James KnightPhD
James Knight siting as his computer
James Knight's descriptionprogrammer and scientist

A brief history

Although formally trained as a molecular biologist, I have been programming since 2000. In 2015 I became a full-time programmer and now work as a bioinformatician at the Lunenfeld-Tanenbaum Research Institute in Toronto creating web apps that help biologists to analyze, manage and visualize their data.

Publications

First paper published

My first paper was published in 2007. It documented structural and residue conservation in the protein kinase superfamily and showed how this information could be used to predict unknown protein kinase structures.

Protein kinase
First review article

The first review article I wrote discussed the role of protein kinases in skeletal muscle cell proliferation and differeniation.

Kinases in muscle differeniation logo
First Nature paper

My first Nature paper describes the suite of web tools we built to aid molecular biologists in visualizing protein-protein interaction data.

Dotplot

Career

NSERC USRA holder

While an undergraduate student I was funded by the Natural Sciences and Engineering Research Council with an Undergraduate Student Research Award to perform research during my Summers in the laboratories of Dr. G. Brian Golding and Dr. David J. D. Earn.

NSERC logo
Graduate student at the OHRI

My graduate studies were conducted in the laboratory of Dr. Rashmi Kothary at the Ottawa Hospital Research Institute where I developed new computational and experimental techniques for studying the protein kinase superfamily.

OHRI logo
Postdoctoral fellow at the LTRI

After completing my PhD I began postdoctoral studies in the laboratory of Dr. Anne-Claude Gingras at the Lunenfeld-Tanenbaum Research Institute studying cerebral cavernous malformations using proteomic approaches.

LTRI logo
Bioinformatician at the LTRI

I am currently employed as a Bioinformatician at the Lunenfeld-Tanenbaum Research Institute in the laboratory of Dr. Anne-Claude Gingras. My principal role is to create web apps and develop new approaches to aid molecular biologists with data analysis.

LTRI logo

Education

BSc in Biology and Mathematics

I attended McMaster University for my first undergadute degree, studying mathematics and biology. The emphases were algebra and anatomy respectively.

McMaster logo
BA in English and History

I attended the University of York in the UK for my second undergraduate degree in English and History, focusing on Victorian literature and Medieval European history.

University of York logo
Vanier Scholarship

During my PhD I was awarded a Vanier Canada Graduate Scholarship that is given for scholarly achievement and leadership in graduate studies.

Vanier scholarship logo
PhD in Cellular and Molecular Medicine

At the University of Ottawa I recieved my PhD, developing computational and methodological approaches for studying the protein kinase superfamily.

University of Ottawa logo

Projects

ProHits-viz

ProHits-viz is a suite of interactive webtools for analyzing and visualizing protein-protein interaction data. This is the project that started my web development career. I am currently working on a new implementation of the site using React with Node.js and Golang on the backend. The current version of the site can be seen at prohits-viz.org (in progress 2020), while the previous version can be seen at prohits-viz.lunenfeld.ca (created 2017), and the first version can be seen at prohitstools.mshri.on.ca (created 2015).

Gene Info is a Chrome Extension that allows molecular biologists to retrieve gene information on any webpage simply by double clicking a gene name. It was built with vanilla JavaScript.

Gene Info
Cell map logo
The human cell map is a Gingras lab project to map a human cell using proteomic techniques. The humancellmap.org is a repository for that data built with Angular and Node.js.
Checkout GitHub for my other public projects.
GitHub
CSSGoReactCSSNodeJS

Skills

coding.js

constskills= {
backEnd:{
current:[
'Express'
'MongoDB'
'Node.js'
],
past:[
'MySQL'
'PHP'
],
},
frontEnd:{
current:[
'CSS'
'Gatsby'
'HTML5'
'React'
'Vanilla JS'
],
past:[
'AngularJS'
'D3.js'
'jQuery'
'SCSS'
],
},
languages:{
current:[
'Go'
'JavaScript'
'Perl'
'R'
],
past:[
'C'
'Java'
'MATLAB'
'Python'
],
},
learning:[
'Docker'
'WebAssembly'
],
};
export defaultskills;
PerlRHTMLSassDocker
Contact bannerbuildings
Contact bannercountryside

Questions or comments?

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© James Knight, 2020.