Ole Winther
Professor with special responsibilities, Visiting professor, Professor MSO
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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-W234Research output: Contribution to journal › Journal article › Research › peer-review
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DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning
Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2024, In: Bioinformatics. 40, 2, 10 p., btae065.Research output: Contribution to journal › Journal article › Research › peer-review
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DeepPeptide predicts cleaved peptides in proteins using conditional random fields
Teufel, Felix Georg, Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.Research output: Contribution to journal › Journal article › Research › peer-review
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Deorphanizing Peptides Using Structure Prediction
Teufel, Felix Georg, Refsgaard, J. C., Kasimova, M. A., Deibler, K., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Journal of Chemical Information and Modeling. 63, 9, 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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DermX: An end-to-end framework for explainable automated dermatological diagnosis
Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, Ole & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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
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DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations
Høie, M. H., Gade, F. S., Johansen, J., Würtzen, C., Winther, Ole, Nielsen, M. & Marcatili, P., 2024, In: Frontiers in Immunology. 15, 12 p., 1322712.Research output: Contribution to journal › Journal article › Research › peer-review
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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. e1000562Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells
Strickertsson, J. A. B., Desler, Claus, 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 journal › Journal article › Research › peer-review
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Explainable Image Quality Assessments in Teledermatological Photography
Jalaboi, R., Winther, Ole & Galimzianova, A., 2023, In: Telemedicine and e-Health. 29, 9, p. 1342-1348 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M. & 4 others, , 2009, In: Genome Research. 19, 2, p. 255-65 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces
Busk, J., Schmidt, M. N., Winther, Ole, Vegge, T. & Jørgensen, P. B., 2023, In: Physical Chemistry Chemical Physics. 25, p. 25828-25837 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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GraphPart: homology partitioning for biological sequence analysis
Teufel, Felix Georg, Gíslason, M. H., Almagro Armenteros, J. J., Johansen, A. R., Winther, Ole & Nielsen, H., 2023, In: NAR Genomics and Bioinformatics. 5, 4, 9 p., lqad088.Research output: Contribution to journal › Journal article › Research › peer-review
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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. R107Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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
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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. 555-560Research output: Contribution to journal › Journal article › Research › peer-review
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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, 21Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
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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. 515Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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. D102-6Research output: Contribution to journal › Journal article › Research › peer-review
ID: 171145930
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2987
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Multivariate Hawkes process models of the occurrence of regulatory elements
Research output: Contribution to journal › Journal article › Research › peer-review
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2491
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HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
984
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Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells
Research output: Contribution to journal › Journal article › Research › peer-review
Published