Functional Genomics

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  1. 2007
  2. Published

    Transcriptional Analysis of the Genetic Element pSSVx: Differential and Temporal Regulation of Gene Expression Reveals Correlation between Transcription and Replication

    Contursi, P., Cannio, R., Prato, S., She, Q., Rossi, M. & Bartolucci, S., 2007, In: Journal of Bacteriology. 189, 17, p. 6339-50 11 p.

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

  3. Published

    Theoretical analysis of epigenetic cell memory by nucleosome modification

    Dodd, I. B., Micheelsen, M. A., Sneppen, Kim & Thon, Genevieve, 2007, In: Cell. 129, 4, p. 813-22 10 p.

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

  4. Published

    Rad52 and Rad59 exhibit both overlapping and distinct functions

    Feng, Q., Düring, L., Mayolo, A. A. D., Lettier, G., Lisby, Michael, Erdeniz, N., Mortensen, U. H. & Rothstein, R., 2007, In: DNA Repair. 6, 1, p. 27-37

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

  5. Published

    Rad52 and Rad59 exhibit both overlapping and distinct functions

    Feng, Q., Düring, L., de Mayolo, A. A., Buchhorn, G. L., Lisby, Michael, Erdeniz, N., Mortensen, U. H. & Rothstein, R., 2007, In: DNA Repair. 6, 1, p. 27-37 11 p.

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

  6. Published

    Using an alignment of fragment strings for comparing protein structures.

    Friedberg, I., Harder, T., Kolodny, R., Sitbon, E., Li, Z. & Godzik, A., 2007, In: Bioinformatics. 23, 2, p. e219-24

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

  7. Published

    Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver.

    Gao, H., Fält, S., Sandelin, Albin Gustav, Gustafsson, J. & Dahlman-Wright, K., 2007, In: Molecular Endocrinology. 22, 1, p. 10-22 12 p.

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

  8. Published

    FOXP3+ regulatory T cells in cutaneous T-cell lymphomas: association with disease stage and survival

    Gjerdrum, L. M., Woetmann, Anders , Ødum, Niels, Burton, C. M., Rossen, K., Skovgaard, G. L., Ryder, L. P. & Ralfkiaer, E., 2007, In: Leukemia. 21, 12, p. 2512-2518 6 p.

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

  9. Published

    Cholecystokinin-2 receptor mediated gene expression in neuronal PC12 cells

    Hansen, T. V. O., Borup, R., Marstrand, T., Rehfeld, Jens Frederik & Nielsen, Finn Cilius, 2007, In: Journal of Neurochemistry. 104, 6, p. 1450-65 15 p.

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

  10. Published

    Four weeks one-leg training and high fat diet does not alter PPAR alpha protein or mRNA expression in human skeletal muscle

    Helge, Jørn Wulff, Bentley, D., Schjerling, Peter, Willer, M., Gibala, M. J., Franch, J., Tapia-Laliena, M. A., Daugaard, J. R. & Andersen, J. L., 2007, In: European Journal of Applied Physiology. 101, 1, p. 105-114 9 p.

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

  11. Published

    Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing.

    Irimia, M., Rukov, J. L., Penny, D. & Roy, S. W., 2007, In: BMC Evolutionary Biology. 7, p. 188

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

  12. Published

    Molecular composition of IMP1 ribonucleoprotein granules.

    Jønson, L., Vikesaa, J., Krogh, Anders, Nielsen, Lars Kamp, Hansen, T. V., Borup, R., Johnsen, A. H., Christiansen, Jan & Nielsen, Finn Cilius, 2007, In: Molecular and Cellular Proteomics. 6, 5, p. 798-811 13 p.

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

  13. Published

    The UCSC Genome Browser Database: 2008 update.

    Karolchik, D., Kuhn, R. M., Baertsch, R., Barber, G. P., Clawson, H., Diekhans, M., Giardine, B., Harte, R. A., Hinrichs, A. S., Hsu, F., Kober, K. M., Miller, W., Pedersen, J. S., Pohl, A., Raney, B. J., Rhead, B., Rosenbloom, K. R., Smith, K. E., Stanke, M., Thakkapallayil, A. & 5 others, Trumbower, H., Wang, T., Zweig, A. S., Haussler, D. & Kent, W. J., 2007, In: Nucleic Acids Research. 36, Database issue, p. D773-9

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

  14. Published

    Cdk phosphorylation of the Ste11 transcription factor constrains differentiation-specific transcription to G1.

    Kjaerulff, S., Andersen, N. R., Borup, M. T. & Nielsen, Olaf, 2007, In: Genes & Development. 21, 3, p. 347-59 12 p.

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

  15. Published

    Drosophila deoxyribonucleoside kinase mutants with enhanced ability to phosphorylate purine analogs

    Knecht, W., Rozpedowska, E., Breton, C. L., Willer, M., Gojkovic, Z., Sandrini, M. P. B., Jørgensen, T., Hasholt, Lis Frydenreich, Munch-Petersen, B. & Piskur, J., 2007, In: Gene Therapy. 14, 17, p. 1278-1286 8 p.

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

  16. Published

    The cell biology of mitotic recombination in saccharomyces cerevisiae

    Lisby, Michael & Rothstein, R., 2 May 2007, Molecular Genetics of Recombination. Aquilera, A. & Rothstein, R. (eds.). p. 335-362 28 p. (Topics in Current Genetics, Vol. 17).

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

  17. Published

    Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob)

    Lorenzen, E. D., De Neergaard, R., Arctander, P. & Siegismund, Hans Redlef, 2007, In: Molecular Ecology. 16, 15, p. 3241-52 11 p.

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

  18. Published

    Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

    Muwanka, V. B., Nyakaana, S., Siegismund, Hans Redlef & Arctander, P., 2007, In: African Journal of Ecology. 45, 1, p. 22-30

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

  19. Published

    Fission yeast goes synthetic.

    Nielsen, Olaf, 2007, In: Nature Methods. 4, 10, p. 777-8 1 p.

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

  20. Published

    Deubiquitination of FANCD2 Is Required for DNA Crosslink Repair

    Østergaard, Vibe Hallundbæk, Langevin, F., Kuiken, H. J., Pace, P., Niedzwiedz, W., Simpson, L. J., Ohzeki, M., Takata, M., Sale, J. E. & Patel, K. J., 14 Dec 2007, In: Molecular Cell. 28, 5, p. 798-809 12 p.

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

  21. Published

    Editing modifies the GABA(A) receptor subunit alpha3.

    Ohlson, J., Pedersen, Jakob Skou, Haussler, D. & Ohman, M., 2007, In: RNA: A publication of the RNA Society. 13, 5, p. 698-703 5 p.

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

  22. Published

    Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms

    Peng, Xu, Basta, T., Häring, M., Garrett, Roger Antony & Prangishvili, D., 2007, In: Virology. 364, 1, p. 237-43 6 p.

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

  23. Published

    Rad52 multimerization is important for its nuclear localization in Saccharomyces cerevisiae.

    Plate, I., Albertsen, L., Lisby, Michael, Hallwyl, S. C. L., Feng, Q., Seong, C., Rothstein, R., Sung, P. & Mortensen, U. H., 2007, In: DNA Repair. 7, 1, p. 57-66 9 p.

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

  24. Published

    Mammalian RNA polymerase II core promoters: insights from genome-wide studies.

    Sandelin, Albin Gustav, Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y. & Hume, D. A., 2007, In: Nature Reviews. Genetics. 8, 6, p. 424-36 12 p.

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

  25. Published

    Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

    Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S-W., Han, M. V. & 26 others, Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M. & Kellis, M., 2007, In: Nature. 450, 7167, p. 219-32 13 p.

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

  26. Published

    KBERG: KnowledgeBase for Estrogen Responsive Genes.

    Tang, S., Zhang, Z., Tan, S. L., Tang, M. E., Kumar, A. P., Ramadoss, S. K. & Bajic, V. B., 2007, In: Nucleic Acids Research. 35, Database issue, p. D732-6

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

  27. Published

    Anaphase onset before complete DNA replication with intact checkpoint responses.

    Torres-Rosell, J., De Piccoli, G., Cordon-Preciado, V., Farmer, S., Jarmuz, A., Machin, F., Pasero, P., Lisby, Michael, Haber, J. E. & Aragón, L., 2007, In: Science. 315, 5817, p. 1411-5 4 p.

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

  28. Published

    The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus.

    Torres-Rosell, J., Sunjevaric, I., De Piccoli, G., Sacher, M., Eckert-Boulet, N., Reid, R., Jentsch, S., Rothstein, R., Aragón, L. & Lisby, Michael, 2007, In: Nature Cell Biology. 9, 8, p. 923-31 8 p.

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

  29. Published

    A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

    Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. & Huang, L., 2007, In: Virology. 363, 1, p. 124-33 9 p.

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

  30. Published

    Structured RNAs in the ENCODE selected regions of the human genome.

    Washietl, S., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S. E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T. R., Guigó, R., Snyder, M. & 4 others, Gerstein, M. B., Reymond, A., Hofacker, I. L. & Stadler, P. F., 2007, In: Genome Research. 17, 6, p. 852-64 12 p.

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

  31. Published

    Nonmalignant T cells stimulate growth of T-cell lymphoma cells in the presence of bacterial toxins

    Woetmann, Anders , Lovato, P., Eriksen, K. W., Krejsgaard, T., Labuda, T., Zhang, Q., Mathiesen, A., Geisler, Carsten, Svejgaard, A., Wasik, M. A. & Ødum, Niels, 2007, In: Blood. 109, 8, p. 3325-32 7 p.

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

  32. Published

    New locus important for Myxococcus social motility and development

    Zhang, C. Y., Cai, K., Liu, H., ZHANG, YONG, Pan, H. W., Wang, B., Wu, Z. H., Hu, W. & Li, Y. Z., Nov 2007, In: Journal of Bacteriology. 189, 21, p. 7937-7941 5 p.

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

  33. Published

    Dss1 interaction with Brh2 as a regulatory mechanism for recombinational repair.

    Zhou, Q., Kojic, M., Cao, Z., Lisby, Michael, Mazloum, N. A. & Holloman, W. K., 2007, In: Molecular and Cellular Biology. 27, 7, p. 2512-26 14 p.

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

  34. 2008
  35. Published

    EGFR induces expression of IRF-1 via STAT1 and STAT3 activation leading to growth arrest of human cancer cells

    Andersen, P., Pedersen, M. W., Woetmann, Anders , Villingshøj, M., Stockhausen, M., Ødum, Niels & Poulsen, H. S., 2008, In: International Journal of Cancer. 122, 2, p. 342-9 7 p.

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

  36. Published

    Differential regulation of the cellular response to DNA double-strand breaks in G1.

    Barlow, J. H., Lisby, Michael & Rothstein, R., 2008, In: Molecular Cell. 30, 1, p. 73-85 12 p.

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

  37. Published

    Viruses in acidic geothermal environments of the Kamchatka Peninsula

    Bize, A., Peng, Xu, Prokofeva, M., Maclellan, K., Lucas, S., Forterre, P., Garrett, Roger Antony, Bonch-Osmolovskaya, E. A. & Prangishvili, D., 2008, In: Research in Microbiology. 159, 5, p. 358-66 8 p.

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

  38. Published

    Identification of let-7-regulated oncofetal genes.

    Boyerinas, B., Park, S., Shomron, N., Hedegaard, M. M., Vinther, Jeppe, Andersen, J. S., Feig, C., Xu, J., Burge, C. B. & Peter, M. E., 2008, In: Cancer Research. 68, 8, p. 2587-91 4 p.

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

  39. Published

    Revised sequence of foxtail mosaic virus reveals a triple gene block structure similar to potato virus X

    Bruun-Rasmussen, M., Madsen, C. T., Johansen, E. & Albrechtsen, M., 2008, In: Archives of Virology. 153, 1, p. 223-226

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

  40. Published

    JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

    Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T., Winther, Ole, da Piedade, I., Krogh, Anders, Lenhard, B. & Sandelin, Albin Gustav, 2008, In: Nucleic Acids Research. 36, Database issue, p. D102-6

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

  41. Published

    57miRNA regulation during oncogene-induced senescence


    Christoffersen, N. R., Frankel, Lisa, Klausen, M., Jacobsen, A., Krogh, Anders & Lund, Anders H., May 2008.

    Research output: Contribution to conference › Conference abstract for conference › Research

  42. Published

    Protein Structure Prediction Using Bee Colony Optimization Metaheuristic: Extended Abstract

    Fonseca, R., Paluszewski, M. & Winter, Pawel, 2008, In: Koebenhavns Universitet. Datalogisk Institut. Rapport. 12, 11 p.

    Research output: Contribution to journal › Conference abstract in journal › Research

  43. Published

    Characterization and transcriptional analysis of two gene clusters for type IV secretion machinery in Wolbachia of Armadillidium vulgare

    Félix, C., Pichon, S., Braquart-Varnier, C., Braig, H., Chen, L., Garrett, Roger Antony, Martin, G. & Grève, P., 2008, In: Research in Microbiology. 159, 6, p. 481-5 4 p.

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

  44. Published

    Mutation of miRNA target sequences during human evolution.

    Gardner, P. P. & Vinther, Jeppe, 2008, In: Trends in Genetics. 24, 6, p. 262-5 3 p.

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

  45. Published

    Rfam: updates to the RNA families database

    Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths-Jones, S., Eddy, S. R. & Bateman, A., 2008, In: Nucleic Acids Research.

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

  46. Published

    FOXP3 positive regulatory T-cells in cutaneous T-cell lymphomas

    Gjerdrum, L. M., Woetmann, Anders , Ødum, Niels & Ralfkiaer, E., 2008, In: Virchows Archiv. 452, Suppl. 1, p. S4-S4

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

  47. Published

    FOXP3 positive regulatory T-cells in cutaneous and systemic CD30 positive T-cell lymphoproliferations

    Gjerdrum, L. M., Woetmann, Anders , Ødum, Niels, Hother, C., Henrik-Nielsen, R., Gniadecki, R. & Ralfkiaer, E., 2008, In: European Journal of Haematology. 80, 6, p. 483-9 6 p.

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

  48. Published

    Origin of introns by 'intronization' of exonic sequences.

    Irimia, M., Rukov, J. L., Penny, D., Vinther, Jeppe, Garcia-Fernandez, J. & Roy, S. W., 2008, In: Trends in Genetics.

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

  49. Published

    Reading Prokaryotic Genomes

    Iversen, P., 2008, Biologisk Institut: Museum Tusculanum. 168 p.

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

  50. Published

    Gamma c-signaling cytokines induce a regulatory T cell phenotype in malignant CD4+ T lymphocytes

    Kasprzycka, M., Zhang, Q., Witkiewicz, A., Marzec, M., Potoczek, M., Liu, X., Wang, H. Y., Milone, M., Basu, S., Mauger, J., Choi, J. K., Abrams, J. T., Hou, J. S., Rook, A. H., Vonderheid, E., Woetmann, Anders , Ødum, Niels & Wasik, M. A., 2008, In: Journal of Immunology. 181, 4, p. 2506-12 6 p.

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

  51. Published

    Hidden layers of human small RNAs

    Kawaji, H., Nakamura, M., Takahashi, Y., Sandelin, Albin Gustav, Katayama, S., Fukuda, S., Daub, C. O., Kai, C., Kawai, J., Yasuda, J., Carninci, P. & Hayashizaki, Y., 2008, In: BMC Genomics. 9, p. 157

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

  52. Published

    Compensatory role for Rad52 during recombinational repair in Ustilago maydis.

    Kojic, M., Mao, N., Zhou, Q., Lisby, Michael & Holloman, W. K., 2008, In: Molecular Microbiology. 67, 5, p. 1156-68 12 p.

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

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