Dr Ke Yuan

  • Lecturer in Machine Learning and Computational Biology (Computing Science)
  • Affiliate (Institute of Cancer Sciences)

telephone: 01413306034
email: Ke.Yuan@glasgow.ac.uk

School of Computing Science

ORCID iDhttps://orcid.org/0000-0002-2318-1460

Biography

Ke Yuan is a Lecturer in Computing Science at the University of Glasgow. He received a PhD from the University of Southampton in 2013 advised by Mahesan Niranjan. Till 04/2016, He was a postdoctoral research fellow at Cancer Research UK Cambridge Institute at the University of Cambridge working with Florian Markowetz. He joined the School of Computing Science at the University of Glasgow in 05/2016.

Full CV: 08-2017

Publications

List by: Type | Date

Jump to: 2020 | 2018 | 2017 | 2016 | 2015 | 2014 | 2012 | 2011 | 2010 | 2009
Number of items: 15.

2020

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)

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

Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A., Morris, Q. and , (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, I., Liu, W., Yuan, K. , O'Reilly, M., Chilamakuri, C. S. R., Ponder, B. A.J., Meyer, K. B. and Markowetz, F. (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, F., Mouliere, F., Yuan, K. , Rosenfeld, N. and Markowetz, F. (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, K. , Sakoparnig, T., Markowetz, F. and Beerenwinkel, N. (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. 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, X., Yuan, K. , Hellmayr, C., Liu, W. and Markowetz, F. (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, K. , Girolami, M. and Niranjan, M. (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, A. Z., Yuan, K. , Kadirkamanathan, V., Niranjan, M. and Sanguinetti, G. (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, K. and Niranjan, M. (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, K. , Liu, W. and Yang, L.-L. (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)

This list was generated on Sat Jul 11 12:05:01 2020 BST.
Jump to: Articles | Book Sections | Conference Proceedings
Number of items: 15.

Articles

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)

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

Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A., Morris, Q. and , (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)

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)

de Santiago, I., Liu, W., Yuan, K. , O'Reilly, M., Chilamakuri, C. S. R., Ponder, B. A.J., Meyer, K. B. and Markowetz, F. (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)

Marass, F., Mouliere, F., Yuan, K. , Rosenfeld, N. and Markowetz, F. (2016) A phylogenetic latent feature model for clonal deconvolution. Annals of Applied Statistics, 10(4), pp. 2377-2404. (doi: 10.1214/16-AOAS986)

Yuan, K. , Sakoparnig, T., Markowetz, F. and Beerenwinkel, N. (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. , Hellmayr, C., Liu, W. and Markowetz, F. (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)

Yuan, K. , Girolami, M. and Niranjan, M. (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)

Mangion, A. Z., Yuan, K. , Kadirkamanathan, V., Niranjan, M. and Sanguinetti, G. (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)

Yuan, K. and Niranjan, M. (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)

Book Sections

Wang, X., Yuan, K. 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

Conference Proceedings

Yuan, K. , Liu, W. and Yang, L.-L. (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)

This list was generated on Sat Jul 11 12:05:01 2020 BST.

Supervision


Ke Yuan