Guillaume Bourque
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View article: Supplementary Table S2 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma
Supplementary Table S2 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma Open
Somatic mutations detected in 12 interrogated genes for cohorts C1-C3
View article: Supplementary Table S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma
Supplementary Table S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma Open
Clinical information and 12 gene mutation status for cohorts C1-C3
View article: Supplementary Tables S3-S13 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma
Supplementary Tables S3-S13 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma Open
Supplementary Tables S3-S13
View article: Figure S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma
Figure S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma Open
Disease-Free Survival outcomes amongst genomic groups when applied to the 247 VHL mutated ccRCCs from the TCGA dataset
View article: Integrated Metabolic Complex Genetic Interaction Network of Chromosome 4p Loss in Basal Breast Cancer
Integrated Metabolic Complex Genetic Interaction Network of Chromosome 4p Loss in Basal Breast Cancer Open
Basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and exhibits a recurrent large chromosomal deletion in chromosome 4p (chr4p). Chr4p loss is associated with poor survival, evolves early in tumorigenesis and …
View article: Altered sperm DNA methylation in overweight men associates transposable element regulation to paternal origins of disease risk in children
Altered sperm DNA methylation in overweight men associates transposable element regulation to paternal origins of disease risk in children Open
The occurrence of childhood neurodevelopmental disorders has been steadily increasing for decades yet we have little understanding of modes of inheritance implicated in these diseases. Epidemiology studies have revealed an association betw…
View article: REST/NRSF Preserves muscle stem cell identity by repressing alternate cell fate
REST/NRSF Preserves muscle stem cell identity by repressing alternate cell fate Open
Cell fate and identity require timely activation of lineage-specific and concomitant repression of alternate-lineage genes. How this process is epigenetically encoded remains largely unknown. In skeletal muscle stem cells, the myogenic reg…
View article: A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage
A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage Open
Current approaches for classifying and annotating endogenous retroviruses (ERVs) and their long terminal repeats (LTRs) have limited resolution and are inaccurate. Here, we developed an annotation approach based on phylogenetic analysis an…
View article: Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA Open
C is- regulatory elements (CREs) have a major effect on phenotypes including disease. They are identified in a genome-wide manner by analyzing the binding of transcription factors (TFs), various co-factors and histone modifications in DNA …
View article: PARPAL: PARalog Protein redistribution using Abundance and Localization in yeast database
PARPAL: PARalog Protein redistribution using Abundance and Localization in yeast database Open
Whole-genome duplication (WGD) events are common across various organisms; however, the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WG…
View article: Finding an optimal sequencing strategy to detect short and long genetic variants in a human genome
Finding an optimal sequencing strategy to detect short and long genetic variants in a human genome Open
Advances in DNA sequencing have transformed genomics, enabling comprehensive insights into human genetic variation. While short-read sequencing (SRS) remains dominant due to its high accuracy and affordability, its limitations in complex g…
View article: Single-cell imaging of protein dynamics of paralogs reveals sources of gene retention
Single-cell imaging of protein dynamics of paralogs reveals sources of gene retention Open
Gene duplication is common across the Tree of Life and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originatin…
View article: STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation
STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation Open
Variation in short tandem repeats (STRs) is implicated in Mendelian disease and complex traits, but can be difficult to resolve with short-read genome sequencing. We present STRkit , a software package for genotyping STRs using long read s…
View article: Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation
Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation Open
View article: PARPAL: PARalog Protein Redistribution using Abundance and Localization in Yeast Database
PARPAL: PARalog Protein Redistribution using Abundance and Localization in Yeast Database Open
Whole-genome duplication (WGD) events are common across various organisms however the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WGD …
View article: Biobanque québécoise de la COVID-19 (BQC19), a COVID-19 biobank to support Canadian health research
Biobanque québécoise de la COVID-19 (BQC19), a COVID-19 biobank to support Canadian health research Open
View article: Genomics of diffusion-imaging integrating GWAS, exome data and single-cell sequencing unravels lifespan determinants of cerebral small vessel disease
Genomics of diffusion-imaging integrating GWAS, exome data and single-cell sequencing unravels lifespan determinants of cerebral small vessel disease Open
Peak width of skeletonized mean diffusivity (PSMD) is an emerging automated diffusion imaging marker showing clinically relevant changes in cerebral small vessel disease (cSVD), a leading cause of stroke and dementia with no mechanism-base…
View article: Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells
Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells Open
Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains …
View article: Transcriptome atlases of rat brain regions and their adaptation to diabetes resolution following gastrectomy in the Goto-Kakizaki rat
Transcriptome atlases of rat brain regions and their adaptation to diabetes resolution following gastrectomy in the Goto-Kakizaki rat Open
View article: A unified framework to analyze transposable element insertion polymorphisms using graph genomes
A unified framework to analyze transposable element insertion polymorphisms using graph genomes Open
View article: The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology Open
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 the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global pu…
View article: Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations
Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations Open
Transposable elements (TEs) are DNA sequences able to create copies of themselves within the genome. Despite their limited expression due to silencing, TEs still manage to impact the host genome. For instance, some TEs have been shown to a…
View article: REST/NRSF preserves muscle stem cell identity and survival by repressing alternate cell fates
REST/NRSF preserves muscle stem cell identity and survival by repressing alternate cell fates Open
Cell fate and identity require timely activation of lineage-specific and concomitant repression of alternate-lineage genes. How this process is epigenetically encoded remains largely unknown. In skeletal muscle stem cells (MuSCs), the myog…
View article: Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells
Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells Open
SUMMARY Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it …
View article: The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology Open
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-CoV-2 genome sequences have been deposited in global public…
View article: Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring
Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring Open
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer.…
View article: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA Open
Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation status is rarely characterized due to previous limitations in genome assembly and detection of modified nucleotides. Because of this, the extent to …
View article: EpiVar Browser: advanced exploration of epigenomics data under controlled access
EpiVar Browser: advanced exploration of epigenomics data under controlled access Open
Motivation Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, s…
View article: A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome
A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome Open
View article: CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in TCF3::PBX1 ALL
CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in TCF3::PBX1 ALL Open
Childhood B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous disease comprising multiple molecular subgroups with subtype-specific expression profiles. Recently, a new type of ncRNA, termed circular RNA (circRNA), has emerged a…