samantha g. e. halliday

gist: generative inference of unassembled mRNA taxonomy

topiary: constraints satisfaction for metatranscriptome reconstruction

gargle: multitrack sequence assembly

genepuddle: metatranscriptome simulation toolkit

lincomp: taxonomic grep and compare

University of Toronto
Doctor of Philosophy (PhD)
Computer Science (Computational Biology)

University of Toronto
Master of Science (MSc)
Computer Science (Computational Biology)

Queen's University, Kingston
Bachelor's in Computing with Honours (BCmpH)
Biomedical Computing Specialization

Halliday, S., Parkinson, J. Gist: an ensemble approach to the taxonomic classification of metatranscriptomic sequence data. Under revision.

Halliday, G., Nuin P., Mousavi P. (2012) The comparison of multiple sequence alignments: automation and results. (Unpublished)

Halliday, G., Palmer, C. (2010) BioBrick Foundation RFC (Request for Comments) #77: Promoter and Coding Sequence Considerations for Caenorhabditis elegans and Other Eukaryotes. (Unrefereed)

Halliday, S., Parkinson, J. (2015) An Ensemble Approach to the Taxonomic Classification of Meta-transcriptomic Sequence Data.
Talk given at Great Lakes Bioinformatics Conference (GLBIO) 2015.

Halliday, S., Parkinson, J. (2014) GIST - A novel pipeline for accurate taxonomic assignment.
Poster presented at 12th Annual Rocky Mountain Bioinformatics Conference; won best poster.

Halliday, S., Parkinson, J. (2014) GIST - An Ensemble Approach to the Taxonomic Classification of Metatranscriptomic Reads.
Poster presented at Great Lakes Bioinformatics Conference (GLBIO) 2014.

Halliday, S., Parkinson, J. (2014) GIST - An ensemble approach to the taxonomic classification of metatranscriptomic reads.
Talk and poster presented at Biocuration 2014.

Halliday, G., Parkinson, J. (2013) GIST - an ensemble approach to the taxonomic classification of metatranscriptomic reads.
Talk and poster presented at 11th Annual Rocky Mountain Bioinformatics Conference.

Halliday, G., Goldie S., Shi H., Phi T. (2010) WormGuide: engineering C. elegans.
Resource produced for the International Genetically-Engineered Machine Competition 2010.

Palmer, C., Zhang, Y., Shi, H., Halliday, G. (2010) WormWorks: engineering C. elegans.
Presentation given at International Genetically-Engineered Machine Competition 2010.

research assistant
Autism Spectrum Disorder Canadian–American Research Consortium
Ongwanada Resource Centre, Kingston

CSC318 design of computational media

CSC104 introduction to computer science

CSC309 programming on the web

CSC301 software engineering

CSC324 principles of programming languages