Functional Genomics

  1. 2009
  2. Published

    High-throughput screening of Erwinia chrysanthemi pectin methylesterase variants using carbohydrate microarrays

    Øbro, J., Sørensen, I., Derkx, P., Madsen, C. T., Drews, M., Willer, M., Mikkelsen, J. D. & Willats, W. G. T., 2009, In: Proteomics - Practical Proteomics. 9, 7, p. 1861-1868

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

    Nygaard, S., Jacobsen, A., Lindow, M., Eriksen, J., Balslev, E., Flyger, H., Tolstrup, N., Moller, S., Krogh, Anders & Litman, T., 2009, In: B M C Medical Genomics. 2, 1, p. 35

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Identification and characterization of barley RNA-directed RNA polymerases

    Madsen, C. T., Stephens, J., Hornyik, C., Shaw, J., Collinge, David B., Lacomme, C. & Albrechtsen, M. T., 2009, In: BBA General Subjects. 1789, 5, p. 375-385 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Identification of proteins interacting with Arabidopsis ACD11.

    Petersen, N. H. T., Joensen, J., McKinney, L. V., Brodersen, P., Petersen, Morten, Hofius, D. & Mundy, J., 2009, In: Journal of Plant Physiology. 166, 6

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Investigating non-coding genome content using high-throughput sequencing data

    Nygaard, S., 2009, Biologisk Institut: Museum Tusculanum. 34 p.

    Research output: Book/ReportPh.D. thesisResearch

  7. Published

    JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    Portales-Casamar, E., Thongjuea, S., Kwon, A. T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W. W. & Sandelin, Albin Gustav, 2009, In: Nucleic Acids Research.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Localization of recombination proteins and Srs2 reveals anti-recombinase function in vivo

    Burgess, R. C., Lisby, Michael, Altmannova, V., Krejci, L., Sung, P. & Rothstein, R., 2009, In: Journal of Cell Biology. 185, 6, p. 969-81 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Novel archaeal plasmid pAH1 and its interactions with the lipothrixvirus AFV1

    Basta, T., Smyth, J., Forterre, P., Prangishvili, D. & Peng, Xu, 2009, In: Molecular Microbiology. 71, 1, p. 23-34 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Novel death regulators in plant immunity

    Malinovsky, F. G., 2009, Biologisk Institut: Museum Tusculanum. 55 p.

    Research output: Book/ReportPh.D. thesisResearch

  11. Published

    Polypeptides comprising an ice-binding activity

    Ramløv, H., Wilkens, C. & Løbner-Olesen, Anders, 2009, Patent No. WO/2009/065415

    Research output: Patent

  12. Published

    Posttranscriptional crossregulation between Drosha and DGCR8

    Han, J., Pedersen, Jakob Skou, Kwon, S. C., Belair, C. D., Kim, Y., Yeom, K., Yang, W., Haussler, D., Blelloch, R. & Kim, V. N., 2009, In: Cell. 136, 1, p. 75-84 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Proteins involved in attack and defence in Zygomycete-aphid interactions

    Grell, M. N., Jensen, Annette Bruun & Lange, L., 2009.

    Research output: Contribution to conferenceConference abstract for conferenceResearch

  14. Published

    Quantitative analysis of promoter architecture and gene regulation

    Marstrand, T. T., 2009, Biologisk Institut: Museum Tusculanum. 33 p.

    Research output: Book/ReportPh.D. thesisResearch

  15. Published

    Quantitative regulation of alternative splicing in evolution and development

    Irimia, M., Rukov, J. L., Roy, S. W., Vinther, Jeppe & Garcia-Fernandez, J., 2009, In: BioEssays. 31, 1, p. 40-50 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells

    Doehn, U., Hauge, C., Frank, S. R., Jensen, C. A. J., Duda, K., Nielsen, J. V., Cohen, M. S., Johansen, Jens Vilstrup, Winther, B. R., Lund, L. R., Winther, Ole, Taunton, J., Hansen, S. H. & Frödin, Morten, 2009, In: Molecular Cell. 35, 4, p. 511-22 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Rad10 exhibits lesion-dependent genetic requirements for recruitment to DNA double-strand breaks in Saccharomyces cerevisiae

    Moore, D. M., Karlin, J., González-Barrera, S., Mardiros, A., Lisby, Michael, Doughty, A., Gilley, J., Rothstein, R., Friedberg, E. C. & Fischhaber, P. L., 2009, In: Nucleic Acids Research. 37, 19, p. 6429-38 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Rad52

    Mortensen, U. H., Lisby, Michael & Rothstein, R., 2009, In: Current Biology. 19, 16, p. R676-7

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Regulation of rDNA stability by sumoylation

    Eckert-Boulet, N. & Lisby, Michael, 2009, In: DNA Repair. 8, 4, p. 507-16 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Response to Comment by Goldberg et al. on "DNA from Pre-Clovis Human Coprolites in Oregon, North America"

    Rasmussen, M., Cummings, L., Gilbert, M Thomas P, Bryant, V., Smith, C., Jenkins, D. & Willerslev, Eske, 2009, In: Science. 325, p. 148 1 p.

    Research output: Contribution to journalComment/debateResearch

  21. Published

    Response to Comment by Poinar et al. on "DNA from Pre-Clovis Human Coprolites in Oregon, North America"

    Gilbert, M Thomas P, Jenkins, D., Higham, T., Rasmussen, M., Malmstrom, H., Svensson, E., Sanchez, J., Cummings, L., Yohe, I. R., Hofreiter, M., Götherström, A. & Willerslev, Eske, 2009, In: Science. 325, 5937, p. 148 1 p.

    Research output: Contribution to journalComment/debateResearch

  22. Published

    Self-consuming innate immunity in Arabidopsis

    Hofius, D., Mundy, J. & Petersen, Morten, 2009, In: Autophagy. 5, 8, p. 1206-7 1 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    The DNA damage response at eroded telomeres and tethering to the nuclear pore complex

    Khadaroo, B., Teixeira, M. T., Luciano, P., Eckert-Boulet, N., Germann, S. M., Simon, M. N., Gallina, I., Abdallah, P., Gilson, E., Géli, V. & Lisby, Michael, 2009, In: Nature Cell Biology. 11, 8, p. 980-7 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

    Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., Thomson, N. R., Bason, N., Quail, M. A., Sharp, S., Cherevach, I., Churcher, C., Goodhead, I., Hauser, H., Holroyd, N., Mungall, K., Scott, P., Walker, D., White, B., Rose, H. & 12 others, Iversen, P., Mil-Homens, D., Rocha, E. P. C., Fialho, A. M., Baldwin, A., Dowson, C., Barrell, B. G., Govan, J. R., Vandamme, P., Hart, C. A., Mahenthiralingam, E. & Parkhill, J., 2009, In: Journal of Bacteriology. 191, 1, p. 261-77 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    The life-cycle of ATV and other crenarchaeal viruses

    Vestergaard, G. A., 2009, Biologisk Institut: Museum Tusculanum. 91 p.

    Research output: Book/ReportPh.D. thesisResearch

  26. Published

    The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans

    Klasson, L., Westberg, J., Sapountzis, P., Näslund, K., Lutnaes, Y., Darby, A. C., Veneti, Z., Chen, L., Braig, H. R., Garrett, Roger Antony, Bourtzis, K. & Andersson, S. G. E., 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 14, p. 5725-5730

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

    Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M. & 31 others, Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Jacobsen, A., Krogh, Anders, Nygaard, S., Sandelin, Albin Gustav, Valen, E., Winther, Ole & Riken Omics Science Center, R. O. S. C., 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus

    Deng, L., Zhu, H., Chen, Z., Liang, Y. X. & She, Q., 2009, In: Extremophiles. 13, 4, p. 735-46 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Vesicles in electric fields: some novel aspects of membrane behavior

    Dimova, R., Bezlyepkina, N. & Domange Jordö, M. E., 2009, In: Soft Matter. 5, 17, p. 3201-3212 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Viruses of the Archaea

    Basta, T., Garrett, Roger Antony & Prangishvili, D., 2009, Encyclopedia of Life Sciences. Wiley, p. 1-8

    Research output: Chapter in Book/Report/Conference proceedingEncyclopedia chapterResearch

  31. Published

    Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants

    Wittemyer, G., Okello, J. B. A., Rasmussen, H. B., Arctander, P., Nyakaana, S., Douglas-Hamilton, I. & Siegismund, Hans Redlef, 2009, In: PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-CONTAINING PAPERS OF A BIOLOGICAL CHARACTER. 276, 1672, p. 3513-3521

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. 2008
  33. 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 conferenceConference abstract for conferenceResearch

  34. Published

    Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus

    Qiu, J., Fiil, Berthe Katrine, Petersen, K., Nielsen, H. B., Botanga, C. J., Thorgrimsen, S. P., Palma, K., Suarez Rodriguez, M. C., Sandbech-Clausen, S., Lichota, J., Brodersen, P., Grasser, K. D., Mattsson, O., Glazebrook, J., Mundy, J. & Petersen, Morten, 2008, In: EMBO Journal. 27, 16, p. 2214-2221 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Age- and tactic-related paternity success in male African elephants

    Rasmussen, H. B., Okello, J. B. A., Wittemyer, G., Siegismund, Hans Redlef, Arctander, P., Vollrath, F. & Douglas-Hamilton, I., 2008, In: Behavioral Ecology. 19, 1, p. 9-15

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes.

    Zhu, X., Long, F., Chen, Y., Knoechel, Susanne, She, Q. & Shi, X., 2008, In: Applied and Environmental Microbiology. 74, 24, p. 7675-7683

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    ACD 11: Programmed Cell Death, Sphingolipids and Plant Defense

    Petersen, N. H. T., 2008, Department of Biology: Museum Tusculanum. 143 p.

    Research output: Book/ReportPh.D. thesisResearch

  38. Published

    Algorithms for Protein Structure Prediction

    Paluszewski, M., 2008, København: Department of Computer Science, University of Copenhagen. 196 p.

    Research output: Book/ReportPh.D. thesisResearch

  39. Published

    BayesMD: Flexible Biological Modeling for Motif Discovery

    Tang, M. E., Krogh, Anders & Winther, Ole, 2008, In: Journal of Computational Biology. 15, 10, p. 1347-63 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Cerebral dysautoregulation and the risk of ischemic events in occlusive carotid artery disease

    Reinhard, M., Gerds, Thomas Alexander, Grabiak, D., Zimmermann, P. R., Roth, M., Guschlbauer, B., Timmer, J., Czosnyka, M., Weiller, C. & Hetzel, A., 2008, In: Journal of Neurology. 255, 8, p. 1182-1189 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. 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 journalJournal articleResearchpeer-review

  42. Published

    Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis.

    Petersen, Morten, 2008, In: CSH protocols.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. 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 journalJournal articleResearchpeer-review

  44. Published

    Competing to destroy: a fight between two RNA-degradation systems

    Thon, Genevieve, 2008, In: Nature Structural and Molecular Biology. 15, 10, p. 1001-2 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Conserved CPEs in the p53 3' untranslated region influence mRNA stability and protein synthesis

    Rosenstierne, M. W., Vinther, Jeppe, Mittler, G., Larsen, L., Mann, M. & Norrild, B., 2008, In: Anticancer Research. 28, 5A, p. 2553-9 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Crenarchaeal Viruses: Morphotypes and Genomes,

    Prangishvili, P., Basta, P. & Garrett, Roger Antony, 2008, Encyclopedia of Virology (Third Edition). Mahy, B. W. J. & van Regenmortel, M. H. V. (eds.). Elsevier, Vol. 3rd ed.. p. 587-595

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearch

  47. 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 journalJournal articleResearchpeer-review

  48. Published

    Downstream targets of WRKY33

    Petersen, K., Fiil, Berthe Katrine, Mundy, J. & Petersen, Morten, 2008, In: Plant Signalling & Behavior. 3, 11, p. 1033-1034

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. 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 journalJournal articleResearchpeer-review

  50. Published

    Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants

    Okello, J. B. A., Wittemyer, G., Rasmussen, H. B., Arctander, P., Nyakaana, S., Douglas-Hamilton, I. & Siegismund, Hans Redlef, 2008, In: Molecular Ecology. 17, 17, p. 3788-3799 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival

    Peng, Xu, 2008, In: Microbiology. 154, Pt 2, p. 383-91 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. 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 journalJournal articleResearchpeer-review