Genomics Archives - Page 3 of 4 - Canadian Centre for Computational Genomics

Disambiguating mixed-species of graft samples

As a Bioinformatician, often I get to work with PDX cancer samples. I’ve recently been reading about samples containing genome admixture, and was revisiting strategies that we commonly use for analyzing these biological data. Presented here is a summary of the existing software tools used for this purpose.

genome admixture samples

The ANCHOR pipeline

Emmanuel Gonzalez with another team member

ANCHOR is a high-resolution metagenomics pipeline, the result of a multi-disciplinary collaboration between C3G and researchers at Institut de recherche en biologie végétale (IRBV) at Université de Montreal.

ANCHOR pipeline

Characterizing the landscape of genetic drivers and their clinical impact

Recently published in [Nature Communications], this paper presents work by members of the C3G Toronto node that integrates genomic and transcriptomic analyses to assess the molecular and clinical features of infant glioma patients.

genomic analysis transcriptomic analysis

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.

fibromyalgia microbiome composition

GSoC 2019

flag with code symbol hoisted on the globe

Again this year, C3G was a Google Summer of Code organization. For people unfamiliar with it, GSoC is in Google’s own words: ” a global program that matches students up with open source, free software and technology-related organizations to write code and get paid to do it! ”

code writing for softwares GSoC Open source

Altered differentiation is central to HIV-specific CD4

Another noteworthy publication to which C3G members contributed as authors was published in Nature Immunology this summer.

HIV specific CD4 T-cells study

Methylation signatures investigations

Methylation signature close up of a DNA strand

The C3G Toronto node has also been involved in two projects to investigate methylation signatures for specific conditions.

methylation signatures

GenPipes: an open-source framework

It started in June with the publication of our beloved GenPipes framework and set of NGS data analysis pipelines in GigaScience.

genomic analysis tool

Covid-19 updates at C3G

We would like to provide a quick update amidst the coronavirus pandemic. While our host institutions (McGill University, SickKids Toronto) have put various measures in place to ensure the safety of our staff, our platform remains fully operational and available to support genomics research.

covid-19

ForCasT

ForCas Tool (ForCasT) is a comprehensive tool for the design, evaluation and collection of CRISPR/Cas9 guide RNAs and primers. Using robust parameters, it generates guide RNAs for target loci, assesses their quality for any potential off-target effects and designs associated primers.

open-source pipeline