B. F. Francis Ouellette
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View article: Biological databases in the age of generative artificial intelligence
Biological databases in the age of generative artificial intelligence Open
Summary Modern biological research critically depends on public databases. The introduction and propagation of errors within and across databases can lead to wasted resources as scientists are led astray by bad data or have to conduct expe…
View article: Ten simple rules for writing a PLOS Computational Biology quick tips article
Ten simple rules for writing a PLOS Computational Biology quick tips article Open
At that time, the change in how we communicate sciences had already begun [2]: social media was blooming, the information deluge was ongoing, and the fear of missing information was anchored in each of us.The Ten Simple Rules collection fi…
View article: RNAget: an API to securely retrieve RNA quantifications
RNAget: an API to securely retrieve RNA quantifications Open
Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in ma…
View article: Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations Open
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArt…
View article: Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing
Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing Open
Over the last two decades, molecular biology has been changed by the introduction of high-throughput technologies. Data sharing requirements have prompted the establishment of persistent data archives. A standardized approach for recording…
View article: ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins Open
Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thous…
View article: Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types Open
We present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing…
View article: ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins Open
Interpretation of genetic variation is required for understanding genotype-phenotype associations, mechanisms of inherited disease, and drivers of cancer. Millions of single nucleotide variants (SNVs) in human genomes are known and thousan…
View article: Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments Open
The International Cancer Genome Consortium (ICGC)’s Pan-Cancer Analysis of Whole Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding and non-coding regions in over 2,800 cancer patients. To provide th…
View article: A global perspective on bioinformatics training needs
A global perspective on bioinformatics training needs Open
In the last decade, life-science research has become increasingly data-intensive and computational. Nevertheless, basic bioinformatics and data stewardship are still only rarely taught in life-science degree programmes, creating a widening…
View article: Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers
Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers Open
Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years…
View article: A Quick Guide for Building a Successful Bioinformatics Community
A Quick Guide for Building a Successful Bioinformatics Community Open
"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Com…