Ole Winther

2020

Systematic review of machine learning for diagnosis and prognosis in dermatology

Thomsen, K., Iversen, L., Titlestad, T. L. & Winther, O., 3 Jul 2020, In: Journal of Dermatological Treatment.

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

10 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., Sept 2019, In: Energy Storage Materials. 21, p. 446-456

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

20 Citations (Scopus)

24 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., 8 Jul 2019, In: BMC Bioinformatics. 20, 9 p., 379.

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

4 Citations (Scopus)

13 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

97 Citations (Scopus)

3 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., Jun 2019, In: Proteins: Structure, Function and Bioinformatics. 87, 6, p. 520-527

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

91 Citations (Scopus)

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., 1 Apr 2019, In: Nature Biotechnology. 37, 4, p. 420-423

Research output: Contribution to journal › Journal article › Communication

811 Citations (Scopus)

2018

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., 3 Jul 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

12 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 › peer-review

49 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

281 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

55 Citations (Scopus)

165 Downloads (Pure)

2016

Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients

Urup, T., Michaelsen, S. R., Olsen, L. R., Toft, A., Christensen, I. J., Grunnet, K., Winther, O., Broholm, H., Kosteljanetz, M., Issazadeh-Navikas, S., Poulsen, H. S. & Lassen, U. N., Oct 2016, In: Molecular Oncology. 10, 8, p. 1160-1168

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

16 Citations (Scopus)

89 Downloads (Pure)

Autoencoding beyond pixels using a learned similarity metric

Larsen, A. B. L., Sønderby, S. K., Larochelle, H. & Winther, O., 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

183 Citations (Scopus)

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, S., Sønderby, C. K., Winther, O., Rapin, N. & Porse, B. T., 4 Jan 2016, In: Nucleic Acids Research. 44, D1, p. D917-24 8 p.

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

141 Citations (Scopus)

102 Downloads (Pure)

Competence classification of cumulus and granulosa cell transcriptome in embryos matched by morphology and female age

Borup, R., Thuesen, L. L., Andersen, C. Y., Andersen, A. N., Ziebe, S., Winther, O. & Grøndahl, M. L., Apr 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

18 Citations (Scopus)

117 Downloads (Pure)

Ladder variational autoencoders

Sønderby, C. K., Raiko, T., Maaløe, L., Sønderby, S. K. & Winther, O., 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

167 Citations (Scopus)

Sequential neural models with stochastic layers

Fraccaro, M., Sønderby, S. K., Paquet, U. & Winther, O., 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

112 Citations (Scopus)

The middle ear immune defense changes with age

Nielsen, M. C., Friis, M., Martin-Bertelsen, T., Winther, O., Friis-Hansen, L. J. & Cayé-Thomasen, P., 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

3 Citations (Scopus)

2015

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, O., 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

85 Downloads (Pure)

Airway inflammation in chronic rhinosinusitis with nasal polyps and asthma: the united airways concept further supported

Håkansson, K., Bachert, C., Konge, L., Thomsen, S. F., Pedersen, A. E., Poulsen, S. S., Martin-Bertelsen, T., Winther, O., Backer, V. & von Buchwald, C., 1 Jul 2015, In: PloS one. 10, 7, 11 p., e0127228.

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

43 Citations (Scopus)

126 Downloads (Pure)

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, O., Henao Giraldo, R., Krogh, A., Perell, K., Jensen, F., Daugaard, G. & Nielsen, F. C., 19 Mar 2015, In: B M C Cancer. 15, 14 p., 151.

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

28 Citations (Scopus)

118 Downloads (Pure)

Cellular origin of prognostic chromosomal aberrations in AML patients

Mora-Jensen, H., Jendholm, L. J., Rapin, N. P.J.-P., Andersen, M. K., Roug, A. S., Bagger, F. O., Bullinger, L., Winther, O., Borregaard, N., Porse, B. T. & Theilgaard-Mönch, K., 7 Aug 2015, In: Leukemia. 29, p. 1785-1789 5 p.

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

7 Citations (Scopus)

Convolutional LSTM networks for subcellular localization of proteins

Sønderby, S. K., Sønderby, C. K., Nielsen, H. & Winther, O., 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

57 Citations (Scopus)

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, O., Friis-Hansen, L. J., Rye-Jørgensen, N., Bloch, S. & Sørensen, M. S., 27 Apr 2015, In: Otology & Neurotology. 36, 4, p. 727-732 6 p.

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

4 Citations (Scopus)

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, O., Jensen, O. N. & Helin, K., 1 Nov 2015, In: Cell Research. 25, p. 1205-1218 14 p.

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

20 Citations (Scopus)

2014

Bioinformatics for cancer immunotherapy target discovery

Olsen, L. R., Campos, B., Stein Barnkob, M., Winther, O., Brusic, V. & Andersen, M. H., 4 Dec 2014, In: Cancer Immunology, Immunotherapy. 63, 12, p. 1235-1249 15 p.

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

18 Citations (Scopus)

Bone signaling in middle ear development: a genome-wide differential expression analysis

Nielsen, M. C., Martin-Bertelsen, T., Friis, M., Winther, O., Friis-Hansen, L. J., Cayé-Thomasen, P. & Sørensen, M. S., 1 Dec 2014, In: Anatomical Record. 297, 12, p. 2349-2355 7 p.

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

4 Citations (Scopus)

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

Rapin, N. P.J.-P., Bagger, F. O., Jendholm, L. J., Mora-Jensen, H., Krogh, A., Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, O., Theilgaard-Mönch, K. & Porse, B. T., 6 Feb 2014, In: Blood (online). 123, 6, p. 894-904 11 p.

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

67 Citations (Scopus)

MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma

Larsen, A.-C., Holst, L. M., Kaczkowski, B., Andersen, M. T., Manfé, V., Siersma, V. D., Kolko, M., Kiilgaard, J. F., Winther, O., Prause, J. U., Gniadecki, R. & Heegaard, S., Sept 2014, In: Acta Ophthalmologica. 92, 6, p. 541-549

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

21 Citations (Scopus)

Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

Olsen, L. R., Campos, B., Winther, O., Sgroi, D. C., Karger, B. L. & Brusic, V., 8 Dec 2014, In: B M C Medical Genomics. 7, 3, p. 1-13 13 p.

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

8 Citations (Scopus)

80 Downloads (Pure)

2013

Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells

Strickertsson, J. A. B., Madsen, C. D., Martin-Bertelsen, T., Machado, A. M. D., Wadstrøm, T., Winther, O., Rasmussen, L. J. & Friis-Hansen, L., 30 Apr 2013, In: PLOS ONE. 8, 4, p. 1-13 13 p., e63147.

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

41 Citations (Scopus)

786 Downloads (Pure)

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

Bagger, F. O., Rapin, N. P.J.-P., Theilgaard-Mønch, K., Kaczkowski, B., Thorén, L. A. M., Jendholm, L. J., Winther, O. & Porse, B. T., 1 Jan 2013, In: Nucleic Acids Research. 41, Database issue, p. D1034-D1039 6 p.

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

60 Citations (Scopus)

2220 Downloads (Pure)

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, A., Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, O., Theilgaard-Moench, K. & Porse, B., 2013, In: Blood. 122, 21

Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

Literature classification for semi-automated updating of biological knowledgebases

Olsen, L. R., Kudahl, U. J., Winther, O. & Brusic, V., 2013, In: B M C Genomics. 14(Suppl 5), 10 p., S14.

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

9 Citations (Scopus)

322 Downloads (Pure)

2012

Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma

Rossing, M., Helweg-Larsen, R. B., Henao Giraldo, R., Winther, O., Vikeså, J., Niazi, O., Godballe, C., Krogdahl, A., Glud, M., Sørensen, C. H., Kiss, K., Bennedbæk, F. N. & Nielsen, F. C., Feb 2012, In: Journal of Molecular Endocrinology. 48, 1, p. 11-23 13 p.

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

69 Citations (Scopus)

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, O., Nielsen, F. C. & Norrild, B., 2012, In: Scientific Reports. 2, p. 515

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

23 Citations (Scopus)

Predictive active set selection methods for Gaussian processes

Henao, R. & Winther, O., 15 Mar 2012, In: Neurocomputing. 80, p. 10-18 9 p.

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

10 Citations (Scopus)

2011

Gene expression of the endolymphatic sac

Friis, M., Martin-Bertelsen, T., Friis-Hansen, L., Winther, O., Henao Giraldo, R., Sørensen, M. S. & Qvortrup, K., Dec 2011, In: Acta Oto-Laryngologica. 131, 12, p. 1257-63 7 p.

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

15 Citations (Scopus)

2010

Molecular signatures of thyroid follicular neoplasia

Helweg-Larsen, R. B., Rossing, M., Henao Giraldo, R., Yamamoto, Y., Krogdahl, A., Godballe, C., Winther, O., Kiss, K., Christensen, L. H., Høgdall, E. V. S., Bennedbæk, F. N. & Nielsen, F. C., Sept 2010, In: Endocrine - Related Cancer. 17, 3, p. 691-708 18 p.

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

25 Citations (Scopus)

Multivariate Hawkes process models of the occurrence of regulatory elements

Carstensen, L., Sandelin, A. G., Winther, O. & Hansen, N. R., 9 Sept 2010, In: BMC Bioinformatics. 11, p. 456

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

25 Citations (Scopus)

2753 Downloads (Pure)

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

Ryge, J., Winther, O., Wienecke, J., Sandelin, A., Westerdahl, A.-C., Hultborn, H. & Kiehn, O., 9 Jun 2010, In: BMC Genomics. 11, 1, p. 365 22 p.

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

27 Citations (Scopus)

2009

Discovery of regulatory elements is improved by a discriminatory approach

Valen, E., Sandelin, A., Winther, O. & Krogh, A., 2009, In: PLoS Computational Biology. 5, 11, p. e1000562

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

24 Citations (Scopus)

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, A. & Carninci, P., 2009, In: Genome Research. 19, 2, p. 255-65 10 p.

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

112 Citations (Scopus)

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, J. V., Winther, B. R., Lund, L. R., Winther, O., Taunton, J., Hansen, S. H. & Frödin, M., 2009, In: Molecular Cell. 35, 4, p. 511-22 11 p.

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

154 Citations (Scopus)

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, A., Nygaard, S., Sandelin, A., Valen, E., Winther, O. & Riken Omics Science Center, 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.

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

325 Citations (Scopus)

2008

BayesMD: Flexible Biological Modeling for Motif Discovery

Tang, M.-H. E., Krogh, A. & Winther, O., 2008, In: Journal of Computational Biology. 15, 10, p. 1347-63 16 p.

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

5 Citations (Scopus)

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.-H. E., Marstrand, T., Winther, O., da Piedade, I., Krogh, A., Lenhard, B. & Sandelin, A., 2008, In: Nucleic Acids Research. 36, Database issue, p. D102-6

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

521 Citations (Scopus)

2006

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

Regenberg, B., Grotkjaer, T., Winther, O., Fausbøll, A., Akesson, M., Bro, C., Hansen, L. K., Brunak, S. & Nielsen, J., 2006, In: Genome Biology (Online Edition). 7, 11, p. R107

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

176 Citations (Scopus)

Ole Winther

Research output

Search results