., Guillaumet-Adkins, A., Smets, M., Leonhardt, H., Heyn, H., Hellmann, I. and Enard, W. (2017) Comparative Analysis of Single-Cell RNA Sequencing Methods. Molecular Cell 65 (4): 631–43.e4.

Nissen, J., Lykke, K., Bryk, J., Stridh, M., Zaganas, I., Skytt, D., Schousboe, A., Bak, L., Enard, W., Pääbo, S., Waagepetersen, H. 2017. Expression of the Human Isoform of Glutamate Dehydrogenase, hGDH2, Augments TCA Cycle Capacity and Oxidative Metabolism of Glutamate during Glucose Deprivation in Astrocytes. Glia 65 (3):474–88.

Schreck, C., Istvanffy, R., Ziegenhain, C., Sippenauer, T., Ruf, F., Henkel, L., Gartner, F., Vieth, B., Florian, M.C., Mende, N., Taubenberger, A., Prendergast, A., Wagner, A., Pagel, C., Grziwok, S., Gotze, K.S., Guck, J., Dean, D.C., Massberg, S., Essers, M., Waskow, C., Geiger, H., Schiemann, M., Peschel, C., Enard, W., and Oostendorp, R.A. (2017). Niche WNT5A regulates the actin cytoskeleton during regeneration of hematopoietic stem cells. The Journal of experimental medicine 214, 165-181.


Chen, Y.C., Kuo, H.Y., Bornschein, U., Takahashi, H., Chen, S.Y., Lu, K.M., Yang, H.Y., Chen, G.M., Lin, J.R., Lee, Y.H., Chou, Y.C., Cheng, S.J., Chien, C.T., Enard, W., Hevers, W., Paabo, S., Graybiel, A.M., and Liu, F.C. (2016). Foxp2 controls synaptic wiring of corticostriatal circuits and vocal communication by opposing Mef2c. Nature neuroscience 19, 1513-1522.

Li, Q., Guo, S., Jiang, X., Bryk, J., Naumann, R., Enard, W., Tomita, M., Sugimoto, M., Khaitovich, P., and Paabo, S. (2016). Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. Proc Natl Acad Sci U S A 113, 5358-5363.

Huber, C.D., DeGiorgio, M., Hellmann, I., and Nielsen, R. (2016). Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular ecology 25, 142-156.

Nissen, J.D., Lykke, K., Bryk, J., Stridh, M.H., Zaganas, I., Skytt, D.M., Schousboe, A., Bak, L.K., Enard, W., Paabo, S., and Waagepetersen, H.S. (2016). Expression of the human isoform of glutamate dehydrogenase, hGDH2, augments TCA cycle capacity and oxidative metabolism of glutamate during glucose deprivation in astrocytes. Glia 1098-1136. doi:10.1002/glia.23105.

Ebinger, S.*, Ozdemir, E.Z.*, Ziegenhain, C.*, Tiedt, S.*, Castro Alves, C.*, Grunert, M., Dworzak, M., Lutz, C., Turati, V.A., Enver, T., Horny, H.P., Sotlar, K., Parekh, S., Spiekermann, K., Hiddemann, W., Schepers, A., Polzer, B., Kirsch, S., Hoffmann, M., Knapp, B., Hasenauer, J., Pfeifer, H., Panzer-Grumayer, R., Enard, W., Gires, O., and Jeremias, I. (2016). Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia. Cancer cell 30, 849-862.

Enard, W. (2016). The Molecular Basis of Human Brain Evolution. Current Biology Volume 20, Issue 20: pR1109–R1117.

Ziegenhain, C., Parekh, S., Vieth, B., Smets, M., Leonhardt, H., Hellmann, I., and Enard, W. (2016). Comparative analysis of single-cell RNA-sequencing methods.

Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., and Hellmann, I. (2016). The impact of amplification on differential expression analyses by RNA-seq. Scientific Reports 6, Article number:25533. 

DeGiorgio, M., Huber, C.D., Hubisz, M.J., Hellmann, I., and Nielsen, R. (2016). SWEEPFINDER2: Increased sensitivity, robustness, and flexibility. Bioinformatics. 


Humphrey, S.J., Azimifar, S.B., and Mann, M. (2015). High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics. Nature Biotechnology 33, 990-995.

Ohnuki, M., and Takahashi, K. (2015). Present and future challenges of induced pluripotent stem cells. Philos Trans R Soc Lond B Biol Sci 370, 20140367.

Hammerschmidt, K., Schreiweis, C., Minge, C., Paabo, S., Fischer, J., and Enard, W. (2015). A humanized version of Foxp2 does not affect ultrasonic vocalization in adult mice. Genes, brain, and behavior 14, 583-590.

Enard, W. (2015). Human evolution: enhancing the brain. Curr Biol 25, R421-423.

Huber, C., DeGiogio, M., Hellmann, I. and Nielsen, R. (2015). Detecting recent selective sweeps while controlling for mutation rate and background selection. Mol Ecol.



Enard, W. (2014). Mouse models of human evolution. Curr Opin Genet Dev 29C, 75-80. doi: 10.1016/j.gde.2014.08.008

Schreiweis, C., Bornschein, U., Burguiere, E., Kerimoglu, C., Schreiter, S., Dannemann, M., Goyal, S., Rea, E., French, C.A., Puliyadi, R., Groszer, M., Fisher, S.E., Mundry, R., Winter, C., Hevers, W., Paabo, S., Enard*, W., and Graybiel*, A.M. (2014). Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. Proc Natl Acad Sci USA.

Huber, C.D., Nordborg, M., Hermisson, J., and Hellmann, I. (2014). Keeping it Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana. Molecular biology and evolution.

Enard, W. (2014). Comparative genomics of brain size evolution. Front. Hum. Neursci. 8:345, doi:10.3389/fnhum.2014.00345.

Wunderlich, S., Kircher, M., Vieth, B., Haase, A., Merkert, S., Beier, J., Göhring, G., Glage, S., Schambach, A., Curnow, WE.C., Pääbo, S., Martin, U., and Enard, W. (2014). Primate iPS cells as tools for evolutionary analyses. Stem Cell Research,

Prufer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P.H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J.C., Vohr, S.H., Green, R.E., Hellmann, I., Johnson, P.L., Blanche, H., Cann, H., Kitzman, J.O., Shendure, J., Eichler, E.E., Lein, E.S., Bakken, T.E., Golovanova, L.V., Doronichev, V.B., Shunkov, M.V., Derevianko, A.P., Viola, B., Slatkin, M., Reich, D., Kelso, J., and Paabo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43-49. doi: 10.1038/nature12886


Long, Q., Rabanal, F.A., Meng, D., Huber, C.D., Farlow, A., Platzer, A., Zhang, Q., Vilhjalmsson, B.J., Korte, A., Nizhynska, V., Voronin, V., Korte, P., Sedman, L., Mandakova, T., Lysak, M.A., Seren, U., Hellmann, I., and Nordborg, M. (2013). Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45, 884-890. doi: 10.1038/ng.2678


Clovis, Y.M., Enard, W., Marinaro, F., Huttner, W.B., and De Pietri Tonelli, D. (2012). Convergent repression of Foxp2 3'UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons. Development 139, 3332-3342,

Enard, W. (2012). Functional primate genomics--leveraging the medical potential. J Mol Med (Berl) 90, 471-480,

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

Fietz, S.A., Lachmann, R., Brandl, H., Kircher, M., Samusik, N., Schroder, R., Lakshmanaperumal, N., Henry, I., Vogt, J., Riehn, A., Distler, W., Nitsch, R., Enard, W., Paabo, S., and Huttner, W.B. (2012). Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc Natl Acad Sci U S A 109, 11836-11841,

Maricic, T., Gunther, V., Georgiev, O., Gehre, S., Curlin, M., Schreiweis, C., Naumann, R., Burbano, H.A., Meyer, M., Lazuela-Fox, C., de la Rasilla, M., Rosas, A., Gajovic, S., Kelso, J., Enard, W., Schaffner, W., and Paabo, S. (2012). A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene. Mol Biol Evol,


Lohmueller, K.E., Albrechtsen, A., Li, Y., Kim, S.Y., Korneliussen, T., Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Feder, A.F., Grarup, N., Jorgensen, T., Jiang, T., Witte, D.R., Sandbaek, A., Hellmann, I., Lauritzen T., Hansen, T., Pedersen, O., Wang, J., and  Nielsen, R. (2011). Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 7, e1002326,

Enard, W. (2011). FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution. Curr Opin Neurobiol 21, 415-424,

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

Johnson, P.L., and Hellmann, I. (2011). Mutation rate distribution inferred from coincident SNPs and coincident substitutions. Genome Biol Evol 3, 842-850,


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

Li, Y., Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Jiang, T., Jiang, H., Albrechtsen, A., Andersen, G., Cao, H., Korneliussen, T., Grarup, N., Guo, Y., Hellmann, I., Jin, X., Li, Q., Liu, J., Liu, X., Sparso, T., Tang, M., Wu, H., Wu, R., Yu, C., Zheng, H., Astrup, A., Bolund, L., Holmkvist, J., Jorgensen, T., Kristiansen, K., Schmitz, O., Schwartz, T.W., Zhang, X., Li, R., Yang, H., Wang, J., Hansen, T., Pedersen, O., Nielsen, R., and Wang, J. (2010). Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42, 969-972,

Pool, J.E., Hellmann, I., Jensen, J.D., and Nielsen, R. (2010). Population genetic inference from genomic sequence variation. Genome Res 20, 291-300,

Staubert, C., Boselt, I., Bohnekamp, J., Rompler, H., Enard, W., and Schoneberg, T. (2010). Structural and functional evolution of the trace amine-associated receptors TAAR3, TAAR4 and TAAR5 in primates. PLoS One 5, e11133,


Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z.,  Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D., Li, R., Cheng, T., Jiang, T., Becquet, C., Xu, X., Liu, C., Zha, X., Fan, W., Lin, Y., Shen, Y., Jiang, L., Jensen, J., Hellmann, I., Tang, S., Zhao, P., Xu, H., Yu, C., Zhang, G., Li, J., Cao, J., Liu, S., He, N., Zhou, Y., Liu, H., Zhao, J., Ye, C., Du, Z., Pan, G., Zhao, A., Shao, H., Zeng, W., Wu, P., Li, C., Pan, M., Li, J., Yin, X., Li, D., Wang, J., Zheng, H., Wang, W., Zhang, X., Li, S., Yang, H., Lu, C., Nielsen, R., Zhou, Z., Wang, J., Xiang, Z., Wang, J. (2009). Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326, 433-436,

Ptak, S.E., Enard, W., Wiebe, V., Hellmann, I., Krause, J., Lachmann, M., and Paabo, S. (2009). Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol 26, 2181-2184,

Dannemann, M., Lorenc, A., Hellmann, I., Khaitovich, P., and Lachmann, M. (2009). The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 25, 2772-2779,

Enard, W., Gehre, S., Hammerschmidt, K., Hölter, S.M., Blass, T., Somel, M., Brückner, M.K., Schreiweis, C., Winter, C., Sohr, R., Becker, L., Wiebe, V., Nickel, B., Giger, T., Müller, U., Groszer, M., Adler, T., Aguilar, A., Bolle, I., Calzada-Wack, J., Dalke, C., Ehrhardt, N., Favor, J., Fuchs, H., Gailus-Durner, V., Hans, W., Hölzlwimmer, G., Javaheri, A., Kalaydjiev, S., Kallnik, M., Kling, E., Kunder, S., Moßbrugger, I., Naton, B., Racz, I., Rathkolb, B., Rozman, J., Schrewe, A., Busch, D.H., Graw, J., Ivandic, B., Klingenspor, M., Klopstock, T., Ollert, M., Quintanilla-Martinez, L., Schulz, H., Wolf, E., Wurst, W., Zimmer, A., Fisher, S.E., Morgenstern, R., Arendt, T., Hrabé de Angelis, M., Fischer, J., Schwarz, J., and Pääbo, S. (2009). A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 137, 961-971,

Nielsen, R., Hubisz, M.J., Hellmann, I., Torgerson, D., Andres, A.M., Albrechtsen, A., Gutenkunst, R., Adams, M.D., Cargill, M., Boyko, A., Indap, A., Bustamante, C.D., and Clark, A.G. (2009). Darwinian and demographic forces affecting human protein coding genes. Genome Res 19, 838-849,


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Hellmann, I., Mang, Y., Gu, Z., Li, P., de la Vega, F.M., Clark, A.G., and Nielsen, R. (2008). Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res 18, 1020-1029,


Krause, J., Lalueza-Fox, C., Orlando, L., Enard, W., Green, R.E., Burbano, H.A., Hublin, J.J., Hänni, C., Fortea, J., de la Rasilla, M., Bertranpetit, J., Rosas, A., and Paabo, S. (2007). The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17, 1908-1912,

Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., and Clark, A.G. (2007). Recent and ongoing selection in the human genome. Nat Rev Genet 8, 857-868,

Francks, C., Maegawa, S., Lauren, J., Abrahams, B.S., Velayos-Baeza, A., Medland, S.E., Colella, S., Groszer, M., McAuley, E.Z., Caffrey, T.M., Timmusk, T., Pruunsild, P., Koppel, I., Lind, P.A., Matsumoto-Itaba, N., Nicod, J., Xiong, L., Joober, R., Enard, W., Krinsky, B., Nanba, E., Richardson, A.J., Riley, B.P., Martin, N.G., Strittmatter, S.M., Möller, H.J., Rujescu, D., St Clair, D., Muglia, P., Roos, J.L., Fisher, S.E., Wade-Martins, R., Rouleau, G.A., Stein, J.F., Karayiorgou, M., Geschwind, D.H., Ragoussis, J., Kendler, K.S., Airaksinen, M.S., Oshimura, M., DeLisi, L.E., and Monaco, A.P. (2007). LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Mol Psychiatry 12, 1129-1139, 1057,

Timpson, N., Heron, J., Smith, G.D., and Enard, W. (2007). Comment on papers by Evans et al. and Mekel-Bobrov et al. on Evidence for Positive Selection of MCPH1 and ASPM. Science 317, 1036; author reply 1036,

Weber, M., Hellmann, I., Stadler, M.B., Ramos, L., Paabo, S., Rebhan, M., and Schubeler, D. (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457-466,

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


Khaitovich, P., Enard, W., Lachmann, M., and Paabo, S. (2006a). Evolution of primate gene expression. Nat Rev Genet 7, 693-702,

Khaitovich, P., Tang, K., Franz, H., Kelso, J., Hellmann, I., Enard, W., Lachmann, M., and Paabo, S. (2006b). Positive selection on gene expression in the human brain. Curr Biol 16, R356-358,

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

Fish, J.L., Kosodo, Y., Enard, W., Paabo, S., and Huttner, W.B. (2006). Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells. Proc Natl Acad Sci U S A 103, 10438-10443,


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

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

Woods, C.G., Bond, J., and Enard, W. (2005). Autosomal recessive primary microcephaly (MCPH): a review of clinical, molecular, and evolutionary findings. Am J Hum Genet 76, 717-728,

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


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

Khaitovich, P., Weiss, G., Lachmann, M., Hellmann, I., Enard, W., Muetzel, B., Wirkner, U, Ansorge, W., and Paabo, S. (2004a). A neutral model of transcriptome evolution. PLoS Biol 2, E132,

Enard, W., Fassbender, A., Model, F., Adorjan, P., Paabo, S., and Olek, A. (2004). Differences in DNA methylation patterns between humans and chimpanzees. Curr Biol 14, R148-149,

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

Enard, W., and Paabo, S. (2004). Comparative primate genomics. Annu Rev Genomics Hum Genet 5, 351-378,


Hellmann, I., Zollner, S., Enard, W., Ebersberger, I., Nickel, B., and Paabo, S. (2003a). Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res 13, 831-837,

Hellmann, I., Ebersberger, I., Ptak, S.E., Paabo, S., and Przeworski, M. (2003b). A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet 72, 1527-1535,


Enard, W., Przeworski, M., Fisher, S.E., Lai, C.S., Wiebe, V., Kitano, T., Monaco, A.P., and Paabo, S. (2002a). Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869-872,

Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., Doxiadis, G.M., Bontrop, R.E., and Paabo, S. (2002b). Intra- and interspecific variation in primate gene expression patterns. Science 296, 340-343,


Straube, A., Enard, W., Berner, A., Wedlich-Soldner, R., Kahmann, R., and Steinberg, G. (2001). A split motor domain in a cytoplasmic dynein. Embo J 20, 5091-5100,