Ole Winther

Ole Winther

Professor with special responsibilities

Member of:


    1. 2006
    2. Published

      Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

      Regenberg, Birgitte, Grotkjaer, T., Winther, Ole, Fausbøll, A., Akesson, M., Bro, C., Hansen, L. K., Brunak, Søren & Nielsen, Jens Bo, 2006, In : Genome Biology (Online Edition). 7, 11, p. R107

      Research output: Contribution to journalJournal articleResearchpeer-review

    3. Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm

      Grotkjær, T., Winther, Ole, Regenberg, Birgitte, Nielsen, J. & Hansen, L. K., 2006, In : Bioinformatics. 22, 1, p. 58-67 10 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    4. 2008
    5. 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

    6. 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 journalJournal articleResearchpeer-review

    7. 2009
    8. Published

      Discovery of regulatory elements is improved by a discriminatory approach

      Valen, E., Sandelin, Albin Gustav, Winther, Ole & Krogh, Anders, 2009, In : PloS Computational Biology. 5, 11, p. e1000562

      Research output: Contribution to journalJournal articleResearchpeer-review

    9. Published

      Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

      Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M. E., Zhao, X., Krogh, Anders, Winther, Ole, Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M., Hayashizaki, Y., Gustincich, S., Sandelin, Albin Gustav & Carninci, P., 2009, In : Genome Research. 19, 2, p. 255-65 10 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    10. 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

    11. 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., 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

    12. 2010
    13. Published

      Molecular signatures of thyroid follicular neoplasia

      Helweg-Larsen, R. B., Rossing, M., Henao Giraldo, R., Yamamoto, Y., Krogdahl, A., Godballe, C., Winther, Ole, Kiss, K., Christensen, L. H., Høgdall, E. V. S., Bennedbæk, Finn Noe & Nielsen, Finn Cilius, 2010, In : Endocrine - Related Cancer. 17, 3, p. 691-708 18 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    14. Published

      Multivariate Hawkes process models of the occurrence of regulatory elements

      Carstensen, L., Sandelin, Albin Gustav, Winther, Ole & Hansen, Niels Richard, 2010, In : BMC Bioinformatics. 11, p. 456

      Research output: Contribution to journalJournal articleResearchpeer-review

    15. Published

      Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

      Ryge, J., Winther, Ole, Wienecke, Jacob, Sandelin, Albin Gustav, Westerdahl, A., Hultborn, Hans & Kiehn, O., 2010, In : BMC Genomics. 11, 1, p. 365 22 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    16. 2011
    17. Published

      Gene expression of the endolymphatic sac

      Friis, M., Martin-Bertelsen, T., Friis-Hansen, L., Winther, Ole, Henao Giraldo, R., Sørensen, Mads Sølvsten & Qvortrup, Klaus, 2011, In : Acta Oto-Laryngologica. 131, 12, p. 1257-63 7 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    18. 2012
    19. Published

      Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma

      Rossing, M., Helweg-Larsen, R. B., Henao Giraldo, R., Winther, Ole, Vikeså, J., Niazi, O., Godballe, C., Krogdahl, A., Glud, Martin, Sørensen, C. H., Kiss, K., Bennedbæk, Finn Noe & Nielsen, Finn Cilius, 2012, In : Journal of Molecular Endocrinology. 48, 1, p. 11-23 13 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    20. Published

      Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

      Kaczkowski, B., Rossing, M., Andersen, D. K., Dreher, A., Morevati, M., Visser, M. A., Winther, Ole, Nielsen, Finn Cilius & Norrild, B., 2012, In : Scientific Reports. 2, p. 515

      Research output: Contribution to journalJournal articleResearchpeer-review

    21. Published

      Predictive active set selection methods for Gaussian processes

      Henao, R. & Winther, Ole, 2012, In : Neurocomputing. 80, p. 10-18 9 p.

      Research output: Contribution to journalConference articleResearchpeer-review

    22. 2013
    23. Published

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

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

      Research output: Contribution to journalJournal articleResearchpeer-review

    24. 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 journalJournal articleResearchpeer-review

    25. 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 journalConference abstract in journalResearchpeer-review

    26. 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 journalJournal articleResearchpeer-review

    27. 2014
    28. Published

      Bioinformatics for cancer immunotherapy target discovery

      Olsen, L. R., Campos, B., Stein Barnkob, M., Winther, Ole, Brusic, V. & Andersen, M. H., 2014, In : Cancer Immunology, Immunotherapy. 63, 12, p. 1235-1249 15 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    29. Published

      Bone signaling in middle ear development: a genome-wide differential expression analysis

      Nielsen, M. C., Martin-Bertelsen, T., Friis, M., Winther, Ole, Friis-Hansen, L. J., Cayé-Thomasen, Per & Sørensen, Mads Sølvsten, 2014, In : Anatomical Record. 297, 12, p. 2349-2355 7 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    30. 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, S., 2014, In : Acta Ophthalmologica. 92, 6, p. 541-549

      Research output: Contribution to journalJournal articleResearchpeer-review

    31. 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 journalJournal articleResearchpeer-review

    32. Published

      Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

      Rapin, N. P. J., Bagger, F. O., Jendholm, L. J., Mora-Jensen, H., Krogh, Anders, Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, Ole, Theilgaard-Mønch, Kim & Porse, Bo Torben, 6 Feb 2014, In : Blood (online). 123, 6, p. 894-904 11 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    33. 2015
    34. Published

      A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

      Olsen, L. R., Simon, C., Kudahl, U. J., Bagger, F. O., Winther, Ole, Reinherz, E. L., Zhang, G. L. & Brusic, V., 2015, In : B M C Medical Genomics. 8, Suppl 4, 6 p., 5.

      Research output: Contribution to journalJournal articleResearchpeer-review

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