Ole Winther - Publications, H-index & Citations

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Ole Winther

university of copenhagen

64H-index

383Paper Count

2.6WCitation Count

Published Papers 63

Publication Date

SpatialFormer: universal spatial representation learning from subcellular molecular to multicellular landscapes

Nature Computational Science

IF18.3

2026-07-30

PREAI

Jun Wang; Yuanhua Huang; Ole Winther

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

NUCLEIC ACIDS RESEARCH

IF13.1

2024-04-08

OAAI

Odum, Marius Thrane; Teufel, Felix; Thumuluri, Vineet; Armenteros, Jose Juan Almagro; Johansen, Alexander Rosenberg; Winther, Ole; Nielsen, Henrik

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Can large language models reason about medical questions?

PATTERNS

IF7.4

2024-03-01

OAAI

Lievin, Valentin; Hother, Christoffer Egeberg; Motzfeldt, Andreas Geert; Winther, Ole

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

FRONTIERS IN IMMUNOLOGY

IF5.9

2024-02-08

OAAI

Hoie, Magnus Haraldson; Gade, Frederik Steensgaard; Johansen, Julie Maria; Wurtzen, Charlotte; Winther, Ole; Nielsen, Morten; Marcatili, Paolo

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GraphPart: homology partitioning for biological sequence analysis

genomics proteomics bioinformatics

IF2.8

2023-10-16

OAAI

Teufel, Felix; Gislason, Magnus Halldor; Armenteros, Jose Juan Almagro; Johansen, Alexander Rosenberg; Winther, Ole; Nielsen, Henrik

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

GENOME BIOLOGY

IF9.4

2023-08-04

OAAI

Horlacher, Marc; Wagner, Nils; Moyon, Lambert; Kuret, Klara; Goedert, Nicolas; Salvatore, Marco; Ule, Jernej; Gagneur, Julien; Winther, Ole; Marsico, Annalisa

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

BRIEFINGS IN BIOINFORMATICS

IF7.7

2023-07-18

OAAI

Wang, Jun; Horlacher, Marc; Cheng, Lixin; Winther, Ole

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Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs

ACS OMEGA

IF4.3

2023-06-22

OAAI

Einarson, Kasper A.; Bendtsen, Kristian M.; Li, Kang; Thomsen, Maria; Kristensen, Niels R.; Winther, Ole; Fulle, Simone; Clemmensen, Line; Refsgaard, Hanne H. F.

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Deep integrative models for large-scale human genomics

NUCLEIC ACIDS RESEARCH

IF13.1

2023-05-24

OAAI

Sigurdsson, Arnor, I; Louloudis, Ioannis; Banasik, Karina; Westergaard, David; Winther, Ole; Lund, Ole; Ostrowski, Sisse Rye; Erikstrup, Christian; Pedersen, Ole Birger Vesterager; Nyegaard, Mette; Brunak, Soren; Vilhjalmsson, Bjarni J.; Rasmussen, Simon

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Deorphanizing Peptides Using Structure Prediction

JOURNAL OF CHEMICAL INFORMATION AND MODELING

IF5.3

2023-04-24

PREAI

Teufel, Felix; Madsen, Dennis; Deibler, Kristine; Refsgaard, Jan C.; Kasimova, Marina A.; Madsen, Christian T.; Stahlhut, Carsten; Gronborg, Mads; Winther, Ole

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

genomics proteomics bioinformatics

IF2.8

2023-03-29

OAAI

Salvatore, Marco; Horlacher, Marc; Marsico, Annalisa; Winther, Ole; Andersson, Robin

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Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory

DIGITAL DISCOVERY

IF5.6

2023-01-01

OAAI

Rieger, Laura Hannemose; Flores, Eibar; Nielsen, Kristian Frellesen; Norby, Poul; Ayerbe, Elixabete; Winther, Ole; Vegge, Tejs; Bhowmik, Arghya

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

MEDICAL IMAGE ANALYSIS

IF11.8

2023-01-01

OAAI

Jalaboi, Raluca; Faye, Frederik; Orbes-Arteaga, Mauricio; Jorgensen, Dan; Winther, Ole; Galimzianova, Alfiia

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NeuralNEB-neural networks can find reaction paths fast

MACHINE LEARNING-SCIENCE AND TECHNOLOGY

IF4.6

2022-12-13

OAAI

Schreiner, Mathias; Bhowmik, Arghya; Vegge, Tejs; Jorgensen, Peter Bjorn; Winther, Ole

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NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

NUCLEIC ACIDS RESEARCH

IF13.1

2022-06-01

107

OAAI

Hoie, Magnus Haraldson; Kiehl, Erik Nicolas; Petersen, Bent; Nielsen, Morten; Winther, Ole; Nielsen, Henrik; Hallgren, Jeppe; Marcatili, Paolo

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

NUCLEIC ACIDS RESEARCH

IF13.1

2022-04-30

262

OAAI

Thumuluri, Vineet; Armenteros, Jose Juan Almagro; Johansen, Alexander Rosenberg; Nielsen, Henrik; Winther, Ole

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

NATURE BIOTECHNOLOGY

IF41.7

2022-01-03

1.2K

OAAI

Teufel, Felix; Almagro Armenteros, Jose Juan; Johansen, Alexander Rosenberg; Gislason, Magnus Halldor; Pihl, Silas Irby; Tsirigos, Konstantinos D.; Winther, Ole; Brunak, Soren; von Heijne, Gunnar; Nielsen, Henrik

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

CELLS

IF5.2

2021-12-28

OAAI

Walbech, Julie Sparholt; Kinalis, Savvas; Winther, Ole; Nielsen, Finn Cilius; Bagger, Frederik Otzen

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

MACHINE LEARNING-SCIENCE AND TECHNOLOGY

IF4.6

2021-12-22

OAAI

Busk, Jonas; Bjorn Jorgensen, Peter; Bhowmik, Arghya; Schmidt, Mikkel N.; Winther, Ole; Vegge, Tejs

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

COMMUNICATIONS BIOLOGY

IF5.1

2021-09-10

OAAI

Montemurro, Alessandro; Schuster, Viktoria; Povlsen, Helle Rus; Bentzen, Amalie Kai; Jurtz, Vanessa; Chronister, William D.; Crinklaw, Austin; Hadrup, Sine R.; Winther, Ole; Peters, Bjoern; Jessen, Leon Eyrich; Nielsen, Morten

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Research Directions