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

    32. 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

    33. 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

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

      Research output: Contribution to journalJournal articleResearchpeer-review

    35. 2014
    36. 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

    37. 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

    38. 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

    39. 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 journalJournal articleResearchpeer-review

    40. 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 journalJournal articleResearchpeer-review

    41. 2013
    42. 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

    43. Published

      HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

      Bagger, F. O., Rapin, N. P. J., Theilgaard-Mønch, Kim, Kaczkowski, B., Thorén, L. A. M., Jendholm, L. J., Winther, Ole & Porse, Bo Torben, 2013, In : Nucleic Acids Research. 41, Database issue, p. D1034-D1039 6 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    44. 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 journalConference abstract in journalResearchpeer-review

    45. 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 journalJournal articleResearchpeer-review

    46. 2012
    47. 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

    48. Published

      Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

      Kaczkowski, B., Rossing, M., Andersen, D. K., Dreher, A., Morevati, M., Visser, M. A., Winther, Ole, Nielsen, Finn Cilius & Norrild, B., 2012, In : Scientific Reports. 2, p. 515

      Research output: Contribution to journalJournal articleResearchpeer-review

    49. 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 journalConference articleResearchpeer-review

    50. 2011
    51. Published

      Gene expression of the endolymphatic sac

      Friis, M., Martin-Bertelsen, T., Friis-Hansen, L., Winther, Ole, Henao Giraldo, R., Sørensen, Mads Sølvsten & Qvortrup, Klaus, 2011, In : Acta Oto-Laryngologica. 131, 12, p. 1257-63 7 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    52. 2010
    53. Published

      Molecular signatures of thyroid follicular neoplasia

      Helweg-Larsen, R. B., Rossing, M., Henao Giraldo, R., Yamamoto, Y., Krogdahl, A., Godballe, C., Winther, Ole, Kiss, K., Christensen, L. H., Høgdall, Estrid Vilma Solyom, Bennedbæk, Finn Noe & Nielsen, Finn Cilius, 2010, In : Endocrine - Related Cancer. 17, 3, p. 691-708 18 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    54. Published

      Multivariate Hawkes process models of the occurrence of regulatory elements

      Carstensen, L., Sandelin, Albin Gustav, Winther, Ole & Hansen, Niels Richard, 2010, In : BMC Bioinformatics. 11, p. 456

      Research output: Contribution to journalJournal articleResearchpeer-review

    55. 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 journalJournal articleResearchpeer-review

    56. 2009
    57. 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

    58. Published

      Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

      Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M. E., Zhao, X., Krogh, Anders, Winther, Ole, Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M., Hayashizaki, Y., Gustincich, S., Sandelin, Albin Gustav & Carninci, P., 2009, In : Genome Research. 19, 2, p. 255-65 10 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    59. 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 journalJournal articleResearchpeer-review

    60. 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., 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 journalJournal articleResearchpeer-review

    61. 2008
    62. 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

    63. Published

      JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

      Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T., Winther, Ole, da Piedade, I., Krogh, Anders, Lenhard, B. & Sandelin, Albin Gustav, 2008, In : Nucleic Acids Research. 36, Database issue, p. D102-6

      Research output: Contribution to journalJournal articleResearchpeer-review

    64. 2006
    65. Published

      Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm

      Grotkjær, T., Winther, Ole, Regenberg, Birgitte, Nielsen, J. & Hansen, Lars, 1 Jan 2006, In : Bioinformatics. 22, 1, p. 58-67 10 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    66. 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 journalJournal articleResearchpeer-review

    ID: 171145930