List of works - Mathieu Blanchette

A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels ⬇️

scientific article published on September 27, 2011

A call for benchmarking transposable element annotation methods

scientific article published on 4 August 2015

A critical assessment of topologically associating domain prediction tools

scientific article published on 2 March 2017

A flexible ancestral genome reconstruction method based on gapped adjacencies ⬇️

scientific article published on December 19, 2012

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

scientific article

A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity

scientific article

A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error.

scientific article published in January 2010

A probabilistic approach for SNP discovery in high-throughput human resequencing data

scientific article

A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses

scientific article published in October 2009

Algorithms for phylogenetic footprinting

scientific article

An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria

scientific article

An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures

scientific article published on 8 February 2018

An approximation algorithm for the Noah's Ark problem with random feature loss

scientific article

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

scientific article published on 30 June 2013

Ancestors 1.0: a web server for ancestral sequence reconstruction

scientific article

BH3-ligand regulates access of MCL-1 to its E3 ligase

scientific article

BigDataScript: a scripting language for data pipelines

scientific article

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells

scientific article published on 27 October 2017

Chromatin conformation signatures of cellular differentiation

scientific article

Classifying leukemia types with chromatin conformation data

scientific article

Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish

scientific article (publication date: 2011)

Computation and analysis of genomic multi-sequence alignments

scientific article published on January 2007

Computational analysis of whole-genome differential allelic expression data in human

scientific article

Computational prediction of the localization of microRNAs within their pre-miRNA ⬇️

scientific article published on 08 June 2013

Computing Chromosome Conformation ⬇️

scientific article published on January 1, 2010

Detecting non-coding selective pressure in coding regions

scientific article published on 8 February 2007

Detection of locally over-represented GO terms in protein-protein interaction networks

scientific article

Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry

scientific article published on 4 December 2012

Discovery of regulatory elements by a computational method for phylogenetic footprinting

scientific article (publication date: May 2002)

Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells

scholarly article

Exact and heuristic algorithms for the Indel Maximum Likelihood Problem

scientific article published in May 2007

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites ⬇️

scientific article published on December 19, 2012

FootPrinter3: phylogenetic footprinting in partially alignable sequences

scientific article published on July 2006

FootPrinter: A program designed for phylogenetic footprinting

scientific article

French Intensive Care Society, International congress - Réanimation 2016

scientific article published in June 2016

Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks

scientific article

Gene maps linearization using genomic rearrangement distances

scientific article published in May 2007

Genetic map refinement using a comparative genomic approach

scientific article published in October 2009

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

scientific article published on 10 April 2006

Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma

scientific article published in May 2007

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

scientific article published on 18 October 2009

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

scientific article published on 14 January 2020

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

scientific article published on 18 May 2009

Hox in motion: tracking HoxA cluster conformation during differentiation

scientific article published on 29 October 2013

Identification and characterization of multi-species conserved sequences

scientific article

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania

scientific article

Into the heart of darkness: large-scale clustering of human non-coding DNA.

scientific article published in August 2004

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players

scientific article published on 05 July 2024

Long-range regulation is a major driving force in maintaining genome integrity

scientific article

Mapping association between long-range cis-regulatory regions and their target genes using synteny

scientific article published on September 1, 2011

Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin.

scientific article published on 16 October 2013

Modeling contaminants in AP-MS/MS experiments

scientific article published on 31 December 2010

Models and algorithms for genome rearrangement with positional constraints

scientific article published on 17 May 2016

Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2

scientific article published on 30 May 2013

On the inference of parsimonious indel evolutionary scenarios

scientific article published in June 2006

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment

scientific article (publication date: 2013)

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing

scientific article

PReMod: a database of genome-wide mammalian cis-regulatory module predictions

scientific article published on 5 December 2006

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

scientific article

Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment ⬇️

scientific article published on March 7, 2012

Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

scientific article

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

scientific article

Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancer

scientific article

Predicting direct protein interactions from affinity purification mass spectrometry data ⬇️

scientific article published on October 29, 2010

Predicting site-specific human selective pressure using evolutionary signatures ⬇️

scientific article published on July 1, 2011

Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

scientific article

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

scientific article

Presence of Candida cell wall derived polysaccharides in the sera of intensive care unit patients: relation with candidaemia and Candida colonisation

scientific article

Proceedings of Réanimation 2017, the French Intensive Care Society International Congress

scientific article

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada

scientific article

Reconstructing contiguous regions of an ancestral genome

scientific article

Reconstructing large regions of an ancestral mammalian genome in silico

scientific article

Reconstruction of full-length LINE-1 progenitors from ancestral genomes

scientific article published in 2022

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences

scientific article published on 8 June 2013

Seeder: discriminative seeding DNA motif discovery

scientific article published on 21 August 2008

Specific dysregulation of IFNγ production by natural killer cells confers susceptibility to viral infection

scientific article (publication date: December 2014)

Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)

scientific article published on April 2008

StructMiner: a tool for alignment and detection of conserved secondary structure.

scientific article published in January 2004

Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme

scientific article

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

scientific article

The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II

scientific article published on 20 September 2010

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

scientific article published on 20 February 2014

The three-dimensional architecture of Hox cluster silencing

scientific article

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling ⬇️

scientific article published on October 25, 2011

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning

scientific article published on November 2005

[Triple fungal infection in a patient with liver cirrhosis]

scientific article published on 01 January 2012

List of works by Mathieu Blanchette

A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels ⬇️

A call for benchmarking transposable element annotation methods

A critical assessment of topologically associating domain prediction tools

A flexible ancestral genome reconstruction method based on gapped adjacencies ⬇️

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity

A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error.

A probabilistic approach for SNP discovery in high-throughput human resequencing data

A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses

Algorithms for phylogenetic footprinting

An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria

An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures

An approximation algorithm for the Noah's Ark problem with random feature loss

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Ancestors 1.0: a web server for ancestral sequence reconstruction

BH3-ligand regulates access of MCL-1 to its E3 ligase

BigDataScript: a scripting language for data pipelines

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells

Chromatin conformation signatures of cellular differentiation

Classifying leukemia types with chromatin conformation data

Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish

Computation and analysis of genomic multi-sequence alignments

Computational analysis of whole-genome differential allelic expression data in human

Computational prediction of the localization of microRNAs within their pre-miRNA ⬇️

Computing Chromosome Conformation ⬇️

Detecting non-coding selective pressure in coding regions

Detection of locally over-represented GO terms in protein-protein interaction networks

Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry

Discovery of regulatory elements by a computational method for phylogenetic footprinting

Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells

Exact and heuristic algorithms for the Indel Maximum Likelihood Problem

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites ⬇️

FootPrinter3: phylogenetic footprinting in partially alignable sequences

FootPrinter: A program designed for phylogenetic footprinting

French Intensive Care Society, International congress - Réanimation 2016

Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks

Gene maps linearization using genomic rearrangement distances

Genetic map refinement using a comparative genomic approach

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

Hox in motion: tracking HoxA cluster conformation during differentiation

Identification and characterization of multi-species conserved sequences

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania

Into the heart of darkness: large-scale clustering of human non-coding DNA.

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players

Long-range regulation is a major driving force in maintaining genome integrity

Mapping association between long-range cis-regulatory regions and their target genes using synteny

Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin.

Modeling contaminants in AP-MS/MS experiments

Models and algorithms for genome rearrangement with positional constraints

Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2

On the inference of parsimonious indel evolutionary scenarios

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing

PReMod: a database of genome-wide mammalian cis-regulatory module predictions

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment ⬇️

Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

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

Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancer

Predicting direct protein interactions from affinity purification mass spectrometry data ⬇️

Predicting site-specific human selective pressure using evolutionary signatures ⬇️

Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

Presence of Candida cell wall derived polysaccharides in the sera of intensive care unit patients: relation with candidaemia and Candida colonisation

Proceedings of Réanimation 2017, the French Intensive Care Society International Congress

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada

Reconstructing contiguous regions of an ancestral genome

Reconstructing large regions of an ancestral mammalian genome in silico

Reconstruction of full-length LINE-1 progenitors from ancestral genomes

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences

Seeder: discriminative seeding DNA motif discovery

Specific dysregulation of IFNγ production by natural killer cells confers susceptibility to viral infection

Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)

StructMiner: a tool for alignment and detection of conserved secondary structure.

Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme