Ole Winther
Professor with special responsibilities, Visiting professor, Professor MSO
- 2024
- Published
Can large language models reason about medical questions?
Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- Published
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
- 2023
- Published
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
- Published
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
- Published
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
- Published
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
- Published
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
- Published
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
- Published
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
- Published
Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs
Einarson, K. A., Bendtsen, K. M., Li, K., Thomsen, M., Kristensen, N. R., Winther, Ole, Fulle, S., Clemmensen, L. & Refsgaard, H. H. F., 2023, In: ACS Omega. 8, 26, p. 23566-23578 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- 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
- 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
- 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
- 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
- 2022
- 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 journal › Journal article › Research › peer-review
- 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-W234Research output: Contribution to journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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. 1023-1025Research output: Contribution to journal › Comment/debate › Research
- 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
- 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
- 2021
- 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 paper › Preprint › Research
- 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 journal › Journal article › Research › peer-review
ID: 171145930
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Multivariate Hawkes process models of the occurrence of regulatory elements
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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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989
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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