elliottlab.ca

V. Lammi et al. Genome-wide association study of long COVID. 2025. Nature Genetics. Supplementary information, tables & data
E. Sidrow, A. Bouchard-Côté and L.T. Elliott. Variational phylogenetic inference with products over bipartitions. 2025. Proceedings of the 42nd International Conference on Machine Learning. Accepted. Preprint version & Code
J. Min, O. Vishnyakova, A. Brooks-Wilson and L.T. Elliott. A joint Bayesian model for change-points and heteroskedasticity applied to the Canadian Longitudinal Study on Aging. Journal of Computational Biology. 2025. 32(4). p374-93. Supplementary material 1 & 2
G. Morgan, C.Y.J. Fung, A.C. Gingras, K. Colwill, L. Briollais, E. Frangione, D. Wolday, F. Qi, A. Pasculescu, M. Delgado-Brand, G. Mailhot, T. Tursun, S. Arnoldo, E. Bearrs, A. Binnie, B. Borgundvaag, S. Casalino, S. Chowdhary, M. Dagher, L. Devine, L.T. Elliott, S.M. Friedman, Z. Khan, E. Lapadula, G. MacDonald, T. Mazzulli, S.L. McLeod, C. Mighton, K. Nirmalanathan, D. Richardson, S. Stern, A. Taher, J. Young, J. Lerner-Ellis and J. Taher. Characterizing the SARS-CoV-2 antibody response and associations with patient factors: Serological profiling of participants enrolled in the GENCOV study. 2024. Clinical Biochemistry. 135. Manuscript
M.R.P. Parker, J. Cao, L.L.E. Cowen, L.T. Elliott and J. Ma. Multi-site disease analytics with applications to estimating COVID-19 undetected cases in Canada. Annals of Applied Statistics. 2024. 18(4). p2928-49. Supplementary material, Code & Preprint version
J. Bambi, H. Sadri, K. Moselle, E. Chang, Y. Santoso, J. Howie, A. Rudnick, L.T. Elliott and A. Kuo. Approaches to extracting patterns of service utilization for patients with complex conditions: Graph community detection vs. natural language processing clustering. 2024. BioMedInformatics. 4(3). p1884-900
M.R.P. Parker, J. Cao, L.L.E. Cowen and L.T. Elliott. Faster asymptotic solutions for N-mixtures on large populations. 2024. Journal of Agricultural, Biological and Environmental Statistics. Manuscript, Code & Supplementary material
J. Manuello, J. Min, P. McCarthy, F. Alfaro-Almagro, S. Lee, S. Smith, L.T. Elliott, A.M. Winkler and G. Douaud. The effects of genetic and modifiable risk factors on brain regions vulnerable to ageing and disease. 2024. Nature Communications. 15(2576). Manuscript, Code, Supplementary material 1, 2, 3, Washington Post article, Newsweek article, SFU's Scholarly Impact of the Week & University of Oxford News article
E. Garg, P. Arguello-Pascualli, O. Vishnyakova, A.R. Halevy, S. Yoo, J.D. Brooks, S.B. Bull, F. Gagnon, C.M.T. Greenwood, R.J. Hung, J.F. Lawless, J. Lerner-Ellis, J.K. Dennis, R.J.S. Abraham, J.-M. Garant, B. Thiruvahindrapuram, S.J.M. Jones, CGEn HostSeq Initiative, L.J. Strug, A.D. Paterson, L. Sun and L.T. Elliott. Canadian COVID-19 host genetics cohort replicates known severity associations. 2024. PLOS Genetics. 20(3). Manuscript, Code, Correction & Mention in the CGEn Annual Report 2023-24
The COVID-19 Host Genetics Initiative. A second update on mapping the human genetic architecture of COVID-19. 2023. Nature. 621(7977). pE7-26. Manuscript, Supplementary material 1, 2, 3, Results browser, Jerusalem Post article & Preprint version
O. Vishnyakova, X. Song, K. Rockwood, L.T. Elliott and A. Brooks-Wilson. Physiological phenotypes have optimal values relevant to healthy aging: Sweet spots deduced from the Canadian Longitudinal Study on Aging. 2023. GeroScience. 46(2). p1589-605. Manuscript, Supplementary material, Vancouver Sun interview & SFU News article
J. Schneider, D. Stenning and L.T. Elliott. Efficient galaxy classification through pretraining. 2023. Frontiers in Astronomy and Space Sciences. 10. Manuscript, Code & Thesis
S. Yoo, E. Garg et al. HostSeq: A Canadian whole genome sequencing and clinical data resource. 2023. BMC Genomic Data. 24(26). Manuscript, Supplementary material, COVID-19 Immunity Task Force summary & Data
S. Wang, S. Ge, B. Sobkowiak, L. Wang, L. Grandjean, C. Colijn and L.T. Elliott. Genome-wide association with uncertainty in the genetic similarity matrix. 2023. Journal of Computational Biology. 30(2). p117-243. Manuscript & Code
S. Ge, S. Wang and L.T. Elliott. Shape modeling with spline partitions. 2023. Statistics and Computing. 33(13). Supplementary material & Code
S. Lee, J.D. Bijsterbosch F. Alfaro Almagro, L.T. Elliott, P. McCarthy, B. Taschler, R. Sala-Llonche, C.F. Beckmann, E.P. Duff, S.M. Smith and G. Douaud. Amplitudes of resting-state functional networks—investigation into their correlates and biophysical properties. 2022. NeuroImage. 265. Manuscript, Supplementary material 1 & 2
M.R.P. Parker, L.L.E. Cowen, J. Cao and L.T. Elliott. Computational efficiency and precision for replicated-count and batch-marked hidden population models. 2022. Journal of Agricultural, Biological and Environmental Statistics. 28(1). p43-58. Manuscript, Supplementary material 1, 2, 3 & CRAN package
L. Wang, J. Min, R. Doig, L.T. Elliott and C. Colijn. Estimation of SARS-CoV-2 antibody prevalence through integration of serology and incidence data. 2022. Canadian Journal of Statistics. 50(3). p734-50. Manuscript & Supplementary material
C. Wang, A.B. Martins-Bach, F. Alfaro-Almagro, G. Douaud, J.C. Klein, A. Llera, C. Fiscone, R. Bowtell, L.T. Elliott, S.M. Smith, B.C. Tendler and K.L. Miller. Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging. 2022. Nature Neuroscience. 25(5583). p818-31. Manuscript, Supplementary material 1 & 2
J. Min and L.T. Elliott. Q-learning with online random forests. 2022. arxiv preprint 2204.03771. Manuscript, Supplementary material & Thesis
M.R.P. Parker, Y. Li, L.T. Elliott, J. Ma and L.L.E. Cowen. Under-reporting of COVID-19 in the Northern Health Authority region of British Columbia. 2021. Canadian Journal of Statistics. 49(4). p1018-38. Manuscript, Supplementary material & CBC Radio One (Prince George) interview
J.E. Stockdale, R. Doig, J. Min, N. Mulberry, L. Wang, L.T. Elliott and C. Colijn. Long time frames to detect the impact of changing COVID-19 measures, Canada, March to July 2020. 2021. Eurosurveillance. 26(4). Code & Supplementary material
W. Chen and L.T. Elliott. Compression for population genetic data through finite-state entropy. 2021. Journal of Bioinformatics and Computational Biology. 19(5). Manuscript, Supplementary material, Thesis & Website
S. Wang, S. Ge, C. Colijn, P. Biller, L. Wang and L.T. Elliott. Estimating genetic similarity matrices using phylogenies. 2021. Journal of Computational Biology. 28(6). p587–600. Manuscript, Code & Supplementary material
S.M. Smith, G. Douaud, W. Chen, T. Hanayik, F. Alfaro-Almagro, K. Sharp and L.T. Elliott. An expanded set of genome-wide association studies of brain imaging phenotypes in UK Biobank. 2021. Nature Neuroscience. 24(5). p737-45. Data, EBI Accessions & SFU Scholarly Impact of the Week
L.T. Elliott. Kinship solutions for partially observed multiphenotype data. 2020. Journal of Computational Biology. 27(9). p1461-70. Code & Supplementary material
N.J. Armstrong et al. Common genetic variation indicates separate causes for periventricular and deep white matter hyperintensities. 2020. Stroke. 51(7). p2111-21. Manuscript, Supplementary material 1 & 2
S.M. Smith, L.T. Elliott, F. Alfaro-Almagro, P. McCarthy, T.E. Nichols, G. Douaud and K.L. Miller. Brain aging comprises many modes of structural and functional change with distinct genetic and biophysical associations. 2020. eLife. doi:10.7554/eLife.52677. Data & Code
S. Ge, S. Wang, Y.W. Teh, L. Wang and L.T. Elliott. Random tessellation forests. 2019. Proceedings of the 33rd Conference on Neural Information Processing Systems. Manuscript, Artwork, Code, Supplementary material & Preprint version
J. Mollink, S.M. Smith, L.T. Elliott, M. Kleinnijenhuis, M. Hiemstra, F. Alfaro-Almagro, J. Marchini, A.-M. van Cappellen van Walsum, S. Jbabdi and K.L. Miller. The spatial correspondence and genetic influence of interhemispheric connectivity with white matter microstructure. 2019. Nature Neuroscience. 22(5). p809-19. Manuscript & Supplementary material
L.T. Elliott, M. De Iorio, S. Favaro, K. Adhikari and Y.W. Teh. Modeling population structure under hierarchical Dirichlet processes. 2019. Bayesian Analysis. 14(2). p313-39. Code & Supplementary material
L.T. Elliott, K. Sharp, F. Alfaro-Almagro, S. Shi, K.L. Miller, G. Douaud, J. Marchini and S.M. Smith. Genome-wide association studies of brain imaging phenotypes in UK Biobank. 2018. Nature. 562(7726). p210-6. Data, Code, Winner's curse correction & Wired article
C. Bycroft, C. Freeman, D. Petkova, G. Band, L.T. Elliott, K. Sharp, A. Motyer, D. Vukcevic, O. Delaneau, J. O’Connell, A. Cortes, S. Welsh, A. Young, M. Effingham, G. McVean, S. Leslie, N. Allen, P. Donnelly and J. Marchini. The UK Biobank resource with deep phenotyping and genomic data. 2018. Nature. 562(7726). p203-9. Data, Nature News and Views article, Supplementary material & Preprint version
S. Schwab, R. Harbord, V. Zerbi, L.T. Elliott, S. Afyouni, J.Q. Smith, M.W. Woolrich, S.M. Smith and T.E. Nichols. Directed functional connectivity using dynamic graphical models. 2018. NeuroImage. 175. p340-53
L.T. Elliott. Bayesian nonparametric models of genetic variation. 2016. Doctoral thesis, University College London Mathematica code
L.T. Elliott and Y.W. Teh. A nonparametric HMM for genetic imputation and coalescent inference. 2016. Electronic Journal of Statistics. 10(2). p3425-51. Preprint version & Code
R.M. Cichy, P. Sterzer, J. Heinzle, L.T. Elliott and F. Ramirez and J.-D. Haynes. Probing principles of large-scale object representation: Category preference and location encoding. 2013. Human Brain Mapping. 34(7). p1636-51. Supplementary material
L.T. Elliott and Y.W. Teh. Scalable imputation of genetic data with a discrete fragmentation-coagulation process. 2012. Proceedings of the 25th Conference on Neural Information Processing Systems. Code
I. Murray and L.T. Elliott. Driving Markov chain Monte Carlo with a dependent random stream. 2012. arxiv preprint 1204.3187. Manuscript, Code, Mention in Radford Neal's blog
Y.W. Teh, C. Blundell and L.T. Elliott. Modelling genetic variations using fragmentation-coagulation processes. 2011. Proceedings of the 24th Conference on Neural Information Processing Systems
Y. Chen, P. Namburi, L.T. Elliott, J. Heinzle, C.S Soon, M.W.L. Chee and J.-D. Haynes. Cortical surface-based searchlight decoding. 2011. NeuroImage. 56(2). p582-92. Supplementary material

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