Home | James Knight, PhD

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

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.

First review article

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

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.

First Nature paper

My first publication in Nature itself is a co-first authored publication with my colleague Dr Chris Go, describing our novel large-scale attempt at mapping the cell using proteomic techniques.

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.

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.

Vanier Scholarship

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

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.

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.

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.

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.

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

Principal Software Engineer at Cultivarium

I currently work as a principal software engineer at Cultivarium, developing resources to support their mission of accelerating the adoption of non-model microorganisms for biotechnology.