Ole Winther

Ole Winther

Professor with special responsibilities, Visiting professor, Professor MSO

Member of:

    ORCID: 0000-0002-1966-3205

    Publication year:
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    1. 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 journal › Journal article › Research › peer-review

    2. 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

    3. 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

    4. Published

      Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals

      Wu, X., Bekker-Jensen, I. H., Christensen, J., Rasmussen, K. D., Sidoli, S., Qi, Y., Kong, Y., Wang, X., Cui, Y., Xiao, Z., Xu, G., Williams, K., Rappsilber, J., Sønderby, C. K., Winther, Ole, Jensen, O. N. & Helin, K., 2015, In: Cell Research. 25, p. 1205-1218 14 p.

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

    5. 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

    6. Published

      Transition1x: a dataset for building generalizable reactive machine learning potentials

      Schreiner, M., Bhowmik, A., Vegge, T., Busk, J. & Winther, Ole, 2022, In: Scientific Data. 9, 1, 9 p., 779.

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

    7. 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 › Research

    8. Published

      Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility

      Salvatore, Marco, Horlacher, M., Marsico, A., Winther, Ole & Andersson, Robin, 2023, In: NAR Genomics and Bioinformatics. 5, 2, 10 p., 026.

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

    9. 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

    10. Published

      Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

      Horlacher, M., Wagner, N., Moyon, L., Kuret, K., Goedert, N., Salvatore, Marco, Ule, J., Gagneur, J., Winther, Ole & Marsico, A., 2023, In: Genome Biology. 24, 1, 37 p., 180.

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

    11. Published

      The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

      Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M. & 31 others, Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Jacobsen, A., Krogh, Anders, Nygaard, S., Sandelin, Albin Gustav, Valen, E., Winther, Ole & Riken Omics Science Center, R. O. S. C., 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.

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

    12. 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

    13. 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, M. L., Faurholt-Jepsen, Maria , 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 journal › Journal article › Research › peer-review

    14. Published

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

      Kessing, Lars Vedel, Munkholm, K., Faurholt-Jepsen, M., Miskowiak, Kamilla, 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 journal › Journal article › Research › peer-review

    15. 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 journal › Review › Research › peer-review

    16. Published

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

      Sidiropoulos, N., 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 journal › Journal article › Research › peer-review

    17. Published

      SignalP 6.0 predicts all five types of signal peptides using protein language models

      Teufel, Felix Georg, Almagro Armenteros, J. J., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, Konstantinos, Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 2022, In: Nature Biotechnology. 40, p. 1023-1025

      Research output: Contribution to journal › Comment/debate › Research

    18. 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 journal › Journal article › Communication

    19. 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 proceeding › Article in proceedings › Research › peer-review

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

    21. Published

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

      Faurholt-Jepsen, M., Lindbjerg Tønning, M., 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 journal › Journal article › Research › peer-review

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

    23. Published

      RNA trafficking and subcellular localization—a review of mechanisms, experimental and predictive methodologies

      Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2023, In: Briefings in Bioinformatics. 24, 5, 14 p., bbad249.

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

    24. 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 journal › Conference article › Research › peer-review

    25. 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

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