Ole Winther
Professor with special responsibilities, Visiting professor, Professor MSO
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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
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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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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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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
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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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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
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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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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
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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
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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
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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
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Deep integrative models for large-scale human genomics
Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, D., Winther, Ole, Lund, O., Ostrowski, Sisse Rye, Erikstrup, C., Pedersen, Ole Birger Vesterager, Nyegaard, Mette, Brunak, Søren, Vilhjálmsson, B. & Rasmussen, Simon, 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 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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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, , 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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 proceeding › Article in proceedings › Research › peer-review
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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 proceeding › Article in proceedings › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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. 1023-1025Research output: Contribution to journal › Comment/debate › Research
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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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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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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 journal › Journal article › Research › peer-review
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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. 496-510Research output: Contribution to journal › Review › Research › peer-review
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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
ID: 171145930
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2989
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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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2498
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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
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987
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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