Platform 5 | Resources
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New Paper: Simultaneous SNP Selection and Adjustment for Population Structure in High Dimensional Prediction Models
![Table 1. Simulation study results. Mean (standard deviation) from 200 simulations stratified by the number of causal SNPs (null, 1%), the overlap between causal SNPs and kinship matrix (no overlap, all causal SNPs in kinship), and true heritability (10%, 30%). For all simulations, sample size is n = 1000, the number of covariates is p = 5000, and the number of SNPs used to estimate the kinship matrix is k = 10000. TPR at FPR = 5% is the true positive rate at a fixed false positive rate of 5%. Model Size () is the number of selected variables in the training set using the high-dimensional BIC for ggmix and 10-fold cross validation for lasso and twostep. RMSE is the root mean squared error on the test set. Estimation error is the squared distance between the estimated and true effect sizes. Error variance (σ2) for twostep is estimated from an intercept only LMM with a single random effect and is modeled explicitly in ggmix. For the lasso we use [28] as an estimator for σ2. Heritability (η) for twostep is estimated as from an intercept only LMM with a single random effect where and are the variance components for the random effect and error term, respectively. η is explictly modeled in ggmix. There is no positive way to calculate η for the lasso since we are using a PC adjustment. show less](https://i0.wp.com/www.impactt-microbiome.ca/wp-content/uploads/2020/05/journal.pgen_.1008766.t001.png?fit=800%2C443&ssl=1)
ggmix, general penalized linear mixed effects model with a single random effect for simultaneous SNP selection and adjustment for population structure in high dimensional prediction models.
New Paper: PSORTm : A Bacterial and Archaeal Protein Subcellular Localization Prediction Tool for Metagenomics Data
Congratulation to our Platform 5 Co-Lead Dr. Fiona Brinkman on this recent publication! Abstract We report PSORTm, the first bioinformatic tool designed for prediction of diverse bacterial and archaeal protein subcellular lo from metagenomics data. PSORTm incorporates components of PSORTb, one of the most precise and widely used protein SCL predictors, with an automated classification […]
New Paper: Open Data Revolution in Clinical Research: Opportunities and Challenges
Congratulations to our Ethics and Policy Lead Dr. Diego Silva on this recent publication! Abstract Efforts for sharing individual clinical data are gaining momentum due to a heightened recognition that integrated datasets can catalyze biomedical discoveries and drug development. Among the benefits are the fact that data sharing can help generate and investigate new research […]
New Paper: MDiNE: A Model to Estimate Differential Co-Occurrence Networks in Microbiome Studies
Congratulations to Dr. Celia Greenwood (Platform 5 Lead), Kevin McGregor et al.MDiNE is implemented in a freely available R package: https://github.com/kevinmcgregor/mdine MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Bioinformatics. 2019 Nov 7. PMID: 31697315 DOI: 10.1093/bioinformatics/btz824 Abstract We propose a new model called Microbiome Differential Network Estimation (MDiNE) to estimate network changes with respect […]
Platform 5 | Computational Development
Platform 5 Computational Development Our Platform 5 Experts Dr. Celia Greenwood Dr. Brinkman Fiona Dr. William Hsiao “We aim to develop novel computational tools and enhance availability and usage of open-source bioinformatics and statistical modelling platforms to advance capability in innovative and high-quality analysis of microbiome data.” Additional expertise provided by Dr. Irina Dinu at […]
