List of works - Guillaume Bourque

A call for benchmarking transposable element annotation methods

scientific article published on 4 August 2015

A coordinated progression of progenitor cell states initiates urinary tract development

scientific article published on 11 May 2021

A draft human pangenome reference

scientific article published on 10 May 2023

A population-based LD map of the human chromosome 6p.

scientific article published on 29 September 2005

A replication study for association of 53 single nucleotide polymorphisms in ScoliScore test with adolescent idiopathic scoliosis in French-Canadian population

scientific article published on April 2015

A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19

scientific article published on 01 June 2022

ABCA7 rare variants and Alzheimer disease risk

scientific article published on April 2016

Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

scientific article published on 07 August 2020

Benefits and barriers in the design of harmonized access agreements for international data sharing

scientific article published on 02 December 2019

CTCF-mediated functional chromatin interactome in pluripotent cells

scientific article

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

scientific article

Comparing Apples to Apples and Oranges to Oranges

scientific article published on 28 May 2018

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

scientific article

Computational tools for the analysis of rearrangements in mammalian genomes

scientific article published on January 2008

Computational tools for the analysis of rearrangements in mammalian genomes

scientific article published in January 2008

Computational tools to unmask transposable elements

scientific article published on 01 November 2018

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes

scientific article

Conserved expression of transposon-derived non-coding transcripts in primate stem cells

scientific article

Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls

scientific article published on 14 July 2017

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

scientific article published on 24 October 2016

CpG deamination creates transcription factor-binding sites with high efficiency

scientific article published on 19 October 2011

Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo

scientific article published on 14 February 2020

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

scientific article

Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors

scientific article published on 19 January 2012

Epigenome data release: a participant-centered approach to privacy protection

scientific article

Evolution of the mammalian transcription factor binding repertoire via transposable elements

scientific article published on 5 August 2008

Evolving data access policy: The Canadian context

scientific article

Functional characterization of the human dendritic cell immunodeficiency associated with the IRF8(K108E) mutation

scientific journal article

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

scientific article published on 10 March 2017

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

scientific article (publication date: June 2007)

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-scale evolution: reconstructing gene orders in the ancestral species ⬇️

scientific article published on January 1, 2002

Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations

scientific article published on 24 October 2019

Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development

scientific article

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations

scientific article (publication date: May 2014)

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

scientific article published on 12 April 2018

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies

scientific article published in November 2017

High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism

scientific article

Human copy number variants are enriched in regions of low mappability

Identification of Elongated Primary Cilia with Impaired Mechanotransduction in Idiopathic Scoliosis Patients

scientific article published on 14 March 2017

Identifying co-opted transposable elements using comparative epigenomics

scientific article

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

scientific article

Improving gene network inference by comparing expression time-series across species, developmental stages or tissues

scientific article published in December 2004

In Silico Methods to Identify Exapted Transposable Element Families

scientific article

In silico tandem affinity purification refines an Oct4 interaction list ⬇️

scientific article published on May 13, 2011

Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge

scientific article published on March 2009

Initial sequence and comparative analysis of the cat genome

scientific article

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

scientific article

K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas

scientific article

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma ⬇️

scientific article published on 23 March 2017

Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion

scientific article published on 13 March 2018

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.

scientific article published in July 2018

Mobile genetic elements and genome evolution 2014

Molecular and genetic crosstalks between mTOR and ERRα are key determinants of rapamycin-induced nonalcoholic fatty liver

scientific article published in April 2013

Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines

scientific article

Molecular convergence of neurodevelopmental disorders

scientific article

Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives

scientific article

Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

scientific article published on January 2006

Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer

scientific article published on 19 July 2017

Optimization of temporal versus spatial replication in the development of habitat use models to explain among-reach variations of fish density estimates in rivers

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning

scientific article published on 24 October 2016

PPARG Binding Landscapes in Macrophages Suggest a Genome-Wide Contribution of PU.1 to Divergent PPARG Binding in Human and Mouse ⬇️

scientific article published on October 31, 2012

Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells

scientific article published on 09 November 2020

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

scientific article published on 05 February 2020

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

scientific article

RNA-Seq as a Tool to Study the Tumor Microenvironment

scientific article

Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes

scientific article published on April 2004

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps

scientific article

Recovering genome rearrangements in the mammalian phylogeny

scientific article published in May 2009

Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements

scientific article

Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons

scientific article published on 05 August 2015

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver

scientific article published on 09 June 2020

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

scientific article published on 08 July 2020

Single-cell analysis of human adipose tissue identifies depot and disease specific cell types

scientific article published on 23 December 2019

Stalled developmental programs at the root of pediatric brain tumors

scientific article published on 25 November 2019

Success in the DREAM3 signaling response challenge using simple weighted-average imputation: lessons for community-wide experiments in systems biology

scientific article

Ten things you should know about transposable elements

scientific article published on 19 November 2018

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

scientific article

The Effects of Regional Hydrologic Alteration on Fish Community Structure in Regulated Rivers

The International Human Epigenome Consortium Data Portal

scientific article

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements ⬇️

scientific article published on May 9, 2013

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

scientific journal article

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction

scientific article published in March 2006

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

scientific article published on 30 March 2014

Transcriptional consequences of genomic structural aberrations in breast cancer

scientific article

Transient DNMT1 suppression reveals hidden heritable marks in the genome

scientific article

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs

scientific article

Transposable elements have rewired the core regulatory network of human embryonic stem cells

scientific article published on 6 June 2010

Transposable elements in gene regulation and in the evolution of vertebrate genomes

scientific article

Ultrafast functional profiling of RNA-seq data for nonmodel organisms

scientific article published on 17 March 2021

Using fish guilds to assess community responses to temperature and flow regimes in unregulated and regulated Canadian rivers

article

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

scientific article published on 29 October 2014

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes

scientific article published in PLoS ONE

Whole-Genome Cartography of Estrogen Receptorα Binding Sites

Whole-genome cartography of estrogen receptor alpha binding sites

scientific article

Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells

scientific article

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

scientific article

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

scientific article published on 01 November 2019

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

scientific article

webMGR: an online tool for the multiple genome rearrangement problem

scientific article

List of works by Guillaume Bourque

A call for benchmarking transposable element annotation methods

A coordinated progression of progenitor cell states initiates urinary tract development

A draft human pangenome reference

A population-based LD map of the human chromosome 6p.

A replication study for association of 53 single nucleotide polymorphisms in ScoliScore test with adolescent idiopathic scoliosis in French-Canadian population

A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19

ABCA7 rare variants and Alzheimer disease risk

Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

Benefits and barriers in the design of harmonized access agreements for international data sharing

CTCF-mediated functional chromatin interactome in pluripotent cells

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Comparing Apples to Apples and Oranges to Oranges

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

Computational tools for the analysis of rearrangements in mammalian genomes

Computational tools for the analysis of rearrangements in mammalian genomes

Computational tools to unmask transposable elements

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes

Conserved expression of transposon-derived non-coding transcripts in primate stem cells

Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

CpG deamination creates transcription factor-binding sites with high efficiency

Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors

Epigenome data release: a participant-centered approach to privacy protection

Evolution of the mammalian transcription factor binding repertoire via transposable elements

Evolving data access policy: The Canadian context

Functional characterization of the human dendritic cell immunodeficiency associated with the IRF8(K108E) mutation

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome-scale evolution: reconstructing gene orders in the ancestral species ⬇️

Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations

Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies

High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism

Human copy number variants are enriched in regions of low mappability

Human copy number variants are enriched in regions of low mappability

Identification of Elongated Primary Cilia with Impaired Mechanotransduction in Idiopathic Scoliosis Patients

Identifying co-opted transposable elements using comparative epigenomics

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

Improving gene network inference by comparing expression time-series across species, developmental stages or tissues

In Silico Methods to Identify Exapted Transposable Element Families

In silico tandem affinity purification refines an Oct4 interaction list ⬇️

Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge

Initial sequence and comparative analysis of the cat genome

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma ⬇️

Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.

Mobile genetic elements and genome evolution 2014

Molecular and genetic crosstalks between mTOR and ERRα are key determinants of rapamycin-induced nonalcoholic fatty liver

Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines

Molecular convergence of neurodevelopmental disorders

Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives

Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer

Optimization of temporal versus spatial replication in the development of habitat use models to explain among-reach variations of fish density estimates in rivers

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning

PPARG Binding Landscapes in Macrophages Suggest a Genome-Wide Contribution of PU.1 to Divergent PPARG Binding in Human and Mouse ⬇️

Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

RNA-Seq as a Tool to Study the Tumor Microenvironment

Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps

Recovering genome rearrangements in the mammalian phylogeny

Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements

Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

Single-cell analysis of human adipose tissue identifies depot and disease specific cell types

Stalled developmental programs at the root of pediatric brain tumors