David Lougheed GitHub

I am a Human Genetics M.Sc. student in Prof. Guillaume Bourque's lab at McGill University, studying short tandem repeats (STRs). I can be emailed at contact@dlougheed.com.

From May 2019 until August 2020, I worked as a software developer at the Canadian Centre for Computational Genomics (C3G) in Montréal.

I have a B.Sc. in Computer Science and Biology from McGill (graduated May 2019 with First Class Honours.)

Publications

• Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection (2022 preprint)

  Katherine A Aracena, Yen-Lung Lin, Kaixuan Luo, Alain Pacis, Saideep Gona, Zepeng Mu, Vania Yotova, Renata Sindeaux, Albena Pramatarova, Marie-Michelle Simon, Xun Chen, Cristian Groza, David Lougheed, Romain Gregoire, David Brownlee, Yang Li, Xin He, David Bujold, Tomi Pastinen, Guillaume Bourque, Luis B Barreiro. bioRxiv Preprint. DOI: 10.1101/2022.05.10.491413

• baRcodeR: An open‐source R package for sample labelling (2020)

  Yihan Wu, David R. Lougheed, Stephen C. Lougheed, Kristy Moniz, Virginia K. Walker, Robert I. Colautti. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.13405

• Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations (2019)

  Janin Grajcarek, Jean Monlong, Yoko Nishinaka-Arai, Michiko Nakamura, Miki Nagai, Shiori Matsuo, David Lougheed, Hidetoshi Sakurai, Megumu K. Saito, Guillaume Bourque & Knut Woltjen. Nature Communications. DOI: 10.1038/s41467-019-12829-8

Software & Projects

• STRkit (work in progress)

  An STR genotyper for long read sequencing data. This is an ongoing project created as part of my Master's degree in Human Genetics at McGill.

• EpiVar Browser (2022)

  A browser for exploring quantitative trait loci and their associations with genotype and ancestry. Part of an upcoming publication by Aracena et al. (currently in preprint; 2022)

• Bento

  A platform for storing, analyzing, and visualizing genomic and epigenomic data, created while working at C3G.

• PyTrackDat

  A utility for creating online databases for scientific data.

• MHCut Browser (2019)

  A browser for microhomologies at variant CRISPR/Cas9 cut sites. Part of a publication by Grajcarek et al. (2019)

• McGill Network (2018)

  A visualization tool and API for examining shared interests between McGill researchers.

• Elbow Lake Trail Guide (2015, revised 2016)

  An interactive trail guide app available on Android and iOS.