Peer reviewed
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
N Eling, AC Richard, S Richardson, JC Marioni and CA Vallejos (2018)
Cell Systems
Extends BASiCS with a residual measure of variability that is not confounded by mean expression and with a robust procedure for quantifying technical noise in experiments without technical spike-in molecules.
Normalizing single-cell RNA sequencing data: challenges and opportunities
CA Vallejos, D Risso, A Scialdone, S Dudoit and JC Marioni (2017)
Nature Methods
Discusses commonly used normalization approaches for single-cell RNA sequencing data and illustrate how some of these can produce misleading results.
Bayesian survival analysis of university outcomes
CA Vallejos and MFJ Steel (2017)
Journal of the Royal Statistical Society - Series A
Introduces and applies a competing risks framework to identify risk factors associated to university dropouts and delayed graduations.
Aging increases cell-to-cell transcriptional variability upon immune stimulation
CP Martinez-Jimenez, N Eling, H Chen, CA Vallejos, AA Kolodziejczyk, F Connor, L Stojic, TF Rayner, MJT Stubbington, SA Teichmann, M de la Roche, JC Marioni and DT Odom (2017)
Science
Studies transcriptional heterogeneity in CD4+T cells using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4+ T cells.
Incorporating unobserved heterogeneity in Weibull survival models: A Bayesian approach
CA Vallejos and MFJ Steel (2017)
Econometrics and Statistics
Extends Weibull regression survival models to account for outliers and other forms of unobserved heterogeneity.
Beyond comparisons of means: understanding changes in gene expression at the single-cell level
CA Vallejos, S Richardson and JC Marioni (2016)
Genome Biology
Extends BASiCS with a probabilistic framework to assess differential expression patterns (mean and variability) between cell populations using single-cell RNA sequencing data.
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
CA Vallejos, JC Marioni and S Richardson (2015)
PLOS Computational Biology
Presents BASiCS as an integrated statistical framework for single-cell RNA sequencing data: normalisation, technical noise quantification as well as highly and lowly genes variable identification.
Objective Bayesian survival analysis using scale mixtures of log-normal distributions
CA Vallejos and MFJ Steel (2015)
Journal of the American Statistical Association
Introduces the family of shape mixtures of log-normal distributions as a flexible framework for survival modelling, studying Bayesian inference under nonsubjective priors based on the Jeffreys’ rule.
Others
Shrinkage estimation of large covariance matrices using multiple shrinkage targets
H Gray, GGR Leday, CA Vallejos, S Richardson (2018)
arXiv
Disentangling transcriptional heterogeneity among single-cells: a Bayesian approach
CA Vallejos, S Richardson and JC Marioni (2015)
Mini workshop: Recent Developments in Statistical Methods with Applications to Genetics and Genomics. Eds. I. Ionita-Laza, M. Krawczak, X. Lin, M. Nothnagel. Mathematisches Forschungsinstitut Oberwolfach Reports 52. DOI: 10.4171/OWR/2015/52
On posterior propriety for the Student-t linear regression model under Jeffreys priors
CA Vallejos and MFJ Steel (2013)
arXiv (CRiSM Working Paper 13-15)