Ole Winther

Ole Winther

Professor with special responsibilities, Visiting professor, Professor MSO

Member of:

    ORCID: 0000-0002-1966-3205

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    1. Published

      Transfer learning reveals sequence determinants of regulatory element accessibility

      Salvatore, Marco, Horlacher, M., Winther, Ole & Andersson, Robin, 2022, bioRxiv, 24 p.

      Research output: Working paper › Preprint

    2. 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 journal › Journal article › Research › peer-review

    3. 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, M., Sørensen, C. H., Kiss, K., Bennedbæk, F. N. & Nielsen, Finn Cilius, 2012, In: Journal of Molecular Endocrinology. 48, 1, p. 11-23 13 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    4. Published

      Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory

      Rieger, L. H., Flores, E., Nielsen, K. F., Norby, P., Ayerbe, E., Winther, Ole, Vegge, T. & Bhowmik, A., 2023, In: Digital Discovery. 2, 1, p. 112-122 11 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    5. 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 journal › Journal article › Research › peer-review

    6. 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 journal › Journal article › Research › peer-review

    7. 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 journal › Conference abstract in journal › Research › peer-review

    8. 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 journal › Journal article › Research › peer-review

    9. 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 journal › Journal article › Research › peer-review

    10. 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 journal › Journal article › Research › peer-review

    11. 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 journal › Journal article › Research › peer-review

    12. 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 journal › Journal article › Research › peer-review

    13. Published

      Improved metagenome binning and assembly using deep variational autoencoders

      Nissen, J. N., Johansen, Joachim, Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2021, In: Nature Biotechnology. 39, p. 555-560

      Research output: Contribution to journal › Journal article › Research › peer-review

    14. Published

      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, (bioRxiv).

      Research output: Working paper › Preprint

    15. 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, Lennart Jan, Cayé-Thomasen, Per & Sørensen, Mads Sølvsten, 2014, In: Anatomical Record. 297, 12, p. 2349-2355 7 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    16. Published

      The middle ear immune defense changes with age

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

      Research output: Contribution to journal › Journal article › Research › peer-review

    17. 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, Lennart Jan, Rye-Jørgensen, N., Bloch, S. & Sørensen, Mads Sølvsten, 2015, In: Otology & Neurotology. 36, 4, p. 727-732 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    18. 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 journal › Journal article › Research › peer-review

    19. Published

      NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data

      Montemurro, A., Schuster, Viktoria, Povlsen, H. R., Bentzen, A. K., Jurtz, V., Chronister, W. D., Crinklaw, A., Hadrup, S. R., Winther, Ole, Peters, B., Jessen, L. E. & Nielsen, M., 2021, In: Communications Biology . 4, 13 p., 1060.

      Research output: Contribution to journal › Journal article › Research › peer-review

    20. Published

      Can large language models reason about medical questions?

      Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.

      Research output: Contribution to journal › Journal article › Research › peer-review

    21. Published

      Optimal Variance Control of the Score-Function Gradient Estimator for Importance Weighted Bounds

      Liévin, V., Dittadi, A., Christensen, Anders & Winther, Ole, 2020, In: Advances in Neural Information Processing Systems. 2020-December, 12 p.

      Research output: Contribution to journal › Conference article › Research › peer-review

    22. Published

      Variational Open-Domain Question Answering

      Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, Ole, 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.

      Research output: Contribution to journal › Conference article › Research › peer-review

    23. 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, Steffen, 2014, In: Acta Ophthalmologica. 92, 6, p. 541-549

      Research output: Contribution to journal › Journal article › Research › peer-review

    24. 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 proceeding › Article in proceedings › Research › peer-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 journal › Journal article › Research › peer-review

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