Ole Winther

Ole Winther

Professor with special responsibilities

Member of:


    1. 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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. Submitted

      Binning microbial genomes using deep learning

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

      Research output: Contribution to journalJournal articleResearch

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. Published

      Convolutional LSTM networks for subcellular localization of proteins

      Sønderby, S. K., Sønderby, C. K., Nielsen, H. & Winther, Ole, 2015, Algorithms for Computational Biology. Dediu, A-H., Hernández-Quiroz, F., Martín-Vide, C. & Rosenblueth, D. A. (eds.). Springer, p. 68-80 13 p. (Lecture notes in computer science, Vol. 9199).

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

    17. 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

    18. 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

    19. 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

    20. 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

    21. 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

    22. Published

      Differential gene expression in the otic capsule and the middle ear-an annotation of bone-related signaling genes

      Nielsen, M. C., Martin-Bertelsen, T., Friis, M., Winther, Ole, Friis-Hansen, L. J., Rye-Jørgensen, N., Bloch, S. & Sørensen, Mads Sølvsten, 2015, In : Otology & Neurotology. 36, 4, p. 727-732 6 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    23. 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

    24. 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

    25. 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

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