Browse by Glasgow Author

2025

Ji, Yanni, Cutiongco, Marie F.A. ORCID: https://orcid.org/0000-0002-4873-9643, Jensen, Bjørn Sand ORCID: https://orcid.org/0000-0001-8074-228X and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2025) Generating realistic single-cell images from CellProfiler representations. Medical Image Analysis, 103, 103574. (doi: 10.1016/j.media.2025.103574) (PMID:40393380)

Farndale, Lucas, Insall, Robert ORCID: https://orcid.org/0000-0003-4898-040X and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2025) TriDeNT: Triple deep network training for privileged knowledge distillation in histopathology. Medical Image Analysis, 102, 103479. (doi: 10.1016/j.media.2025.103479) (PMID:40174325)

Coudray, N. et al. (2025) Self supervised artificial intelligence predicts poor outcome from primary cutaneous squamous cell carcinoma at diagnosis. npj Digital Medicine, 8(1), 105. (doi: 10.1038/s41746-025-01496-3) (PMID:39955424) (PMCID:PMC11830021)

Lytras, Spyros, Lamb, Kieran D., Ito, Jumpei, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Sato, Kei, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)

Coudray, Nicolas, Occidental, Michael A., Mantilla, Jose G., Claudio Quiros, Adalberto, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Balko, Jan, Tsirigos, Aristotelis and Jour, George (2025) Quantitative and morphology-based deep convolutional neural network approaches for osteosarcoma survival prediction in the neoadjuvant and metastatic settings. Clinical Cancer Research, 31(2), pp. 365-375. (doi: 10.1158/1078-0432.ccr-24-2599) (PMID:39561274)

2024

Seyedshahi, F. et al. (2024) A histomorphological atlas of resected mesothelioma discovered by self-supervised learning from 3446 whole-slide images. bioRxiv, (doi: 10.1101/2024.11.18.624103)

Liu, Dan, Young, Francesca, Lamb, Kieran D., Claudio Quiros, Adalberto, Pancheva, Alexandrina, Miller, Crispin ORCID: https://orcid.org/0000-0003-4341-1283, Macdonald, Craig ORCID: https://orcid.org/0000-0003-3143-279X, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv, (doi: 10.1101/2024.11.05.622169)

Liu, Dan, Young, Francesca, Lamb, Kieran D., Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2024) Prediction of virus-host associations using protein language models and multiple instance learning. PLoS Computational Biology, 20(11), e1012597. (doi: 10.1371/journal.pcbi.1012597) (PMID:39561204) (PMCID:PMC11614202)

Lamb, Kieran D., Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Lytras, Spyros, Young, Francesca, Koci, Orges, Herzig, James, Lovell, Simon C,, Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)

Quiros, A. C. et al. (2024) Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unannotated pathology slides. Nature Communications, 15, 4596. (doi: 10.1038/s41467-024-48666-7) (PMID:38862472) (PMCID:PMC11525555)

Liu, B. et al. (2024) Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer. bioRxiv, (doi: 10.1101/2024.02.26.582106) (PMID:PPR813774)

Lamb, Kieran D., Luka, Martha M., Saathoff, Megan, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Phan, My V.T., Cotten, Matthew ORCID: https://orcid.org/0000-0002-3361-3351, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)

2023

Ji, Yanni, Cutiongco, Marie F.A., Jensen, Bjorn Sand ORCID: https://orcid.org/0000-0001-8074-228X and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2023) CP2Image: Generating High-Quality Single-Cell Images Using CellProfiler Representations. In: Medical Imaging with Deep Learning (MIDL 2023), Nashville, TN, USA, 10-12 July 2023, pp. 1-12.

2022

Ji, Yanni, Cutiongco, Marie F.A., Jensen, Bjorn Sand ORCID: https://orcid.org/0000-0001-8074-228X and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2022) CP2Image: Generating High-Quality Single-Cell Images Using CellProfiler Representations. NeurIPS 2022 Workshop on Learning Meaningful Representations of Life (LMRL 2022), 12 Sept 2022.

Liu, Xiangling, Yang, Xinyu, Ouyang, Linkun, Guo, Guibing, Su, Jin, Xi, Ruibin, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Yuan, Fajie (2022) Protein Language Model Predicts Mutation Pathogenicity and Clinical Prognosis. NeurIPS 2022 Workshop on Learning Meaningful Representations of Life (LMRL 2022), 12 Sept 2022.

2021

Claudio Quiros, Adalberto, Coudray, Nicolas, Yeaton, Anna, Sunhem, Wisuwat, Murray-Smith, Roderick ORCID: https://orcid.org/0000-0003-4228-7962, Tsirigos, Aristotelis and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2021) Adversarial Learning of Cancer Tissue Representations. In: 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021), 27 Sept-1 Oct 2021, pp. 602-612. ISBN 9783030872366 (doi: 10.1007/978-3-030-87237-3_58)

Claudio Quiros, Adalberto, Murray-Smith, Roderick ORCID: https://orcid.org/0000-0003-4228-7962 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2021) PathologyGAN: Learning deep representations of cancer tissue. Journal of Machine Learning for Biomedical Imaging, 2021(4), pp. 1-48.

Dentro, S. C. et al. (2021) Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell, 184(8), 2239-2254.e39. (doi: 10.1016/j.cell.2021.03.009) (PMID:33831375) (PMCID:PMC8054914)

Macintyre, G. et al. (2021) FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections. JCO Clinical Cancer Informatics, 5, pp. 176-186. (doi: 10.1200/cci.20.00075) (PMID:33570999)

2020

Claudio Quiros, Adalberto, Murray-Smith, Roderick ORCID: https://orcid.org/0000-0003-4228-7962 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2020) Learning a Low Dimensional Manifold of Real Cancer Tissue with PathologyGAN. NeurIPS 2020 Learning Meaningful Representations of Life, 11 Dec 2020.

Bailey, M. H. et al. (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11, 4748. (doi: 10.1038/s41467-020-18151-y) (PMID:32958763) (PMCID:PMC7505971)

Claudio Quiros, Adalberto, Murray-Smith, Roderick ORCID: https://orcid.org/0000-0003-4228-7962 and Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 (2020) PathologyGAN: Learning Deep Representations of Cancer Tissue. In: Third Conference on Medical Imaging with Deep Learning, Montreal, Canada, 6-9 Jul 2020, pp. 669-695.

Li, C. H. et al. (2020) Sex differences in oncogenic mutational processes. Nature Communications, 11, 4330. (doi: 10.1038/s41467-020-17359-2) (PMID:32859912) (PMCID:PMC7455744)

Gerstung, M. et al. (2020) The evolutionary history of 2,658 cancers. Nature, 578(7793), pp. 122-128. (doi: 10.1038/s41586-019-1907-7) (PMID:32025013)

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, et al. (2020) Pan-cancer analysis of whole genomes. Nature, 578(7793), pp. 82-93. (doi: 10.1038/s41586-020-1969-6) (PMID:32025007) (PMCID:PMC7025898)

Cmero, M. et al. (2020) Inferring structural variant cancer cell fraction. Nature Communications, 11, 730. (doi: 10.1038/s41467-020-14351-8) (PMID:32024845) (PMCID:PMC7002525)

Rubanova, Yulia, Shi, Ruian, Harrigan, Caitlin F., Li, Roujia, Wintersinger, Jeff, Sahin, Nil, Deshwar, Amit and Morris, Quaid (2020) Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications, 11, 731. (doi: 10.1038/s41467-020-14352-7) (PMID:32024834) (PMCID:PMC7002414)

2018

Tarabichi, M. et al. (2018) Neutral tumor evolution? Nature Genetics, 50(12), pp. 1630-1633. (doi: 10.1038/s41588-018-0258-x) (PMID:30374075) (PMCID:PMC6548558)

Dong, L.-Q. et al. (2018) Spatial and temporal clonal evolution of intrahepatic cholangiocarcinoma. Journal of Hepatology, 69(1), pp. 89-98. (doi: 10.1016/j.jhep.2018.02.029) (PMID:29551704)

2017

de Santiago, Ines, Liu, Wei, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, O'Reilly, Martin, Chilamakuri, Chandra Sekhar Reddy, Ponder, Bruce A.J., Meyer, Kerstin B. and Markowetz, Florian (2017) BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. Genome Biology, 18, 39. (doi: 10.1186/s13059-017-1165-7) (PMID:28235418) (PMCID:PMC5326502)

2016

Marass, Francesco, Mouliere, Florent, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Rosenfeld, Nitzan and Markowetz, Florian (2016) A phylogenetic latent feature model for clonal deconvolution. Annals of Applied Statistics, 10(4), pp. 2377-2404. (doi: 10.1214/16-AOAS986)

2015

Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Sakoparnig, Thomas, Markowetz, Florian and Beerenwinkel, Niko (2015) BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biology, 16(1), p. 36. (doi: 10.1186/s13059-015-0592-6) (PMID:25786108) (PMCID:PMC4359483)

Wang, X., Yuan, K. ORCID: https://orcid.org/0000-0002-2318-1460 and Markowetz, F. (2015) Joining the dots: network analysis of gene perturbation data. In: Markowetz, F. and Boutros, M. (eds.) Systems Genetics: Linking Genotypes and Phenotypes. Series: Cambridge series in systems genetics. Cambridge University Press. ISBN 9781107013841

2014

Wang, Xin, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Hellmayr, Christoph, Liu, Wei and Markowetz, Florian (2014) Reconstructing evolving signalling networks by hidden Markov nested effects models. Annals of Applied Statistics, 8(1), pp. 448-480. (doi: 10.1214/13-AOAS696)

2012

Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Girolami, Mark and Niranjan, Mahesan (2012) Markov chain Monte Carlo methods for state-space models with point process observations. Neural Computation, 24(6), pp. 1462-1486. (doi: 10.1162/NECO_a_00281) (PMID:22364499)

2011

Mangion, Andrew Zammit, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Kadirkamanathan, Visakan, Niranjan, Mahesan and Sanguinetti, Guido (2011) Online variational inference for state-space models with point-process observations. Neural Computation, 23(8), pp. 1967-1999. (doi: 10.1162/NECO_a_00156)

2010

Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Niranjan, Mahesan (2010) Estimating a state-space model from point process observations: a note on convergence. Neural Computation, 22(8), pp. 1993-2001. (doi: 10.1162/neco.2010.07-09-1047) (PMID:20337540)

2009

Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460, Liu, Wei and Yang, Lie-Liang (2009) Reliability-Aided Multiuser Detection in Time-Frequency-Domain Spread Multicarrier DS-CDMA Systems. In: IEEE 69th Vehicular Technology Conference, 26-29 April 2009, pp. 1-5. (doi: 10.1109/VETECS.2009.5073833)