Ole Winther

Ole Winther

Professor with special responsibilities

Member of:


    1. Published

      Detecting sequence signals in targeting peptides using deep learning

      Almagro Armenteros, J. J., Salvatore, Marco, Emanuelsson, O., Winther, Ole, von Heijne, G., Elofsson, A. & Nielsen, H., 2019, In : Life Science Alliance. 2, 5, 14 p., 201900429.

      Research output: Contribution to journalJournal articleResearchpeer-review

    2. Published

      DeepLoc: prediction of protein subcellular localization using deep learning

      Almagro Armenteros, J. J., Sønderby, C. K., Sønderby, S. K., Nielsen, H. & Winther, Ole, 1 Nov 2017, In : Bioinformatics. 33, 21, p. 3387-3395 9 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    3. Published

      SignalP 5.0 improves signal peptide predictions using deep neural networks

      Armenteros, J. J. A., Tsirigos, Konstantinos, Sønderby, C. K., Petersen, T. N., Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 18 Feb 2019, In : Nature Biotechnology. 37, 4, p. 420-423

      Research output: Contribution to journalJournal articleCommunication

    4. 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

    5. Published

      BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

      Bagger, F. O., Sasivarevic, D., Hadi Sohi, S., Laursen, L. G., xfd783, xfd783, Sønderby, C. K., Winther, Ole, Rapin, N. & Porse, Bo Torben, 4 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D917-24 8 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    6. Published

      A perspective on inverse design of battery interphases using multi-scale modelling, experiments and generative deep learning

      Bhowmik, A., Castelli, I. E., Garcia-Lastra, J. M., Bjørn-Jørgensen, P., Winther, Ole & Vegge, T., 2019, In : Energy Storage Materials. 21, p. 446-456

      Research output: Contribution to journalReviewResearchpeer-review

    7. Published

      Competence classification of cumulus and granulosa cell transcriptome in embryos matched by morphology and female age

      Borup, R., Thuesen, L. L., tcg964, tcg964, Andersen, Anders Nyboe, Ziebe, S., Winther, Ole & Grøndahl, M. L., 2016, In : P L o S One. 11, 4, p. 1-19 19 p., e0153562.

      Research output: Contribution to journalJournal articleResearchpeer-review

    8. 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

    9. Published

      Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments

      Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, Lars Vedel & Winther, Ole, 2020, In : Translational Psychiatry. 10, 12 p., 194.

      Research output: Contribution to journalJournal articleResearchpeer-review

    10. Published

      Forecasting Mood in Bipolar Disorder From Smartphone Self-assessments: Hierarchical Bayesian Approach

      Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, Lars Vedel & Winther, Ole, 1 Apr 2020, In : JMIR mHealth and uHealth. 8, 4, 14 p., e15028.

      Research output: Contribution to journalJournal articleResearchpeer-review

    11. 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

    12. 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

    13. Published

      Reducing the rate of psychiatric re-admissions in bipolar disorder using smartphones - The RADMIS trial

      Faurholt-Jepsen, M., Tønning, Morten Lindbjerg, Fros, M., Martiny, Klaus, Tuxen, N., Rosenberg, N., Busk, J., Winther, Ole, Thaysen-Petersen, D., Aamund, K. A., Tolderlund, L., Bardram, J. E. & Kessing, Lars Vedel, 2021, In : Acta Psychiatrica Scandinavica. 143, 5, p. 453-465 13 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    14. Published

      Sequential neural models with stochastic layers

      Fraccaro, M., Sønderby, S. K., Paquet, U. & Winther, Ole, 2016, Neural Information Processing Systems 2016. Lee, D. D., Sugiyama, M., Luxburg, U. V., Guyon, I. & Garnett, R. (eds.). Neural Information Processing Systems Foundation, p. 2207-2215 9 p. (Advances in Neural Information Processing Systems, Vol. 29).

      Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

    15. 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

    16. 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

    17. Published

      scVAE: variational auto-encoders for single-cell gene expression data

      Grønbech, Christopher Heje, Vording, M. F., Timshel, P., Sønderby, C. K., Pers, Tune H & Winther, Ole, 2020, In : Bioinformatics. 36, 16, p. 4415-4422 8 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    18. 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

    19. 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

    20. Published

      Airway inflammation in chronic rhinosinusitis with nasal polyps and asthma: the united airways concept further supported

      Håkansson, K., Bachert, C., Konge, Lars, Thomsen, Simon Francis, Pedersen, Anders Elm, Poulsen, Steen Seier, Martin-Bertelsen, T., Winther, Ole, Backer, Vibeke & von Buchwald, Christian, 2015, In : PloS one. 10, 7, 11 p., e0127228.

      Research output: Contribution to journalJournal articleResearchpeer-review

    21. Published

      An introduction to deep learning on biological sequence data: examples and solutions

      Jurtz, V. I., Johansen, A. R., Nielsen, M., Almagro Armenteros, J. J., Nielsen, H., Sønderby, C. K., Winther, Ole & Sønderby, S. K., 15 Nov 2017, In : Bioinformatics. 33, 22, p. 3685-3690 6 p.

      Research output: Contribution to journalReviewResearchpeer-review

    22. 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

    23. Published

      The Bipolar Illness Onset study: research protocol for the BIO cohort study

      Kessing, Lars Vedel, Munkholm, K., Faurholt-Jepsen, M., Miskowiak, Kamilla Woznica, Nielsen, L. B., Frikke-Schmidt, Ruth, Ekstrøm, Claus Thorn, Winther, Ole, Pedersen, Bente Klarlund, Poulsen, Henrik Enghusen, McIntyre, R. S., Kapczinski, F., Gattaz, W. F., Bardram, J., Frost, M., Mayora, O., Knudsen, Gitte Moos, Phillips, M. & Vinberg, Maj, 2017, In : BMJ Open. 7, 6, 12 p., e015462.

      Research output: Contribution to journalJournal articleResearchpeer-review

    24. Published

      Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data

      Kinalis, S., Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2019, In : BMC Bioinformatics. 20, 9 p., 379.

      Research output: Contribution to journalJournal articleResearchpeer-review

    25. Published

      NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning

      Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, Ole, Nielsen, M., Petersen, Bent & Marcatili, P., 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 6, p. 520-527

      Research output: Contribution to journalJournal articleResearchpeer-review

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