Computational and RNA Biology

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  1. 2014
  2. Published

    Genome-wide analysis of noncoding regulatory mutations in cancer

    Weinhold, N., Skanderup, A. M. J., Schultz, N., Sander, C. & Lee, W., 2014, In: Nature Genetics. 46, 11, p. 1160-1165 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., Andersson, R., Jones, P. A., Hoover, C. A., Tikhonov, A., Prokhortchouk, E., Rubin, E. M., Sandelin, A. G., Gilbert, M. T. P., Krogh, A., Willerslev, E. & 1 others, Orlando, L. A. A., 2014, In: Genome Research. 24, 3, p. 454-466 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Genomic structure in Europeans dating back at least 36,200 years

    Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A. S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., Goebel, T., Westaway, M., Lambert, D., Khartanovich, V., Wall, J. D., Nigst, P. R., Foley, R. A., Lahr, M. M., Nielsen, R., Orlando, L. A. A. & 1 others, Willerslev, Eske, 2014, In: Science. 346, 6213, p. 1113-1118 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    High-Throughput Sequencing Based Methods of RNA Structure Investigation

    Kielpinski, L. J., 2014, Department of Biology, Faculty of Science, University of Copenhagen. 137 p.

    Research output: Book/Report › Ph.D. thesis › Research

  6. Published

    Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

    Lykke-Andersen, S., Chen, Y., Ardal, B., Lilje, B., Waage, J. E., Sandelin, Albin Gustav & Jensen, T. H., 2014, In: Genes & Development. 28, p. 2498-2517 20 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

    Jønson, L., Christiansen, Jan, Hansen, Thomas van Overeem, Vikeså, J., Yamamoto, Y. & Nielsen, Finn Cilius, 2014, In: Cell Reports. 7, 2, p. 539-551 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2

    Boyd, M., Coskun, M., Lilje, B., Andersson, Robin, Hoof, I., Lange, Jette Bornholdt, Dahlgaard, K., Olsen, Jørgen, Vitezic, M., Bjerrum, Jakob Tveiten , Seidelin, Jakob Benedict, Nielsen, Ole Haagen, Troelsen, J. & Sandelin, Albin Gustav, 2014, In: D N A Research. 21, 6, p. 569-583 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    Olsen, Morten Tange, Andersen, L. W., Dietz, R., Teilmann, J., Härkönen, T. & Siegismund, Hans Redlef, 2014, In: Molecular Ecology. 23, 4, p. 815-831 17 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Involvement of CDX2 in the cross talk between TNF-α and Wnt signaling pathway in the colon cancer cell line Caco-2

    Coskun, M., Olsen, A. K., Bzorek, M., Holck, S., Engel, U. H., Nielsen, Ole Haagen & Troelsen, J. T., 2014, In: Carcinogenesis. 35, 5, p. 1185-1192 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Is diagnosability an indicator of speciation? Response to "Why one century of phenetics is enough"

    Heller, Rasmus, Frandsen, P., Lorenzen, Eline & Siegismund, Hans Redlef, 2014, In: Systematic Biology. 63, 5, p. 833-837 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

    Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C., Chou, A., Ienasescu, H., Lim, J., Shyr, C., Tan, G., Zhou, M., Lenhard, B., Sandelin, Albin Gustav & Wasserman, W. W., 2014, In: Nucleic Acids Research. 42, p. D142-D147 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

    Kielpinski, L. J. & Vinther, Jeppe, 2014, In: Nucleic Acids Research. 42, 8, 12 p., e70.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma

    Larsen, A., Holst, L. M., Kaczkowski, B., Andersen, M. T., Manfé, V., Siersma, Volkert Dirk, Kolko, Miriam, Kiilgaard, Jens Folke, Winther, Ole, Prause, J. U., Gniadecki, R. & Heegaard, Steffen, 2014, In: Acta Ophthalmologica. 92, 6, p. 541-549

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Modification of T cell responses by stem cell mobilization requires direct signaling of the T cell by G-CSF and IL-10

    MacDonald, K. P. A., Le Texier, L., Zhang, P., Morris, H., Kuns, R. D., Lineburg, K. E., Leveque, L., Don, A. L., Markey, K. A., Vuckovic, S., Bagger, F. O., Boyle, G. M., Blazar, B. R. & Hill, G. R., 2014, In: Journal of Immunology. 192, 7, p. 3180-3189 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Molecular architecture of transcription factor hotspots in early adipogenesis

    Siersbæk, R., Baek, S., Rabiee, A., Nielsen, R., Traynor, S., Clarke, N., Sandelin, Albin Gustav, Jensen, O. N., Sung, M., Hager, G. L. & Mandrup, S., 2014, In: Cell Reports. 7, 5, p. 1434-1442 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Nuclear stability and transcriptional directionality separate functionally distinct RNA species

    Andersson, Robin, Refsing Andersen, P., Valen, E., Core, L. J., Lange, Jette Bornholdt, Boyd, M., Jensen, T. H. & Sandelin, Albin Gustav, 2014, In: Nature Communications. 5, 10 p., 5336.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    On detecting incomplete soft or hard selective sweeps using haplotype structure

    Ferrer-Admetlla, A., Liang, M., Korneliussen, Thorfinn Sand & Nielsen, Rasmus, 2014, In: Molecular Biology and Evolution. 31, 5, p. 1275-1291 17 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    Oncogenic fusion proteins expressed in immature hematopoietic cells fail to recapitulate the transcriptional changes observed in human AML

    Rapin, N. & Porse, Bo Torben, 2014, In: Oncogenesis. 3, p. 1-5 5 p., e106.

    Research output: Contribution to journal › Letter › Research › peer-review

  20. Published

    Pharmaco-miR: linking microRNAs and drug effects

    Rukov, J. L., Wilentzik, R., Jaffe, I., Vinther, Jeppe & Shomron, N., 2014, In: Briefings in Bioinformatics. 15, 4, p. 648-659 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

    Liu, S., Lorenzen, E., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., Wray, G., Li, J., He, W., Wang, Z., Fu, W., Xiang, X., Morgan, C. C., Doherty, A., O'Connell, M. J., McInerney, J. O. & 9 others, Born, E. W., Dalén, L., Dietz, R., Orlando, L. A. A., Sonne, C., KU, thw266, Nielsen, Rasmus, Willerslev, Eske & Wang, J., 2014, In: Cell. 157, 4, p. 785-794 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Prehistoric genomes reveal the genetic foundation and cost of horse domestication

    Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., Fumagalli, M., Raghavan, M., Seguin-Orlando, A., Korneliussen, T. S., Velazquez, A. M. V., Stenderup, J., Hoover, C. A., Rubin, C-J., Alfarhan, A. H., Alquraishi, S. A. & 15 others, Al-Rasheid, K. A. S., MacHugh, D. E., Kalbfleisch, T., MacLeod, J. N., Rubin, E. M., Sicheritz-Ponten, T., Andersson, L., Hofreiter, M., Marques-Bonet, T., Gilbert, M Thomas P, Nielsen, R., Excoffier, L., Willerslev, Eske, Shapiro, B. & Orlando, L. A. A., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 52, p. E5661–E5669 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Probabilistic determination of native state ensembles of proteins

    Olsson, S., Vögeli, B. R., Cavalli, A., Boomsma, Wouter, Ferkinghoff-Borg, J., Lindorff-Larsen, Kresten & Hamelryck, Thomas Wim, 2014, In: Journal of Chemical Theory and Computation. 10, 8, p. 3484-3491 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

    Ohmiya, H., Vitezic, M., Frith, M. C., Itoh, M., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Lassmann, T. & The FANTOM Consortium, T. F. C., 2014, In: B M C Genomics. 15, 15 p., 269.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

    Cao, H., Hastie, A. R., Cao, D., Lam, E. T., Sun, Y., Huang, H., Liu, X., Lin, L., Andrews, W., Chan, S., Huang, S., Tong, X., Requa, M., Anantharaman, T., Krogh, Anders, Yang, H., Cao, H. & Xu, X., 2014, In: GigaScience. 3, 11 p., 34.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    RelateAdmix: a software tool for estimating relatedness between admixed individuals

    Moltke, Ida & Albrechtsen, Anders, 2014, In: Bioinformatics. 30, 7, p. 1027-1028 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Published

    Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling

    Lindgreen, S., Umu, S. U., Lai, A. S., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N. E., Biggs, P. J., Thomson, N. R., Barquist, L., Poole, A. M. & Gardner, P. P., 2014, In: P L o S One. 10, 10, 10 p., e1003907.

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    SNPest: a probabilistic graphical model for estimating genotypes

    Lindgreen, S., Krogh, Anders & Pedersen, J. S., 2014, In: BMC Research Notes. 7, 12 p., 298.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Speciation with gene flow in equids despite extensive chromosomal plasticity

    Jónsson, H., Schubert, M., Seguin-Orlando, A., Ginolhac, A., Petersen, L., Fumagalli, M., Albrechtsen, A., Petersen, B., Korneliussen, T. S., Mouatt, J. T. V., Lear, T., Myka, J. L., Lundquist, J., Miller, D. C., Alfarhan, A. H., Alquraishi, S. A., Al-Rasheid, K. A. S., Stagegaard, J., Strauss, G., Bertelsen, M. F. & 6 others, Sicheritz-Ponten, T., Antczak, D. F., Bailey, E., Nielsen, R., Willerslev, Eske & Orlando, L. A. A., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 52, p. 18655–18660 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    Telomerase inhibition effectively targets mouse and human AML stem cells and delays relapse following chemotherapy

    Bruedigam, C., Bagger, F. O., Heidel, F. H., Kuhn, C. P., Guignes, S., Song, A., Austin, R., Vu, T., Lee, E., Riyat, S., Moore, A. S., Lock, R. B., Bullinger, L., Hill, G. R., Armstrong, S. A., Williams, D. A. & Lane, S. W., 2014, In: Cell Stem Cell. 15, 6, p. 775-790 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    The genetic prehistory of the New World Arctic

    Raghavan, M., DeGiorgio, M., Albrechtsen, A., Moltke, I., Skoglund, P., Korneliussen, T. S., Grønnow, B., Appelt, M., Gulløv, H. C., Friesen, T. M., Fitzhugh, W., Malmström, H. S., Rasmussen, S., Olsen, J., Melchior, L. C., Fuller, B. T., Fahrni, S. M., Stafford jr., T., Grimes, V., Renouf, M. A. P. & 36 others, Cybulski, J., Lynnerup, Niels, Lahr, M. M., Britton, K., Knecht, R., Arneborg, J., Metspalu, M., Cornejo, O. E., Malaspinas, A. S., Wang, Y., Rasmussen, M., Raghavan, V., Hansen, Thomas van Overeem, Khusnutdinova, E., Pierre, T. L., Dneprovsky, K., Andreasen, C., Lange, H., Hayes, M. G., Coltrain, J., Spitsyn, V. A., Götherström, A., Orlando, L. A. A., Kivisild, T., Villems, R., Crawford, M. H., Nielsen, Finn Cilius, Dissing, J., Heinemeier, J., Meldgaard, Morten, Bustamante, C., O'Rourke, D. H., Jakobsson, M., Gilbert, M Thomas P, Nielsen, R. & Willerslev, Eske, 2014, In: Science. 345, 6200, 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    The genome of a Late Pleistocene human from a Clovis burial site in western Montana

    Rasmussen, M., Anzick, S. L., Waters, M. R., Skoglund, P., DeGiorgio, M., Stafford jr., T., Rasmussen, S., Moltke, I., Albrechtsen, A., Doyle, S. M., Poznik, G. D., Gudmundsdottir, V., Yadav, R., Malaspinas, A. S., White, S. S., Allentoft, M. E., Cornejo, O. E., Tambets, K., Eriksson, A., Heintzman, P. D. & 22 others, Karmin, M., Korneliussen, Thorfinn Sand, Meltzer, D. J., Pierre, T. L., Stenderup, Jesper Tandberg, Saag, L., Warmuth, V. M., Lopes, M. C., Malhi, R. S., Brunak, S., Sicheritz-Pontén, T., Barnes, I., Collins, M., Orlando, L. A. A., Balloux, F., Manica, A., Gupta, R., Metspalu, M., Bustamante, C. D., Jakobsson, M., Nielsen, R. & Willerslev, Eske, 2014, In: Nature. 506, 7487, p. 225-229 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  33. Published

    Toward Larger DNA Origami

    Marchi, A. N., Saaem, I., Vogen, B. N., Brown, Stanley & LaBean, T. H., 2014, In: Nano Letters. 14, 10, p. 5740-5747 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions

    Davis, M. R., Andersson, Robin, Severin, J., de Hoon, M., Bertin, N., Baillie, J. K., Kawaji, H., Sandelin, Albin Gustav, Forrest, A. R. R. & Summers, K. M., 2014, In: Molecular Genetics and Metabolism. 112, 3, p. 73-83 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

    Olsen, L. R., Campos, B., Winther, Ole, Sgroi, D. C., Karger, B. L. & Brusic, V., 2014, In: B M C Medical Genomics. 7, 3, p. 1-13 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. Published

    Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Malaspinas, A. S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P., Sagredo, F. S., Rasmussen, S., Gonçalves, V. F., Albrechtsen, A., Allentoft, M. E., Johnson, P. L. F., Li, M., Reis, S., Bernardo, D. V., DeGiorgio, M., Duggan, A. T., Bastos, M., Wang, Y. & 20 others, Stenderup, Jesper Tandberg, Moreno Mayar, J. Víctor, Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G. J., Orlando, L. A. A., Price, T. D., Jensen, J. D., Nielsen, Rasmus, Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M. M., Neves, W. A., Kayser, M., Higham, T., Stoneking, M., Pena, S. D. J. & Willerslev, Eske, 2014, In: Current biology : CB. 24, 21, p. R1035-R1037 3 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Upper palaeolithic Siberian genome reveals dual ancestry of Native Americans

    Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford jr., T., Orlando, L. A. A., Metspalu, E., Karmin, M., Tambets, K., Rootsi, S., Mägi, R., Campos, P., Balanovska, E., Balanovsky, O., Khusnutdinova, E., Litvinov, S., Osipova, L. P. & 11 others, Fedorova, S. A., Voevoda, M. I., Degiorgio, M., Sicheritz-Ponten, T., Brunak, S., Demeshchenko, S., Kivisild, T., Villems, R., Nielsen, R., Jakobsson, M. & Willerslev, Eske, 2014, In: Nature. 505, 7481, p. 87-91 4 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  38. Published

    Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

    Li, S., Besenbacher, S., Li, Y., Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, T. H., Korneliussen, Thorfinn Sand, Hansen, Torben, Wang, J., Nielsen, Rasmus, Pedersen, Oluf Borbye, Bolund, L. & Schierup, M. H., 2014, In: European Journal of Human Genetics. 22, p. 1040-1045 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. Published

    Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

    Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Ling-Hu, C., Zhou, H., Lin, H., Gonzalez-Morales, S., Trejo-Saavedra, D. L., Tian, H. & 53 others, Tang, X., Zhao, M., Huang, Z., Zhou, A., Yao, X., Cui, J., Li, W., Chen, Z., Feng, Y., Niu, Y., Bi, S., Yang, X., Li, W., Cai, H., Luo, X., Montes-Hernandez, S., Leyva-Gonzalez, M. A., Xiong, Z., He, X., Bai, L., Tan, S., Tang, X., Liu, D., Liu, J., Zhang, S., Chen, M., Zhang, L., Zhang, L., Zhang, Y., Liao, W., Zhang, Y., Wang, M., Lv, X., Wen, B., Liu, H., Luan, H., Zhang, Y., Yang, S., Wang, X., Xu, J., Li, X., Li, S., Wang, J., Palloix, A., Bosland, P. W., Li, Y., Krogh, Anders, Rivera-Bustamante, R. F., Herrera-Estrella, L., Yin, Y., Yu, J., Hu, K. & Zhang, Z., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 14, p. 5135-5140 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  40. Published

    spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

    Vitting-Seerup, K., Porse, Bo Torben, Sandelin, Albin Gustav & Waage, J., 2014, In: B M C Bioinformatics. 15, p. 1-7 7 p., 81.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. 2013
  42. Published

    Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes

    Lohmueller, K. E., Sparsø, T. H., Li, Q., Galijatovic, E. A. A., Korneliussen, T. S., Albrechtsen, A., Banasik, K., Grarup, N., Hallgrimsdottir, I., Kiil, K., Oskari Kilpeläinen, T., Krarup, N. T., Pers, T. H., Sanchez, G., Hu, Y., DeGiorgio, M., Jørgensen, T., Sandbæk, A., Lauritzen, T., Brunak, S. & 6 others, Kristiansen, Karsten, Li, Y., Hansen, Torben, Wang, J., Nielsen, Rasmus & Pedersen, Oluf Borbye, 5 Dec 2013, In: American Journal of Human Genetics. 93, 6, p. 1072-1086 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Bacterial natural transformation by highly fragmented and damaged DNA

    Overballe-Petersen, S., Harms, K., Orlando, L. A. A., Moreno Mayar, J. Víctor, Rasmussen, Simon, Dahl, Tais Wittchen, Rosing, Minik Thorleif, Poole, A. M., Sicheritz-Ponten, T., Brunak, S., Inselmann, S., de Vries, J., Wackernagel, W., Pybus, O. G., Nielsen, Rasmus, Johnsen, P. J., Nielsen, K. M. & Willerslev, Eske, 3 Dec 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 49, p. 19860–19865 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. Published

    Estimating individual admixture proportions from next generation sequencing data

    Skotte, L., Korneliussen, Thorfinn Sand & Albrechtsen, Anders, Nov 2013, In: Genetics. 195, 3, p. 693-702 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Quantifying population genetic differentiation from next-generation sequencing data

    Fumagalli, M., Vieira, Filipe Garrett, Korneliussen, Thorfinn Sand, Linderoth, T., Huerta-Sánchez, E., Albrechtsen, Anders & Nielsen, Rasmus, Nov 2013, In: Genetics. 195, 3, p. 979-992 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. Published

    DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

    Norregaard, K., Andersson, M., Sneppen, Kim, Nielsen, Peter E., Brown, Stanley & Oddershede, L. B., 22 Oct 2013, In: Proceedings of the National Academy of Sciences USA (PNAS). 110, 43, p. 17386-91 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Published

    Lack of the p42 form of C/EBPα leads to spontaneous immortalization and lineage infidelity of committed myeloid progenitors

    Schuster, Mikkel Bruhn, Frank, Anne-Katrine, Bagger, F. O., Rapin, N., Vikesaa, J. & Porse, Bo Torben, Oct 2013, In: Experimental Hematology. 41, 10, p. 882-893 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Published

    MiR-492 impairs the angiogenic potential of endothelial cells

    Patella, F., Leucci, E., Evangelista, M., Parker, B., Wen, J., Mercatanti, A., Rizzo, M., Chiavacci, E., Lund, Anders H. & Rainaldi, G., Aug 2013, In: Journal of Cellular and Molecular Medicine. 17, 8, p. 1006-15 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Published

    Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

    Martin, M. D., Cappellini, Enrico, Samaniego Castruita, J. A., Zepeda Mendoza, M. L., Campos, P., Seguin-Orlando, A., Wales, N., Orlando, L. A. A., Ho, S. Y. W., Dietrich, F. S., Mieczkowski, P. A., Heitman, J., Willerslev, Eske, Krogh, Anders, Ristaino, J. B. & Gilbert, M Thomas P, 18 Jul 2013, In: Nature Communications. 4, 7 p., 2172.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

    Orlando, L. A. A., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, T. S., Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J. & 36 others, Dolocan, A., Stenderup, Jesper Tandberg, Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Røed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. A. S., Ryder, O., Andersson, L., Mundy, J., Krogh, Anders, Gilbert, M Thomas P, Kjær, Kurt H., Sicheritz-Pontén, T., Jensen, Lars Juhl, Olsen, Jesper Velgaard, Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J. & Willerslev, Eske, 4 Jul 2013, In: Nature. 499, 7456, p. 74-78 5 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  51. Published

    Hepatocyte growth factor activator inhibitor-2 prevents shedding of matriptase

    Larsen, B. R., Steffensen, S. D. R., Nielsen, N. V. L., Friis, S., Godiksen, S., Lange, Jette Bornholdt, Soendergaard, C., Nonboe, Annika Weile, Andersen, M. N., Poulsen, Steen Seier, Szabo, R., Bugge, T. H., Lin, C., Skovbjerg, H., Jensen, J. K. & Vogel, Lotte, 1 Apr 2013, In: Experimental Cell Research. 319, 6, p. 918-929 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries

    Jakobsen, J. S., Waage, J., Rapin, N., Bisgaard, Hanne Cathrine, Larsen, F. S. & Porse, Bo Torben, Apr 2013, In: Genome Research. 23, 4, p. 592-603 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  53. Published

    Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation

    Wu, X., Johansen, Jens Vilstrup & Helin, K., 28 Mar 2013, In: Molecular Cell. 49, 6, p. 1134-46 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  54. Published

    Are there really twice as many bovid species as we thought?

    Heller, Rasmus, Frandsen, P., Lorenzen, Eline & Siegismund, Hans Redlef, Mar 2013, In: Systematic Biology. 62, 3, p. 490-493 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  55. Published

    SigniSite: identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

    Jessen, L. E., Hoof, I., Lund, O. & Nielsen, M., 2013, In: Nucleic Acids Research. 41, W1, p. W286-W291 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  56. Published

    A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies: [plus] Erratum

    Cao, H., Wang, Y., Zhang, W., Chai, X., Zhang, X., Chen, S., Yang, F., Zhang, C., Guo, Y., Liu, Y., Tang, Z., Chen, C., Xue, Y., Zhen, H., Xu, Y., Rao, B., Liu, T., Zhao, M., Zhang, W., Li, Y. & 6 others, Zhang, X., Tellier, L. C. A. M., Krogh, Anders, Kristiansen, Karsten, Wang, J. & Li, J., 2013, In: Human Mutation. 34, 12, p. 1715-1720 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  57. Published

    A simple probabilistic model of multibody interactions in proteins

    Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 2013, In: Proteins: Structure, Function, and Bioinformatics. 81, 8, p. 1340-1350 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  58. Published

    A study of bacterial gene regulatory mechanisms: Dynamic features of gene regulatory mechanisms in EscherichEia coli and small RNA post-transcriptional regulation in Vibrio cholerae

    Hansen, S., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 134 p.

    Research output: Book/Report › Ph.D. thesis › Research

  59. Published

    Acute Genome-wide effects of Rosiglitazone on PPARγ transcriptional networks in Adipocytes

    Haakonsson, A. K., Madsen, M. S., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2013, In: Molecular Endocrinology. 27, 9, p. 1536-1549 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  60. Published

    Alterations in polyadenylation and its implications for endocrine disease

    Rehfeld, Anders Aagaard, Plass, M., Krogh, Anders & Friis-Hansen, Lennart Jan, 2013, In: Frontiers in Endocrinology. 4, 23 p., 53.

    Research output: Contribution to journal › Review › Research › peer-review

  61. Published

    BlockLogo: visualization of peptide and sequence motif conservation

    Olsen, L. R., Kudahl, U. J., Simon, C., Sun, J., Schönbach, C., Reinherz, E. L., Zhang, G. L. & Brusic, V., 2013, In: Journal of Immunological Methods. 400-401, p. 37-44 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  62. Published

    Body fluid identification of blood, saliva and semen using second generation sequencing of micro-RNA

    Petersen, C. H., Hjort, B. B., Tvedebrink, T., Kielpinski, L. J., Vinther, Jeppe & Morling, Niels, 2013, In: Forensic Science International: Genetics Supplement Series. 4, 1, p. e204-5 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  63. Published

    Bringing genetic diversity to the forefront of conservation policy and management

    Hoban, S. M., Hauffe, H. C., Pérez-Espona, S., Arntzen, J. W., Bertorelle, G., Bryja, J., Frith, K., Gaggiotti, O. E., Galbusera, P., Godoy, J. A., Hoelzel, A. R., Nichols, R. A., Primmer, C. R., Russo, I., Segelbacher, G., Siegismund, Hans Redlef, Sihvonen, M., Vernesi, C., Vilà, C. & Bruford, M. W., 2013, In: Conservation Genetics Resources. 5, 2, p. 593-598 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  64. Published

    Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

    Korneliussen, Thorfinn Sand, Moltke, Ida, Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: B M C Bioinformatics. 14, 14 p., 289.

    Research output: Contribution to journal › Journal article › Research › peer-review

  65. Published

    Combining the multicanonical ensemble with generative probabilistic models of local biomolecular structure

    Frellsen, J., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2013, Proceedings of the 59th World Statistics Congress of the International Statistical Institute, 2013 . Hague, p. 139-144 6 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research

  66. Published

    Conservation genetic resources for effective species survival (ConGRESS): bridging the divide between conservation research and practice

    Hoban, S., Arntzen, J. W., Bertorelle, G., Bryja, J., Fernandes, M., Frith, K., Gaggiotti, O., Galbusera, P., Godoy, J. A., Hauffe, H. C., Hoelzel, A. R., Nichols, R. A., Perez-Espona, S., Primmer, C., Russo, I-R. M., Segelbacher, G., Siegismund, H. R., Sihvonen, M., Sjogren-Gulve, P., Vernesi, C. & 2 others, Vila, C. & Bruford, M. W., 2013, In: Journal for Nature Conservation. 21, 6, p. 433-437 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  67. Published

    Detection of Active Matriptase using a Biotinylated Chloromethyl Ketone Peptide

    Godiksen, S., Soendergaard, C., Friis, S., Jensen, J. K., Lange, Jette Bornholdt, Sales, K. U., Huang, M., Bugge, T. H. & Vogel, Lotte, 2013, In: P L o S One. 8, 10, 10 p., e77146.

    Research output: Contribution to journal › Journal article › Research › peer-review

  68. Published

    Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing

    Kielpinski, L. J., Boyd, M., Sandelin, Albin Gustav & Vinther, Jeppe, 2013, In: Methods in molecular biology (Clifton, N.J.). 1038, p. 213-31 19 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  69. Published

    Drosha regulates gene expression independently of RNA cleavage function

    Gromak, N., Dienstbier, M., Macias, S., Plass, M., Eyras, E., Cáceres, J. F. & Proudfoot, N. J., 2013, In: Cell Reports. 5, 6, p. 1499-510 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  70. Published

    Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells

    Strickertsson, J. A. B., Desler, Claus, Martin-Bertelsen, T., Machado, A. M. D., Wadstrøm, T., Winther, Ole, Rasmussen, Lene Juel & Friis-Hansen, Lennart Jan, 2013, In: PLOS ONE. 8, 4, p. 1-13 13 p., e63147.

    Research output: Contribution to journal › Journal article › Research › peer-review

  71. Published

    Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation

    Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  72. Published

    Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes

    Albrechtsen, A., Grarup, N., Li, Y., Sparsø, T. H., Tian, G., Cao, H., Jiang, T., Kim, S. Y., Korneliussen, T. S., Li, Q., Nie, C., Wu, R., Skotte, L., Morris, A. P., Ladenvall, C., Cauchi, S., Stancáková, A., Andersen, G., Astrup, A., Banasik, K. & 86 others, Bennett, A. J., Bolund, L., Charpentier, G., Chen, Y., Dekker, J. M., Doney, A. S. F., Dorkhan, M., Forsen, T., Frayling, T. M., Groves, C. J., Gui, Y., Hallmans, G., Hattersley, A. T., He, K., Hitman, G. A., Holmkvist, J., Huang, S., Jiang, H., Jin, X., Justesen, Johanne Marie, Kristiansen, Karsten, Kuusisto, J., Lajer, M., Lantieri, O., Li, W., Liang, H., Liao, Q., Liu, X., Ma, T., Ma, X., Manijak, M. P., Marre, M., Mokrosinski, J., Morris, A. D., Mu, B., Nielsen, A. A., Nijpels, G., Nilsson, P., Palmer, C. N. A., Rayner, N. W., Renström, F., Ribel-Madsen, R., Robertson, N., Rolandsson, O., Rossing, P., Schwartz, Thue W., Slagboom, P. E., Sterner, M., Tang, M., Tarnow, L., Tuomi, T., Van't Riet, E., van Leeuwen, N., V Varga, Tibor, Vestmar, M. A., Walker, M., Wang, B., Wang, Y., Wu, H., Xi, F., Yengo, L., Yu, C., Zhang, X., Zhang, J., Zhang, Q., Zhang, W., Zheng, H., Zhou, Y., Altshuler, D., 't Hart, L. M., Franks, P. W., Balkau, B., Froguel, P., McCarthy, M. I., Laakso, M., Groop, L., Christensen, C., Brandslund, I., Lauritzen, T., Witte, D. R., Linneberg, A., Jørgensen, T., Hansen, Torben, Wang, J., Nielsen, Rasmus & Pedersen, Oluf Borbye, 2013, In: Diabetologia. 56, 2, p. 298-310 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  73. Published

    Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

    Grarup, N., Sulem, P., Sandholt, C. H., Thorleifsson, G., Ahluwalia, T. V. S., Steinthorsdottir, V., Bjarnason, H., Gudbjartsson, D. F., Magnusson, O. T., Sparsø, T., Albrechtsen, A., Kong, A., Masson, G., Tian, G., Cao, H., Nie, C., Kristiansen, K., Husemoen, L. L., Thuesen, B., Li, Y. & 10 others, Nielsen, Rasmus, Linneberg, Allan René, Olafsson, I., Eyjolfsson, G. I., Jørgensen, T., Wang, J., Hansen, Torben, Thorsteinsdottir, U., Stefánsson, K. & Pedersen, Oluf Borbye, 2013, In: P L o S Genetics. 9, 6, 12 p., e1003530.

    Research output: Contribution to journal › Journal article › Research › peer-review

  74. Published

    Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations

    Huerta-Sánchez, E., DeGiorgio, M., Pagani, L., Tarekegn, A., Ekong, R., Antao, T., Cardona, A., Montgomery, H. E., Cavalleri, G. L., Robbins, P. A., Weale, M. E., Bradman, N., Bekele, E., Kivisild, T., Tyler-Smith, C. & Nielsen, Rasmus, 2013, In: Molecular Biology and Evolution. 30, 8, p. 1877-1888 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  75. Published

    Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii

    Seim, I., Fang, X., Xiong, Z., Lobanov, A. V., Huang, Z., Ma, S., Feng, Y., Turanov, A. A., Zhu, Y., Lenz, T. L., Gerashchenko, M. V., Fan, D., Yim, S. H., Yao, X., Jordan, D., Xiong, Y., Ma, Y., Lyapunov, A. N., Chen, G., Kulakova, O. I. & 9 others, Sun, Y., Lee, S., Bronson, R. T., Moskalev, A. A., Sunyaev, S. R., Zhang, G., Krogh, Anders, Wang, J. & Gladyshev, V. N., 2013, In: Nature Communications. 4, 8 p., 2212.

    Research output: Contribution to journal › Journal article › Research › peer-review

  76. Published

    Genome-wide association study of genetic variants in LPS-stimulated IL-6, IL-8, IL-10, IL-1ra and TNF-α cytokine response in a Danish Cohort

    Larsen, M. H., Albrechtsen, Anders, Thørner, L. W., Werge, T., Hansen, T., Gether, Ulrik, Haastrup, E. & Ullum, H., 2013, In: PLOS ONE. 8, 6, 6 p., e66262.

    Research output: Contribution to journal › Journal article › Research › peer-review

  77. Published

    Great ape genetic diversity and population history

    Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O'Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I. & 55 others, Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M. L., Stevison, L., Camprubí, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J. A., Bergl, R. A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, Hans Redlef, Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S. A., Mullikin, J. C., Wilson, R. K., Gut, I. G., Gonder, M. K., Ryder, O. A., Hahn, B. H., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schierup, M. H., Hvilsom, C., Andrés, A. M., Wall, J. D., Bustamante, C. D., Hammer, M. F., Eichler, E. E. & Marques-Bonet, T., 2013, In: Nature. 499, 7459, p. 471-475 5 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  78. Published

    HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

    Bagger, F. O., Rapin, N. P. J., Theilgaard-Mønch, Kim, Kaczkowski, B., Thorén, L. A. M., Jendholm, L. J., Winther, Ole & Porse, Bo Torben, 2013, In: Nucleic Acids Research. 41, Database issue, p. D1034-D1039 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  79. Published

    Improving The Analysis Of Gene Expression Profiles By Comparing AML Blasts With Their Nearest Normal Counterparts

    Rapin, N., Bagger, F. O., Jendholm, J., Mora-Jensen, H. I., Krogh, Anders, Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, Ole, Theilgaard-Mønch, Kim & Porse, Bo Torben, 2013, In: Blood. 122, 21

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  80. Published

    Inference of structure ensembles of flexible biomolecules from sparse, averaged data

    Olsson, S., Frellsen, J., Boomsma, Wouter, Mardia, K. V. & Hamelryck, Thomas Wim, 2013, In: PLoS ONE. 8, 11, 7 p., e79439.

    Research output: Contribution to journal › Journal article › Research › peer-review

  81. Published

    Inference problems in structural biology: protein structures and protein structure ensembles

    Olsson, S., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 138 p.

    Research output: Book/Report › Ph.D. thesis › Research

  82. Published

    Inferring demographic history from a spectrum of shared haplotype lengths

    Harris, K. & Nielsen, Rasmus, 2013, In: P L o S Genetics. 9, 6, 20 p., e1003521.

    Research output: Contribution to journal › Journal article › Research › peer-review

  83. Published

    Laboratory capacity for diagnosis of foot-and-mouth disease in Eastern Africa: implications for the progressive control pathway

    Namatovu, A., Wekesa, S. N., Tjørnehøj, K., Dhikusooka, M. T., Muwanika, V. B., Siegismund, Hans Redlef & Ayebazibwe, C., 2013, In: B M C Veterinary Research. 9, 19, 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  84. Published

    Lessons on RNA silencing mechanisms in plants from Eukaryotic Argonaute structures

    Poulsen, C., Vaucheret, H. & Brodersen, Peter, 2013, In: Plant Cell. 25, 1, p. 22-37 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  85. Published

    Literature classification for semi-automated updating of biological knowledgebases

    Olsen, L. R., Kudahl, U. J., Winther, Ole & Brusic, V., 2013, In: B M C Genomics. 14(Suppl 5), 10 p., S14.

    Research output: Contribution to journal › Journal article › Research › peer-review

  86. Published

    Loss of miR-10a activates Lpo and collaborates with activated Wnt signaling in inducing intestinal Neoplasia in female mice

    Stadthagen Gomez, G., Tehler, D. E., Høyland-Kroghsbo, Nina Molin, Wen, J., Krogh, Anders, Jensen, K. T., Santoni Rugiu, Eric, Engelholm, Lars Henning & Lund, Anders H., 2013, In: P L o S Genetics. 9, 10, 12 p., e1003913.

    Research output: Contribution to journal › Journal article › Research › peer-review

  87. Published

    Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

    Li, Y., Zhao, S., Ma, J., Li, D., Yan, L., Li, J., Qi, X., Guo, X., Zhang, L., He, W., Chang, R., Liang, Q., Guo, Y., Ye, C., Wang, X., Tao, Y., Guan, R., Wang, J., Liu, Y., Jin, L. & 15 others, Zhang, X., Liu, Z., Zhang, L., Chen, J., Wang, K., Nielsen, Rasmus, Li, R., Chen, P., Li, W., Reif, J. C., Purugganan, M., Wang, J., Zhang, M., Wang, J. & Qiu, L., 2013, In: BMC Genomics. 14, 12 p., 579.

    Research output: Contribution to journal › Journal article › Research › peer-review

  88. Published

    Nanger (granti) Grant's Gazelle Species Group

    Siegismund, Hans Redlef, Lorenzen, Eline & Arctander, P., 2013, Mammals of Africa: Pigs, Hippopotamuses, Chevrotain, Giraffes, Deer and Bovids. Kingdon, J. & Hoffmann, M. (eds.). London: Bloomsbury Academic, Vol. VI. p. 373–379 7 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  89. Published

    On the accuracy of short read mapping

    Menzel, K. P., Frellsen, J., Plass, M., Rasmussen, S. H. & Krogh, Anders, 2013, Deep Sequencing Data Analysis. Shomron, N. (ed.). Springer Science+Business Media, p. 39-59 21 p. (Methods in Molecular Biology, Vol. 1038).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  90. Published

    PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

    Boomsma, Wouter, Frellsen, J., Harder, T. P., Bottaro, S., Johansson, Kristoffer Enøe, Tian, P., Stovgaard, K., Andreetta, C., Olsson, S., Valentin, J., Antonov, L. D., Christensen, A. S., Borg, M., Jensen, Jan Halborg, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2013, In: Journal of Computational Chemistry. 34, 19, p. 1697-1705 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  91. Published

    Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

    Smitz, N., Berthouly, C., Cornélis, D., Heller, Rasmus, Hooft, P. V., Chardonnet, P., Caron, A., Prins, H., Vuuren, B. J. V., Iongh, H. D. & Michaux, J., 2013, In: P L o S One. 8, 2, p. 1-17 17 p., e56235.

    Research output: Contribution to journal › Journal article › Research › peer-review

  92. Published

    Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

    Antonov, L. D., Andreetta, C. & Hamelryck, Thomas Wim, 2013, Biomedical Engineering Systems and Technologies. Gabriel, J., Schier, J. & Huffel, S. V. (eds.). Springer Science+Business Media, Vol. 357. p. 222-235 14 p. (Communications in Computer and Information Science).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  93. Published

    Phaistos user manual

    Boomsma, Wouter, Bottaro, S., Hamelryck, Thomas Wim, Frellsen, J., Andreetta, C., Borg, M., Harder, T., Johansson, Kristoffer Enøe, Stovgaard, K. & Tian, P., 2013, 90 p.

    Research output: Book/Report › Book › Education

  94. Published

    Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality

    Ntini, E., Järvelin, A. I., Lange, Jette Bornholdt, Chen, Y., Boyd, M., Jørgensen, M., Andersson, Robin, Hoof, I., Schein, A., Andersen, P. R., Andersen, P. K., Preker, P., Valen, E., Zhao, X., Pelechano, V., Steinmetz, L. M., Sandelin, Albin Gustav & Jensen, T. H., 2013, In: Nature Structural and Molecular Biology. 20, p. 923-928 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  95. Published

    Probabilistic Equilibrium Sampling of Protein Structures from SAXS Data and a Coarse Grained Debye Formula

    Andreetta, C., 2013, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  96. Published

    Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2013, In: PLoS ONE. 8, 12, 10 p., e84123.

    Research output: Contribution to journal › Journal article › Research › peer-review

  97. Published

    Sample planning optimization tool for conservation and population genetics (SPOTG): a software for choosing the appropriate number of markers and samples

    Hoban, S., Arntzen, P., Gaggiotti, O., Bertorelle, G., Bryja, J., Fernandes, M., Frith, K., Galbusera, P., Godoy, J. A., Hauffe, H. C., Hoelzel, R., Nichols, R., Perez-Espona, S., Primmer, C., Russo, I-R. M., Segelbacher, G., Siegismund, H. R., Sihvonen, M., Sjoegren-Gulve, P., Vernesi, C. & 2 others, Vila, C. & Bruford, M. W., 2013, In: Methods in Ecology and Evolution. 4, 3, p. 299-303 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  98. Published

    Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

    Simola, D. F., Wissler, L., Donahue, G., Waterhouse, R. M., Helmkampf, M., Roux, J., Nygaard, S., Glastad, K. M., Hagen, D. E., Viljakainen, L., Reese, J. T., Hunt, B. G., Graur, D., Elhaik, E., Kriventseva, E. V., Wen, J., Parker, B. J., Cash, E., Privman, E., Childers, C. P. & 18 others, Muñoz-Torres, M. C., Boomsma, Jacobus J., Bornberg-Bauer, E., Currie, C. R., Elsik, C. G., Suen, G., Goodisman, M. A. D., Keller, L., Liebig, J., Rawls, A., Reinberg, D., Smith, C. D., Smith, C. R., Tsutsui, N., Wurm, Y., Zdobnov, E. M., Berger, S. L. & Gadau, J., 2013, In: Genome Research. 23, 8, p. 1235-1247 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  99. Published

    The Microprocessor controls the activity of mammalian retrotransposons

    Heras, S. R., Macias, S., Plass, M., Fernandez, N., Cano, D., Eyras, E., Garcia-Perez, J. L. & Cáceres, J. F., 2013, In: Nature Structural and Molecular Biology. 20, 10, p. 1173-1181 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  100. Published

    The Prognostic, Diagnostic, and Therapeutic Potential of Tumor Antigens

    Olsen, L. R., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 271 p.

    Research output: Book/Report › Ph.D. thesis › Research

  101. Published

    The confounding effect of population structure on bayesian skyline plot inferences of demographic history

    Heller, Rasmus, Chikhi, L. & Siegismund, Hans Redlef, 2013, In: P L o S One. 8, 5, p. 1-10 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  102. Published

    Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

    Hvilsom, C., Frandsen, P., Børsting, Claus, Carlsen, F., Sallé, B., Simonsen, Bo Thisted & Siegismund, Hans Redlef, 2013, In: Heredity. 110, 6, p. 586-593 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

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