O. Winther

M. S. Sørensen, O. Winther, L. Friis-Hansen, 2015, Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology.

Bone Signaling in Middle Ear Development: A Genome‐Wide Differential Expression Analysis

P. Cayé-Thomasen, M. S. Sørensen, O. Winther, 2014, Anatomical record.

May 09, 2020 Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1,

B. Kaczkowski, O. Winther, Anders Jacobsen, 2014 .

Cellular origin of prognostic chromosomal aberrations in AML patients

B. Porse, L. Bullinger, N. Rapin, 2015, Leukemia.

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

V. Brusic, E. Reinherz, L. Olsen, 2015, BMC Medical Genomics.

Transfer learning reveals sequence determinants of regulatory element accessibility

R. Andersson, O. Winther, M. Salvatore, 2022, bioRxiv.

Down-regulation of miR-129-5p and the let-7 family in neuroendocrine tumors and metastases leads to up-regulation of their targets Egr1, and Bach1

B. Kaczkowski, O. Winther, Anders Jacobsen, 2014 .

Down-regulation of miR-129-5p and the let-7 family in neuroendocrine tumors and metastases leads to up-regulation of their targets Egr1, and

B. Kaczkowski, O. Winther, Anders Jacobsen, 2014 .

Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

J. Ule, J. Gagneur, O. Winther, 2022, bioRxiv.

Improved prediction of blood biomarkers using deep learning

A. Sigurdsson, O. Lund, S. Brunak, 2022, medRxiv.

Identifying endogenous peptide receptors by combining structure and transmembrane topology prediction

Jan C. Refsgaard, O. Winther, M. Kasimova, 2022, bioRxiv.

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

F. O. Bagger, O. Winther, F. Nielsen, 2019, BMC Bioinformatics.

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

Ole Winther, Frederik Otzen Bagger, Finn Cilius Nielsen, 2019, BMC Bioinformatics.

RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells.

Ole Winther, Jack Taunton, Michael S. Cohen, 2009, Molecular cell.

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

L. Olsen, M. Kosteljanetz, I. Christensen, 2016, Molecular oncology.

Transfer learning identifies sequence determinants of regulatory element accessibility

R. Andersson, O. Winther, M. Salvatore, 2023, bioRxiv.

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Ole Winther, Boris Lenhard, Anders Krogh, 2007, Nucleic Acids Res..

Interpretable Autoencoders Trained on Single Cell Sequencing Data Can Transfer Directly to Data from Unseen Tissues

F. O. Bagger, O. Winther, F. Nielsen, 2021, Cells.

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2009, Genome research.

A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data

F. O. Bagger, O. Winther, F. Nielsen, 2021, bioRxiv.

DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks

Konstantinos D. Tsirigos, A. Krogh, Henrik Nielsen, 2022, bioRxiv.

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

B. Kaczkowski, O. Winther, S. Heegaard, 2014, Acta ophthalmologica.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

Ole Winther, Casper Kaae Sønderby, Frederik Otzen Bagger, 2015, Nucleic Acids Res..

COVID-19 vaccine candidates: Prediction and validation of 174 novel SARS-CoV-2 epitopes

Ole Winther, Frederik Otzen Bagger, Sune Justesen, 2020 .

COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes

Ole Winther, Frederik Otzen Bagger, Sune Justesen, 2020, bioRxiv.

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

Anders Krogh, Ole Winther, Frederik Otzen Bagger, 2014, Blood.

Enterococcus faecalis Infection Causes Inflammation, Intracellular Oxphos-Independent ROS Production, and DNA Damage in Human Gastric Cancer Cells

L. Rasmussen, O. Winther, Ana Manuel Dantas Machado, 2013, PloS one.

SignalP 6.0 achieves signal peptide prediction across all types using protein language models

Konstantinos D. Tsirigos, Magnús Halldór Gíslason, S. Brunak, 2021, bioRxiv.

Molecular signatures of thyroid follicular neoplasia.

Ricardo Henao, O. Winther, F. Nielsen, 2010, Endocrine-related cancer.

A Quantitative Study Of Pruning By Optimal Brain Damage

Ole Winther, Lars Kai Hansen, Claus Svarer, 1993, Int. J. Neural Syst..

Neural Networks and Cellular Automata Complexity

Ole Winther, Jan Gorodkin, A. Sørensen, 1993, Complex Syst..

Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons.

F. O. Bagger, O. Winther, F. Nielsen, 2019, Cell reports.

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

Ole Winther, Anders Krogh, Albin Sandelin, 2009, PLoS Comput. Biol..

Airway Inflammation in Chronic Rhinosinusitis with Nasal Polyps and Asthma: The United Airways Concept Further Supported

L. Konge, V. Backer, C. Bachert, 2015, PloS one.

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

V. Brusic, E. Reinherz, L. Olsen, 2015, BMC Medical Genomics.

Literature classification for semi-automated updating of biological knowledgebases

Vladimir Brusic, Ole Winther, Lars Rønn Olsen, 2013, BMC Genomics.

Literature classification for semi-automated updating of biological knowledgebases

V. Brusic, L. Olsen, O. Winther, 2013, BMC Genomics.

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

Ole Winther, Frederik Otzen Bagger, Nicolas Rapin, 2012, Nucleic Acids Res..

Multivariate Hawkes process models of the occurrence of regulatory elements

Ole Winther, Albin Sandelin, Lisbeth Carstensen, 2010, BMC Bioinformatics.

GraphPart: homology partitioning for biological sequence analysis

Magnús Halldór Gíslason, Henrik Nielsen, O. Winther, 2023, bioRxiv.

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

Ricardo Henao, O. Winther, F. Nielsen, 2012, Journal of molecular endocrinology.

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

R. Andersson, O. Winther, M. Salvatore, 2022, NAR genomics and bioinformatics.

Transfer learning reveals sequence determinants of regulatory element accessibility

R. Andersson, O. Winther, M. Salvatore, 2023 .

Transfer learning reveals sequence determinants of regulatory element accessibility

R. Andersson, O. Winther, M. Salvatore, 2022 .

BayesMD: Flexible Biological Modeling for Motif Discovery

Ole Winther, Anders Krogh, Man-Hung Eric Tang, 2008, J. Comput. Biol..

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

Lina A. Thoren, B. Porse, B. Kaczkowski, 2012, Nucleic Acids Res..

HemaExplorer: a Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis.

B. Porse, B. Kaczkowski, N. Rapin, 2012, Blood.

Enterococcus faecalis Infection Causes Inflammation, Intracellular Oxphos-Independent ROS Production, and DNA Damage in Human Gastric Cancer Cells

L. Rasmussen, O. Winther, Ana Manuel Dantas Machado, 2013, PloS one.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

Sina Hadi Sohi, C. Sønderby, B. Porse, 2015, Nucleic Acids Res..

Literature classification for semi-automated updating of biological knowledgebases

V. Brusic, L. Olsen, O. Winther, 2013, BMC Genomics.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Ariel S. Schwartz, 2009, Nature Genetics.

promoters using DeepCAGE Genome-wide detection and analysis of hippocampus core

Man-Hung Eric Tang, A. Krogh, A. Sandelin, 2009 .

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

B. Kaczkowski, O. Winther, S. Heegaard, 2014, Acta ophthalmologica.

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

Lina A. Thoren, B. Porse, B. Kaczkowski, 2012, Nucleic Acids Res..

Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

B. Kaczkowski, O. Winther, F. Nielsen, 2012, Scientific Reports.

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

V. Brusic, E. Reinherz, L. Olsen, 2015, BMC Medical Genomics.

Gene expression of the endolymphatic sac

Ricardo Henao, M. S. Sørensen, O. Winther, 2011, Acta oto-laryngologica.