560 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- University of TorontoCA7 papers
- European Bioinformatics InstituteGB2 papers
- McGill UniversityCA2 papers
- Mila - Quebec Artificial Intelligence InstituteCA2 papers
- Princess Margaret Cancer CentreCA2 papers
- Université de MontréalCA2 papers
- University Health NetworkCA2 papers
- University of British ColumbiaCA2 papers
- Agricultural Research ServiceUS1 paper
- AIDS VancouverCA1 paper
- Alex's Lemonade Stand FoundationUS1 paper
- AVIZ: Analyse et visualisationFR1 paper
14 papers
Transfer Learning and Machine Learning for Training Five Year Survival Prognostic Models in Early Breast Cancer
Lisa Pilgram, Kai Yang, Ana-Alicia Beltran-Bless +22
Prognostic information is essential for decision-making in breast cancer management. Recently trials have predominantly focused on genomic prognostication tools, even though clinic…
Applying the FAIR Principles to computational workflows
Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame +20
Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also…
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
Erin E. Gill, Baofeng Jia, Carmen Lia Murall +67
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-…
Recommendations for extending the GFF3 specification for improved interoperability of genomic data
Surya Saha, Scott Cain, Ethalinda K. S. Cannon +8
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Speci…
Simulated dose painting of hypoxic sub-volumes in pancreatic cancer stereotactic body radiotherapy
Ahmed M. Elamir, Teodor Stanescu, Andrea Shessel +15
Dose painting of hypoxic tumour sub-volumes using positron-emission tomography (PET) has been shown to improve tumour control in silico in several sites. Pancreatic cancer presents…
The importance of transparency and reproducibility in artificial intelligence research
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny +17
In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines…
Checking the Model and the Prior for the Constrained Multinomial
Berthold-Georg Englert, Michael Evans, Gun Ho Jang +3
The multinomial model is one of the simplest statistical models. When constraints are placed on the possible values for the probabilities, however, it becomes much more difficult t…
Ten Simple Rules for Making Research Software More Robust
Morgan Taschuk, Greg Wilson
Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution, or e…
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification
Ivan Borozan, Stuart Watt, Vincent Ferretti
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequence…
Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments
Greg W. Clark, Sharon H. Ackerman, Elisabeth R. Tillier +1
Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about…
On the representation of de Bruijn graphs
Rayan Chikhi, Antoine Limasset, Shaun Jackman +2
The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a comp…
Exploring Genome Characteristics and Sequence Quality Without a Reference
Jared T. Simpson
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are avai…
Inferring clonal evolution of tumors from single nucleotide somatic mutations
Wei Jiao, Shankar Vembu, Amit G. Deshwar +2
High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases…
NodeTrix: Hybrid Representation for Analyzing Social Networks
Nathalie Henry, Jean-Daniel Fekete, Michael Mcguffin
The need to visualize large social networks is growing as hardware capabilities make analyzing large networks feasible and many new data sets become available. Unfortunately, the v…