Diff for "BrendanInnes" - Bader Lab @ The University of Toronto

Differences between revisions 6 and 36 (spanning 30 versions)

Members/binnes.jpg

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.

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've recently built a basic R package to generate and visualize bipartite graphs of cell-cell interactions from single-cell RNAseq data, 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.

Education

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

Publications

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 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

Innes BT & Bader GD. Innes BT and 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

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

CategoryHomepage

-  ⇤ ← Revision 6 as of 2016-05-24 20:37:33 → 
  Size: 1503
  Editor: BrendanInnes
  Comment:
+   ← Revision 36 as of 2019-04-09 15:14:52 → ⇥
  Size: 4090
  Editor: BrendanInnes
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
+{{attachment:Members/binnes.jpg}}
-Line 7:
+Line 9:
-Brendan Innes is a PhD candidate in Molecular Genetics.  He is interested using single-cell RNAseq data to understand intercellular signalling in complex tissues.
+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 [[CellCellInteractions|handy database of ligand-receptor pairs]]. This database has powered analyses such as [[https://doi.org/10.1016/j.neuron.2016.07.037|this one from the Miller/Kaplan lab]], which identified extrinsic regulators of neurogenesis.  

I've recently built a basic R package to generate and visualize bipartite graphs of cell-cell interactions from single-cell RNAseq data, [[https://baderlab.github.io/CCInx|available here]].

=== scClustViz - scRNAseq cluster assessment and visualization ===
I've built an interactive reporting tool for single-cell RNAseq results [[https://baderlab.github.io/scClustViz|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.
-Line 10:
+Line 21:
-MSc in Biochemistry at the University of Western Ontario, supervised by Dr. David Litchfield
+MSc in Biochemistry at the University of Western Ontario, supervised by [[https://www.schulich.uwo.ca/biochem/people/bios/Litchfield.html|Dr. David Litchfield]]
-Line 18:
+Line 29:
-'''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. doi:10.1016/jbbadis.2014.12.025 http://www.ncbi.nlm.nih.gov/pubmed/25595659
+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'' https://doi.org/10.1101/440032
-Line 20:
+Line 31:
-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. doi:10.1139/cjc-2014-0230
+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
-Line 22:
+Line 33:
-'''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. doi:10.3389/fphys.2013.00018.  http://www.ncbi.nlm.nih.gov/pubmed/23407864
+'''Innes BT''' & Bader GD. Innes BT and 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

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