Publications

GenPipes: an open-source framework for
distributed and scalable genomic analyses

It started in June with the publication of our beloved GenPipes framework and set of NGS data analysis pipelines in GigaScience. We use these pipelines on a daily basis for data production and routine analysis and hope the community will find it useful. While GenPipes is the product of several years of teamwork, kudos to co-first authors Mathieu Bourgey and Rola Dali who worked very hard to get this long-awaited paper out!

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Altered microbiome composition in individuals with fibromyalgia

This summer has also been very special for C3G’s metagenome specialist Emmanuel Gonzalez with a publication in Pain highlighting a strong potential link between the microbiome and fibromyalgia, a terrible and elusive disorder affecting a large fraction of the population. This study drew quite a nice amount of media attention, notably from the
Montreal Gazette and the CBC. We are very proud to say that through Emmanuel, C3G provided first-rate analysis services for experimental design, species identification, statistical analysis, machine learning and finally for working hand-in-hand with Drs. Minerbi and Brereton on biological interpretation. Importantly, Emmanuel’s applied ANCHOR here, a method he also
published earlier this year, which enables the identification of microbial species at a resolution higher than for other common 16S sequencing data analysis methods.

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Altered differentiation is central to HIV-specific CD4+ T cell dysfunction in progressive disease

Another noteworthy publication to which C3G contributed as author to was published in Nature Immunology this summer. Among other things, this study contrasted specific HIV specific CD4 T-cells subpopulations between antiretroviral therapy treated and elite controller patients, which contributes to a better understanding of why viral control is lost once antiretroviral therapy is interrupted. For this project, C3G services analyst Éloi Mercier performed careful quality control and complex functional genomics analyses, working closely with the lead authors for interpretation and visualization of results. We are immensely thankful to Drs Mourou and Kaufmann for offering us the opportunity of helping advance HIV research.

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The International Human Epigenome
Consortium Data Portal

The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. To define conventions ensuring the compatibility of datasets and establish an infrastructure enabling data integration, analysis, and sharing, we developed the IHEC Data Portal (http://epigenomesportal.ca/ihec). The portal provides access to >7,000 reference epigenomic datasets, generated from >600 tissues, which have been contributed by seven international consortia:ENCODE, NIH Roadmap, CEEHRC, Blueprint, DEEP, AMED-CREST, and KNIH. The portal enhances the utility of these reference maps by facilitating the discovery, visualization, analysis, download, and sharing of epigenomics data. The IHEC Data Portal is the official source to navigate through IHEC datasets and represents a strategy for unifying the distributed data produced by international research consortia.

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