Ole Winther

Research output

Research output per year 2006 2015 2016 2020 2022 2023 2024

• 10878 Citations
• 72 Journal article
• 4 Article in proceedings
• 3 Conference article
• 3 Review
• 6 More
  • 3 Preprint
  • 1 Paper
  • 1 Comment/debate
  • 1 Conference abstract in journal

Research output per year

Research output per year

Search results

• 2024

  BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks

  Marin, F. I., Teufel, F., Horlacher, M., Madsen, D., Pultz, D., Winther, O. & Boomsma, W., 2024. 36 p.

  Research output: Contribution to conference › Paper › Research

  Open Access

  File
  1 Citation (Scopus)

  9 Downloads (Pure)

• Can large language models reason about medical questions?

  Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, O., 2024, In: Patterns. 5, 3, 12 p., 100943.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  16 Citations (Scopus)

  14 Downloads (Pure)

• DeepLoc 2.1: multi-label membrane protein type prediction using protein language models

  Ødum, M. T., Teufel, F., Thumuluri, V., Armenteros, J. J. A., Johansen, A. R., Winther, O. & Nielsen, H., 2024, In: Nucleic Acids Research. 52, W1, p. W215-W220 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  1 Citation (Scopus)

  3 Downloads (Pure)

• DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning

  Wang, J., Horlacher, M., Cheng, L. & Winther, O., 2024, In: Bioinformatics. 40, 2, 10 p., btae065.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  3 Citations (Scopus)

  10 Downloads (Pure)

• DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

  Høie, M. H., Gade, F. S., Johansen, JM., Würtzen, C., Winther, O., Nielsen, M. & Marcatili, P., 2024, In: Frontiers in Immunology. 15, 12 p., 1322712.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  14 Citations (Scopus)

  11 Downloads (Pure)

• Physician Level Assessment of Hirsute Women and of Their Eligibility for Laser Treatment With Deep Learning

  Thomsen, K., Jalaboi, R., Winther, O., Lomholt, H. B., Lorentzen, H. F., Høgsberg, T., Egekvist, H., Hedelund, L., Jørgensen, S., Frost, S., Bertelsen, T. & Iversen, L., 2024, (E-pub ahead of print) In: Lasers in Surgery and Medicine.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access
• 2023

  Deep integrative models for large-scale human genomics

  Sigurdsson, A. I., Louloudis, I., Banasik, K., Westergaard, D., Winther, O., Lund, O., Ostrowski, S. R., Erikstrup, C., Pedersen, O. B., Nyegaard, M., Brunak, S., Vilhjálmsson, BJ. & Rasmussen, S., 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  51 Downloads (Pure)

• DeepPeptide predicts cleaved peptides in proteins using conditional random fields

  Teufel, F., Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, O. & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  12 Downloads (Pure)

• Deorphanizing Peptides Using Structure Prediction

  Teufel, F., Refsgaard, J. C., Kasimova, M. A., Deibler, K., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, O. & Madsen, D., 2023, In: Journal of Chemical Information and Modeling. 63, 9, 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  File
  11 Citations (Scopus)

• DermX: An end-to-end framework for explainable automated dermatological diagnosis

  Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, O. & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  7 Citations (Scopus)

  20 Downloads (Pure)

• Explainable Image Quality Assessments in Teledermatological Photography

  Jalaboi, R., Winther, O. & 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

  Open Access

  File
  6 Citations (Scopus)

  14 Downloads (Pure)

• FindZebra online search delving into rare disease case reports using natural language processing

  Liévin, V., Hansen, J. M., Lund, A., Elstein, D., Matthiesen, M. E., Elomaa, K., Zarakowska, K., Himmelhan, I., Botha, J., Borgeskov, H. & Winther, O., 2023, In: PLOS Digital Health. 2, 6, e0000269.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access
  2 Citations (Scopus)

• Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces

  Busk, J., Schmidt, M. N., Winther, O., 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

  Open Access

  File
  3 Citations (Scopus)

  17 Downloads (Pure)

• GraphPart: homology partitioning for biological sequence analysis

  Teufel, F., Gíslason, M. H., Almagro Armenteros, J. J., Johansen, A. R., Winther, O. & Nielsen, H., 2023, In: NAR Genomics and Bioinformatics. 5, 4, 9 p., lqad088.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)

  17 Downloads (Pure)

• 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, O., 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

  Open Access

  File
  3 Citations (Scopus)

  14 Downloads (Pure)

• RNA trafficking and subcellular localization—a review of mechanisms, experimental and predictive methodologies

  Wang, J., Horlacher, M., Cheng, L. & Winther, O., 2023, In: Briefings in Bioinformatics. 24, 5, 14 p., bbad249.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  6 Citations (Scopus)

  16 Downloads (Pure)

• 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, M., Ule, J., Gagneur, J., Winther, O. & Marsico, A., 2023, In: Genome Biology. 24, 1, 37 p., 180.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  8 Citations (Scopus)

  13 Downloads (Pure)

• Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility

  Salvatore, M., Horlacher, M., Marsico, A., Winther, O. & Andersson, R., 2023, In: NAR Genomics and Bioinformatics. 5, 2, 10 p., 026.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  6 Citations (Scopus)

  20 Downloads (Pure)

• 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, O., 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

  Open Access

  File
  13 Citations (Scopus)

  18 Downloads (Pure)

• Variational Open-Domain Question Answering

  Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, O., 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.

  Research output: Contribution to journal › Conference article › Research › peer-review

  Open Access

  File
  6 Citations (Scopus)
• 2022

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

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

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  33 Citations (Scopus)

  30 Downloads (Pure)

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

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

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  243 Citations (Scopus)

  22 Downloads (Pure)

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

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

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  4 Citations (Scopus)

  35 Downloads (Pure)

• 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, B., Nielsen, M., Winther, O., 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

  Open Access

  File
  29 Downloads (Pure)

• SignalP 6.0 predicts all five types of signal peptides using protein language models

  Teufel, F., Almagro Armenteros, J. J., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, K. D., Winther, O., Brunak, S., von Heijne, G. & Nielsen, H., 2022, In: Nature Biotechnology. 40, p. 1023-1025

  Research output: Contribution to journal › Comment/debate › Research

  Open Access

  File
  1076 Citations (Scopus)

  45 Downloads (Pure)

• Transfer learning reveals sequence determinants of regulatory element accessibility

  Salvatore, M., Horlacher, M., Winther, O. & Andersson, R., 2022, bioRxiv, 24 p.

  Research output: Working paper › Preprint › Research

  File
  17 Downloads (Pure)

• Transition1x: a dataset for building generalizable reactive machine learning potentials

  Schreiner, M., Bhowmik, A., Vegge, T., Busk, J. & Winther, O., 2022, In: Scientific Data. 9, 1, 9 p., 779.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  29 Citations (Scopus)

  18 Downloads (Pure)
• 2021

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

  Gabrielaite, M., Torp, M. H., Rasmussen, M. S., Andreu-Sánchez, S., Vieira, F. G., 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, M., Nielsen, F. C., Winther, O. & Bagger, F. O., 2021, In: Cancers. 13, 24, 6283.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  45 Citations (Scopus)

  34 Downloads (Pure)

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

  Gabrielaite, M., Torp, MH., Rasmussen, MS., Andreu-Sánchez, S., Vieira, FG., Pedersen, CB., Kinalis, S., Madsen, MB., Yde, CW., Rønn, O. L., Marvig, RL., Østrup, O., Rossing, C. M., Nielsen, F. C., Winther, O. & Bagger, F. O., 2021, bioRxiv, 29 p.

  Research output: Working paper › Preprint › Research

  Open Access

  File
  25 Downloads (Pure)

• Improved metagenome binning and assembly using deep variational autoencoders

  Nissen, J. N., Johansen, J., Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Gronbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O. & Rasmussen, S., 2021, In: Nature Biotechnology. 39, p. 555-560

  Research output: Contribution to journal › Journal article › Research › peer-review

  File
  223 Citations (Scopus)

  33 Downloads (Pure)

• NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data

  Montemurro, A., Schuster, V., Povlsen, H. R., Bentzen, A. K., Jurtz, V., Chronister, W. D., Crinklaw, A., Hadrup, S. R., Winther, O., Peters, B., Jessen, L. E. & Nielsen, M., 2021, In: Communications Biology . 4, 13 p., 1060.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  97 Citations (Scopus)

  54 Downloads (Pure)

• Reducing the rate of psychiatric re-admissions in bipolar disorder using smartphones - The RADMIS trial

  Faurholt-Jepsen, M., Lindbjerg Tønning, M., Fros, M., Martiny, K., Tuxen, N., Rosenberg, N., Busk, J., Winther, O., Thaysen-Petersen, D., Aamund, K. A., Tolderlund, L., Bardram, J. E. & Kessing, L. V., 2021, In: Acta Psychiatrica Scandinavica. 143, 5, p. 453-465 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  20 Citations (Scopus)

  15 Downloads (Pure)

• 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, K., Tuxen, N., Rosenberg, N., Busk, J., Winther, O., Melbye, S. A., Thaysen-Petersen, D., Aamund, K. A., Tolderlundh, L., Bardram, J. E. & Kessing, L. V., 2021, In: Journal of Affective Disorders. 282, p. 354-363 10 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  23 Citations (Scopus)
• 2020

  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, L. V. & Winther, O., 2020, In: Translational Psychiatry. 10, 12 p., 194.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  14 Citations (Scopus)

  27 Downloads (Pure)

• Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases

  Thomsen, K., Christensen, A. L., Iversen, L., Lomholt, H. B. & Winther, O., 2020, In: Frontiers in Medicine. 7, 7 p., 574329.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  28 Citations (Scopus)

  39 Downloads (Pure)

• Forecasting Mood in Bipolar Disorder From Smartphone Self-assessments: Hierarchical Bayesian Approach

  Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, L. V. & Winther, O., 1 Apr 2020, In: JMIR mHealth and uHealth. 8, 4, 14 p., e15028.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  28 Citations (Scopus)

  49 Downloads (Pure)

• Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools

  Prachar, M., Justesen, S., Steen-Jensen, D. B., Thorgrimsen, S., Jurgons, E., Winther, O. & Bagger, F. O., 2020, In: Scientific Reports. 10, 8 p., 20465.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  45 Citations (Scopus)

  42 Downloads (Pure)

• Optimal Variance Control of the Score-Function Gradient Estimator for Importance Weighted Bounds

  Liévin, V., Dittadi, A., Christensen, A. & Winther, O., 2020, In: Advances in Neural Information Processing Systems. 2020-December, 12 p.

  Research output: Contribution to journal › Conference article › Research › peer-review

  Open Access

  File
  2 Citations (Scopus)

  15 Downloads (Pure)

• scVAE: variational auto-encoders for single-cell gene expression data

  Grønbech, C. H., Vording, M. F., Timshel, P., Sønderby, C. K., Pers, T. H. & Winther, O., 2020, In: Bioinformatics. 36, 16, p. 4415-4422 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access
  122 Citations (Scopus)

• Systematic review of machine learning for diagnosis and prognosis in dermatology

  Thomsen, K., Iversen, L., Titlestad, T. L. & Winther, O., 2020, In: Journal of Dermatological Treatment. 31, 5, p. 496-510

  Research output: Contribution to journal › Review › Research › peer-review
  64 Citations (Scopus)
• 2019

  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, O. & Vegge, T., 2019, In: Energy Storage Materials. 21, p. 446-456

  Research output: Contribution to journal › Review › Research › peer-review

  Open Access

  File
  86 Citations (Scopus)

  250 Downloads (Pure)

• Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data

  Kinalis, S., Nielsen, F. C., Winther, O. & Bagger, F. O., 2019, In: BMC Bioinformatics. 20, 9 p., 379.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  19 Citations (Scopus)

  214 Downloads (Pure)

• Detecting sequence signals in targeting peptides using deep learning

  Almagro Armenteros, J. J., Salvatore, M., Emanuelsson, O., Winther, O., 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

  Open Access

  File
  554 Citations (Scopus)

  111 Downloads (Pure)

• 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, O., Nielsen, M., Petersen, B. & Marcatili, P., 2019, In: Proteins: Structure, Function and Bioinformatics. 87, 6, p. 520-527

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  375 Citations (Scopus)

  55 Downloads (Pure)

• SignalP 5.0 improves signal peptide predictions using deep neural networks

  Armenteros, J. J. A., Tsirigos, K., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne, G. & Nielsen, H., 18 Feb 2019, In: Nature Biotechnology. 37, 4, p. 420-423

  Research output: Contribution to journal › Journal article › Communication

  Open Access

  File
  2877 Citations (Scopus)

  1775 Downloads (Pure)
• 2018

  Binning microbial genomes using deep learning

  Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, C. H., Nielsen, H. B., Petersen, T. N., Winther, O. & Rasmussen, S., 2018, (bioRxiv).

  Research output: Working paper › Preprint › Research

  File
  236 Downloads (Pure)

• SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

  Sidiropoulos, N., Sohi, S. H., Pedersen, T. L., Porse, B. T., Winther, O., 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
  31 Citations (Scopus)
• 2017

  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, O. & Sønderby, S. K., 15 Nov 2017, In: Bioinformatics. 33, 22, p. 3685-3690 6 p.

  Research output: Contribution to journal › Review › Research › peer-review
  111 Citations (Scopus)

• DeepLoc: prediction of protein subcellular localization using deep learning

  Almagro Armenteros, J. J., Sønderby, C. K., Sønderby, S. K., Nielsen, H. & Winther, O., 1 Nov 2017, In: Bioinformatics. 33, 21, p. 3387-3395 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  761 Citations (Scopus)

• The Bipolar Illness Onset study: research protocol for the BIO cohort study

  Kessing, L. V., Munkholm, K., Faurholt-Jepsen, M., Miskowiak, K. W., Nielsen, L. B., Frikke-Schmidt, R., Ekstrøm, C. T., Winther, O., Pedersen, B. K., Poulsen, H. E., McIntyre, R. S., Kapczinski, F., Gattaz, W. F., Bardram, J., Frost, M., Mayora, O., Knudsen, G. M., Phillips, M. & Vinberg, M., 2017, In: BMJ Open. 7, 6, 12 p., e015462.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  117 Citations (Scopus)

  447 Downloads (Pure)