Ole Winther

Ole Winther

Professor with special responsibilities

Member of:


    1. 2021
    2. E-pub ahead of print

      Improved metagenome binning and assembly using deep variational autoencoders

      Nissen, J. N., Johansen, Joachim, Allesøe, Rosa Lundbye, Sonderby, C. K., Almagro Armenteros, Jose Juan, Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, Jan 2021, In : Nature Biotechnology. 12 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    3. Accepted/In press

      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, (Accepted/In press) In : Acta Psychiatrica Scandinavica. 13 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    4. Published

      The effect of smartphone-based monitoring and treatment on the rate and duration of psychiatric readmission in patients with unipolar depressive disorder: The RADMIS randomized controlled trial

      Tønning, Morten Lindbjerg, Faurholt-Jepsen, M., Frost, M., Martiny, Klaus, Tuxen, N., Rosenberg, N., Busk, J., Winther, Ole, Melbye, S. A., Thaysen-Petersen, D., Aamund, K. A., Tolderlundh, L., Bardram, J. E. & Kessing, Lars Vedel, 2021, In : Journal of Affective Disorders. 282, p. 354-363 10 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    5. 2020
    6. 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

    7. 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

    8. Published

      Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases

      Thomsen, K., Christensen, A. L., Iversen, L., Lomholt, H. B. & Winther, Ole, 2020, In : Frontiers in Medicine. 7, 7 p., 574329.

      Research output: Contribution to journalJournal articleResearchpeer-review

    9. Published

      Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools

      Prachar, Marek, Justesen, S., Steen-Jensen, D. B., Thorgrimsen, S., Jurgons, E., Winther, Ole & Bagger, F. O., 2020, In : Scientific Reports. 10, 8 p., 20465.

      Research output: Contribution to journalJournal articleResearchpeer-review

    10. Published

      Systematic review of machine learning for diagnosis and prognosis in dermatology

      Thomsen, K., Iversen, L., Titlestad, T. L. & Winther, Ole, 2020, In : Journal of Dermatological Treatment. 31, 5, p. 496-510

      Research output: Contribution to journalReviewResearchpeer-review

    11. 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

    12. 2019
    13. 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

    14. 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

    15. 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

    16. 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

    17. 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

    18. 2018
    19. Submitted

      Binning microbial genomes using deep learning

      Nissen, J. N., Sønderby, C. K., Almagro Armenteros, Jose Juan, Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, (Submitted) In : bioRxiv. 490078.

      Research output: Contribution to journalJournal articleResearch

    20. Published

      SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

      Sidiropoulos, Nikos, Sohi, S. H., Pedersen, T. L., Porse, Bo Torben, Winther, Ole, Rapin, N. & Bagger, F. O., 2018, In : Journal of Computational and Graphical Statistics. 27, 3, p. 673-676 4 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    21. 2017
    22. 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

    23. Published

      DeepLoc: prediction of protein subcellular localization using deep learning

      Almagro Armenteros, Jose Juan, 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

    24. 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

    25. 2016
    26. Published

      Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients

      Urup, T., Michaelsen, Signe Regner, Olsen, L. R., Toft, A., Christensen, I. J., Grunnet, K., Winther, Ole, Broholm, H., Kosteljanetz, M., Issazadeh-Navikas, Shohreh, Poulsen, Hans Skovgaard & Lassen, Ulrik Niels, Oct 2016, In : Molecular Oncology. 10, 8, p. 1160-1168

      Research output: Contribution to journalJournal articleResearchpeer-review

    27. 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

    28. Published

      Autoencoding beyond pixels using a learned similarity metric

      Larsen, A. B. L., Sønderby, S. K., Larochelle, H. & Winther, Ole, 2016, Proceedings of The 33rd International Conference on Machine Learning. Balcan, M. F. & Weinberger, K. Q. (eds.). p. 1558–1566 9 p. (JMLR: Workshop and Conference Proceedings, Vol. 48).

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

    29. 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

    30. Published

      Ladder variational autoencoders

      Sønderby, C. K., Raiko, T., Maaløe, L., Sønderby, S. K. & Winther, Ole, 2016, Advances in Neural Information Processing Systems 29 (NIPS 2016). Lee, D. D., Sugiyama, M., Luxburg, U. V., Guyon, I. & Garnett, R. (eds.). Curran Associates, Inc., p. 3745-3753 9 p. (Advances in Neural Information Processing Systems, Vol. 29).

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

    31. 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

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