Brendan Innes

Email: <brendan DOT innes AT mail DOT utoronto DOT ca>

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.

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.

scClustViz - scRNAseq cluster assessment and visualization

I've built a simple pipeline and visualization tool to help collaborators go from raw gene expression counts per cell to exploring annotated cell-type specific gene expression data in a quick and reproducible way. Below is a quick video of an old prototype of the visualization tool in action, showing the sort of data one can get from this pipeline. See the newest version here!



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

Teaching Experience

TA for MBP1010H - Quantitative Biology and Statistical Methods


Ximerakis M, Lipnick SL, Simmons SK, Adiconis X, Innes BT, 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 transcriptomics of the aged mouse brain reveals convergent, divergent and unique aging signatures. Submitted to Nat Neurosci. Preprint at

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.

Innes BT & Bader GD. Innes BT and Bader GD. scClustViz – Single-cell RNAseq cluster assessment and visualization [version 1; referees: 2 approved with reservations]. F1000Res. 7:1522, 2018.

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.

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.

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.

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.


BrendanInnes (last edited 2018-10-22 14:13:43 by BrendanInnes)

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