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 senior software engineer at Cultivarium. I specialize in developing software for data sharing and analysis, as well as for general scientific productivity purposes.

Publications

First review article

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

Kinases in muscle differentiation logo
First Nature publication

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

Dotplot

Education

BSc in Biology and Mathematics

I attended McMaster University for my first undergraduate 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 the 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 received my PhD, developing computational and methodological approaches for studying the protein kinase superfamily.

University of Ottawa logo
Online education

My education continues in the form of online courses that fill gaps in my expertise and improve my existing skill set. You can view my completed courses on my certificates page.

Computer

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

After my postdoc, I was employed as a Bioinformatician at the Lunenfeld-Tanenbaum Research Institute in the laboratory of Dr. Anne-Claude Gingras, where I performed analysis and created web apps that helped biologists to understand, manage and visualize their own data

LTRI logo

Projects

COVID-19 interactome logo

The COVID-19 interactome is a project mapping interactions between the SARS-CoV-2 virus and proteins found in infected human cells. I did the analysis for this project in Python and built a static website to act as a repository for that data using Gatsby. A preprint for the project is currently available on bioRχiv.

ProHits-viz is a suite of interactive webtools for analyzing and visualizing protein-protein interaction data. This is the project where I first began learning web development. The third (and current) iteration of this site was built using React with Node.js, Golang and Docker on the backend. A paper for this project was published at Nature Methods.

ProHits-viz
Gene Info

GIX is a Browser 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 and was published at Nature Methods.

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, with analysis performed using R and Matlab. A paper for this project was published at Nature.
Cell map logo
GitHub logo
Checkout GitHub for my other public projects.
CSSGoReactTSNodeJSNextJS

Skills

coding.js

constskills= {
languages:{
current:[
'Bash'
'Go'
'JavaScript'
'Python'
'TypeScript'
],
past:[
'C'
'Java'
'MATLAB'
'Perl'
'R'
],
},
frontEnd:{
current:[
'CSS'
'Gatsby'
'HTML5'
'React'
'Vanilla JS'
],
past:[
'AngularJS'
'D3.js'
'jQuery'
'SCSS'
],
},
backEnd:{
current:[
'AWS Lambda'
'Express'
'Node.js'
],
past:[
'PHP'
],
},
databases:{
current:[
'DynamoDB'
'MongoDB'
'PostgreSQL'
],
past:[
'MySQL'
],
},
tools:{
current:[
'AWS'
'Docker'
'Git'
'Webpack'
],
past:[
'Gulp'
],
},
learning:[
'Next.js'
'Rust'
],
};
export defaultskills;
PythonAWSHTMLRustDocker
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Moving car
© James Knight, 2022.