Ole Winther

Ole Winther

Professor with special responsibilities


  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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, A. N., 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

  8. 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

  9. 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

  10. 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

  11. Published

    Calibrated uncertainty for molecular property prediction using ensembles of message passing neural networks

    Busk, J., Jørgensen, P. B., Bhowmik, A., Schmidt, M. N., Winther, Ole & Vegge, T., 2022, In: Machine Learning: Science and Technology. 3, 1, 12 p., 015012.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. 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

  13. 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

  14. 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 journalJournal articleResearchpeer-review

  15. 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

  16. Published

    Gene expression of the endolymphatic sac

    Friis, M., Martin-Bertelsen, T., Friis-Hansen, Lennart Jan, 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

  17. Published

    A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

    Gabrielaite, M., Torp, M., Rasmussen, M., Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C., Kinalis, S., Madsen, M., Yde, C., Rønn, O. L., Marvig, R., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, bioRxiv, 29 p.

    Research output: Working paperPreprintResearch

  18. Published

    A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

    Gabrielaite, M., Torp, M. H., Rasmussen, Malthe Sebro, Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C. B., Kinalis, S., Madsen, M. B., Kodama, M., Demircan, G. S., Simonyan, A., Yde, C. W., Olsen, L. R., Marvig, R. L., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, In: Cancers. 13, 24, 6283.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. 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 journalJournal articleResearchpeer-review

  20. 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 journalJournal articleResearchpeer-review

  21. 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

  22. 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

  23. 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

  24. Published

    NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

    Høie, M. H., Kiehl, E. N., Petersen, Bent, Nielsen, M., Winther, Ole, Nielsen, H., Hallgren, J. & Marcatili, P., 2022, In: Nucleic Acids Research. 50, W1, p. W510-W515 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. 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

  26. 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

  27. 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 journalJournal articleResearchpeer-review

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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 journalConference articleResearchpeer-review

  33. 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 journalJournal articleResearchpeer-review

  34. 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

  35. 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 journalJournal articleResearchpeer-review

  36. 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 journalJournal articleResearchpeer-review

  37. 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 journalJournal articleResearchpeer-review

  38. 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

  39. 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 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. 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

  42. 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

  43. 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

  44. 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 journalJournal articleResearchpeer-review

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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, Lennart Jan, 2013, In: PLOS ONE. 8, 4, p. 1-13 13 p., e63147.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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 journalComment/debateResearch

  57. 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

  58. 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

  59. Published

    DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

    Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, Ole, 2022, In: Nucleic Acids Research. 50, W1, p. W228-W234

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. 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, M., 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 journalJournal articleResearchpeer-review

  61. 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

  62. 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

  63. 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

  64. 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

  65. Published

    Interpretable autoencoders trained on single cell sequencing data can transfer directly to data from unseen tissues

    Walbech, J. S., Kinalis, S., Winther, Ole, Nielsen, Finn Cilius & Bagger, F. O., 2022, In: Cells. 11, 12 p., 85.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. 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, Kristian, 2015, In: Cell Research. 25, p. 1205-1218 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

ID: 171145930