Ole Winther

Ole Winther

Professor with special responsibilities

Member of:


    1. 2020
    2. E-pub ahead of print

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

      Grønbech, Christopher Heje, Vording, M. F., Timshel, Pascal Nordgren, Sønderby, C. K., Pers, Tune H & Winther, Ole, 16 May 2020, In : Bioinformatics. 8 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    3. 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

    4. 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

    5. 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

    6. 2019
    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 2018
    13. 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

    14. 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

    15. 2017
    16. 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

    17. 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

    18. 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

    19. 2016
    20. 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

    21. 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

    22. 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

    23. 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, Søren, 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

    24. 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

    25. 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

    26. Published

      The middle ear immune defense changes with age

      Nielsen, M. C., Friis, M., Martin-Bertelsen, T., Winther, Ole, Friis-Hansen, L. J. & Cayé-Thomasen, Per, 2016, In : European Archives of Oto-Rhino-Laryngology. 273, 1, p. 81-86 6 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    27. 2015
    28. Published

      Cellular origin of prognostic chromosomal aberrations in AML patients

      Mora-Jensen, H., Jendholm, L. J., Rapin, N. P. J., Andersen, M. K., Roug, A. S., Bagger, F. O., Bullinger, L., Winther, Ole, Borregaard, N., Porse, Bo Torben & Theilgaard-Mønch, Kim, 11 Feb 2015, In : Leukemia. 29, p. 1785-1789 5 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    29. 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

    30. 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

    31. Published

      Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin

      Vikeså, J., Møller, A. K. H., Kaczkowski, B., Helweg-Larsen, R. B., Winther, Ole, Henao Giraldo, R., Krogh, Anders, Perell, K., Jensen, F., Daugaard, Gedske & Nielsen, Finn Cilius, 2015, In : B M C Cancer. 15, 14 p., 151.

      Research output: Contribution to journalJournal articleResearchpeer-review

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