Tools

Computational and Analytical Tool

Name	Description	Ref (PMID)
ryp	a Python-R bridge to accelerate (biomedical) data science
LEADER	CelL sEletion viA aDaptivE Reweighting Method to subset cells aiming to capture rare cell types with the goal of creating more balanced datasets. Leader requires a processed seurat object with gene expression data and an optional marker file specifying known marker genes for known cell types.	Nat Commun, 2024
INTEGRAL-Radiomics	Radiomics analysis to predict pulmonary nodule malignancy using machine learning approaches	Thorax, 2024
mixcuref	R language statistical function package for jointly modelling time-to-event and probability of being event-free. The Firth-type penalized likelihood approach was introduced as an alternative to the MLE approach, to handle heavily censored data with imbalanced categorical covariates	Statistics in Medicine, 2023
ALARM	Lung Cancer Absolute Risk Models for Mortality in an Asian Population using the China Kadoorie Biobank	J Natl Cancer Inst., 2022
Astir	Automated inference of cell identity from single-cell multiplexed imaging and proteomics	Cell Systems, 2021
JM-SNP	Characterization of direct and/or indirect genetic associations for multiple traits in longitudinal studies of disease progression with application to diabetes complications	MedRxiv, 2021
TwoPhase_postGWAS	Two-phase sample selection strategies for design and analysis in post-genome-wide association fine-mapping studies with application to lipids in the Northern Finland Birth Cohort	Statistics in Medicine, 2021
FamEvent	Family Age-at-Onset Data Simulation and Cancer Risk Estimation: Simulation and analysis of time-to-event outcomes for various family designs	J. Statistical Software, 2021
rareBF	Performs region-based testing of rare variants in case-control design	Biometrics, 2021
sim1000G	Simulation of genetic variants according to the 1000 Genomes haplotypes	BMC Bioinformatics, 2019
SBDMCMC	The scalable Birth-Death MCMC Algorithm for Mixed Graphical Model Learning with Application to Genomic Data Integration.
REGION-SCAN	Region-based GWAS by Multiple linear combination regression with constraints. Performs genome-wide region-based association testing of common and low-frequency variants with quantitative and binary (case-control) traits, in concert with bigLD/gpart software: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks. Application to lipids traits in the Canadian Longitudinal Study on Aging	Genet Epidemiol., 2017 Bioinformatics, 2018 Bioinformatics, 2019 Genetic Epidemiol., 2022
PMLR	Penalized multinomial logistic regression: Performs sparse data logistic regression for general categorical outcomes under a penalized likelihood, including LR test statistics and profile likelihood confidence interval construction	BMC Proc., 2016 Stat Med., 2007
genMOSS	Bayesian Analysis of GWAS data: Performs multi-SNP analysis in the context of GWAS and fine-mapping studies	Ann Appl Stat., 2016
BRsquared Plug-in	Performs bootstrap bias reduction for effect estimation under the Cox proportional hazards time-to-event model	Genet Epidemiol., 2015 Stat Med., 2011 Hum Genet., 2011
FrailtyPack	General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction- Two functions developed by our group: a) Joint model analysis of recurrent and terminal events in family setting; b) Rare variant analysis in family setting.	Comput Methods Program Biomed. 2005

		Careers
			Postdoctoral Fellow Position in Statistical Genetics and Biostatistics in Toronto