I am a PhD candidate in Molecular Genetics who started in the Bader lab in May, 2016. I am very excited about the possibilities offered by high-throughput single-cell RNA-seq, especially to investigate intercellular signalling in complex tissues.
CCInx - Cell-cell interaction prediction
As part of our ongoing work developing tools to predict cell-cell interaction networks from -omics data, Ruth Isserlin has put together a handy database of ligand-receptor pairs. This database has powered analyses such as this one from the Miller/Kaplan lab, which identified extrinsic regulators of neurogenesis. I'm currently working on CCInx, an R package to generate and visualize bipartite graphs of cell-cell interactions from single-cell RNAseq data. A working development version is available here.
Aging Mouse Brain
CCInx was used to perform the cell-cell interaction prediction and visualization in this collaboration with Lee Rubin's group, comparing the brains of young and old mice. The results are available here.
scClustViz - scRNAseq cluster assessment and visualization
I've built an interactive reporting tool for single-cell RNAseq results available here. Hopefully it will both help biologists and bioinformaticians better collaborate while working with this data, and improve open science by making it easier to publish data in an accessible manner.
Human Liver Atlas
Sonya MacParland and Ian McGilvray led the creation of the first single-cell atlas of a human organ, the liver. Jeff Liu and I were honoured to perform the analysis for this project, the results of which can be viewed in scClustViz here.
Embryonic Mouse Cerebral Cortex
I worked with Scott Yuzwa and Michael Borrett of Freda Miller's group
MSc in Biochemistry at the University of Western Ontario, supervised by Dr. David Litchfield
BMSc in Cell Biology and Biochemistry at the University of Western Ontario
TA for MBP1010H - Quantitative Biology and Statistical Methods
Innes BT & Bader GD. scClustViz – Single-cell RNAseq cluster assessment and visualization [version 2; peer review: 2 approved]. F1000Res. 7:1522, 2019. http://doi.org/10.12688/f1000research.16198.2
Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Nguyen L, Mayweather BA, Ozek C, Niziolek Z, Butty VL, Isserlin R, Buchanan SM, Levine SR, Regev A, Bader GD, Levin JZ, Rubin LL. Single-cell transcriptomic profiling of the aging mouse brain. Submitted to Nat Neurosci. Preprint at https://doi.org/10.1101/440032
MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 9(4383), 2018. https://doi.org/10.1038/s41467-018-06318-7
Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD. Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling. Cell Rep. 21(13):3970-86, 2017. https://doi.org/10.1016/j.celrep.2017.12.017
Innes BT, Sowole MA, Gyenis L, Dubinsky M, Konermann L, Brandl CJ, Litchfield DW, Shilton BH. Peroxide-Mediated Oxidation and Inhibition of the Peptidyl-Prolyl Isomerase Pin1. Biochim Biophys Acta. 1852(5):905-12, 2015. https://doi.org/10.1016/j.bbadis.2014.12.025
Sowole MA, Innes BT, Amunugama M, Brandl CJ, Shilton BH, Litchfield DW, Konermann L. Noncovalent binding of a cyclic peptide inhibitor to the peptidyl-prolyl isomerase Pin1 explored by hydrogen exchange mass spectrometry. Can J Chem. July 2014. https://doi.org/10.1139/cjc-2014-0230
Innes BT, Bailey ML, Brandl CJ, Shilton BH, Litchfield DW. Non-catalytic participation of the Pin1 peptidyl-prolyl isomerase domain in target binding. Front. Physiol. 4:18, 2013. https://doi.org/10.3389/fphys.2013.00018