Ole Winther

Ole Winther

Professor with special responsibilities, Visiting professor, Professor MSO

Member of:

    ORCID: 0000-0002-1966-3205

    Publication year:
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    1 - 84 out of 84Page size: 500
    1. 2024
    2. 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

    3. 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

    4. 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

    5. 2023
    6. Published

      Deep integrative models for large-scale human genomics

      Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, David, 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

    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. 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

    17. 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

    18. 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

    19. 2022
    20. 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

    21. 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 journal › Journal article › Research › peer-review

    22. 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

    23. 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

    24. 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 journal › Comment/debate › Research

    25. 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

    26. 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

    27. 2021
    28. 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

    29. 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

    30. 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 journal › Journal article › Research › peer-review

    31. 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 journal › Journal article › Research › peer-review

    32. 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 journal › Journal article › Research › peer-review

    33. 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, Maria , 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 journal › Journal article › Research › peer-review

    34. 2020
    35. 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 journal › Journal article › Research › peer-review

    36. 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 journal › Journal article › Research › peer-review

    37. 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 journal › Journal article › Research › peer-review

    38. 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 journal › Journal article › Research › peer-review

    39. 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 journal › Conference article › Research › peer-review

    40. 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 journal › Review › Research › peer-review

    41. 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 journal › Journal article › Research › peer-review

    42. 2019
    43. 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 journal › Journal article › Communication

    44. 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 journal › Review › Research › peer-review

    45. 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 journal › Journal article › Research › peer-review

    46. 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 journal › Journal article › Research › peer-review

    47. 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 journal › Journal article › Research › peer-review

    48. 2018
    49. Published

      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, (bioRxiv).

      Research output: Working paper › Preprint › Research

    50. Published

      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

    51. 2017
    52. 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 journal › Review › Research › peer-review

    53. 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 journal › Journal article › Research › peer-review

    54. 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 journal › Journal article › Research › peer-review

    55. 2016
    56. 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, H. S. & Lassen, Ulrik Niels, Oct 2016, In: Molecular Oncology. 10, 8, p. 1160-1168

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

    57. 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., Pundhir, Sachin, 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 journal › Journal article › Research › peer-review

    58. 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 proceeding › Article in proceedings › Research › peer-review

    59. 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 journal › Journal article › Research › peer-review

    60. 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 proceeding › Article in proceedings › Research › peer-review

    61. 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 proceeding › Article in proceedings › Research › peer-review

    62. 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 journal › Journal article › Research › peer-review

    63. 2015
    64. 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 journal › Journal article › Research › peer-review

    65. 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 journal › Journal article › Research › peer-review

    66. 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 journal › Journal article › Research › peer-review

    67. 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, G. & Nielsen, Finn Cilius, 2015, In: B M C Cancer. 15, 14 p., 151.

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

    68. 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 proceeding › Article in proceedings › Research › peer-review

    69. 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 journal › Journal article › Research › peer-review

    70. 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, K., 2015, In: Cell Research. 25, p. 1205-1218 14 p.

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

    71. 2014
    72. 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 journal › Journal article › Research › peer-review

    73. 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 journal › Journal article › Research › peer-review

    74. 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 journal › Journal article › Research › peer-review

    75. 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 journal › Journal article › Research › peer-review

    76. 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 journal › Journal article › Research › peer-review

    77. 2013
    78. Published

      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

    79. 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 journal › Journal article › Research › peer-review

    80. 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 journal › Conference abstract in journal › Research › peer-review

    81. 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 journal › Journal article › Research › peer-review

    82. 2012
    83. 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, 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

    84. 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 journal › Journal article › Research › peer-review

    85. 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 journal › Conference article › Research › peer-review

    86. 2011
    87. 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 journal › Journal article › Research › peer-review

    88. 2010
    89. 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, F. N. & Nielsen, Finn Cilius, 2010, In: Endocrine - Related Cancer. 17, 3, p. 691-708 18 p.

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

    90. 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 journal › Journal article › Research › peer-review

    91. 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 journal › Journal article › Research › peer-review

    92. 2009
    93. 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 journal › Journal article › Research › peer-review

    94. 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-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M. & 4 others, Hayashizaki, Y., Gustincich, S., Sandelin, Albin Gustav & Carninci, P., 2009, In: Genome Research. 19, 2, p. 255-65 10 p.

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

    95. 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 journal › Journal article › Research › peer-review

    96. 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. & 31 others, 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 journal › Journal article › Research › peer-review

    97. 2008
    98. 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 journal › Journal article › Research › peer-review

    99. 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 journal › Journal article › Research › peer-review

    100. 2006
    101. 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 journal › Journal article › Research › peer-review

    102. 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 journal › Journal article › Research › peer-review

    ID: 171145930