Mathieu Blanchette

Mathieu Blanchette 's AcademicInfluence.com Rankings

Mathieu Blanchette

Biology

#5920

World Rank

#8521

Historical Rank

Computational Biology

#199

World Rank

#200

Historical Rank

biology Degrees

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Biology

Why Is Mathieu Blanchette Influential?

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According to Wikipedia, Mathieu Daniel Blanchette is a computational biologist and Director of the School of Computer Science at McGill University. His research focuses on developing new algorithms for the detection of functional regions in DNA sequences.

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Mathieu Blanchette 's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Aligning multiple genomic sequences with the threaded blockset aligner. (2004) (1439)
Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning (2005) (482)
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (2007) (426)
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts (2014) (395)
The Capsella rubella genome and the genomic consequences of rapid mating system evolution (2013) (364)
Genome-wide Orchestration of Cardiac Functions by the Orphan Nuclear Receptors ERRα and γ (2007) (359)
Discovery of regulatory elements by a computational method for phylogenetic footprinting. (2002) (357)
Identification and characterization of multi-species conserved sequences. (2003) (356)
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions (2013) (321)
Reconstructing contiguous regions of an ancestral genome. (2006) (292)
Multiple Genome Rearrangement and Breakpoint Phylogeny (1998) (282)
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. (2006) (278)
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. (2007) (234)
Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment (2012) (231)
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis (2009) (227)
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences (2004) (213)
Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny (1999) (207)
Algorithms for phylogenetic footprinting (2001) (207)
FootPrinter: a program designed for phylogenetic footprinting (2003) (188)
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling (2011) (166)
Reconstructing large regions of an ancestral mammalian genome in silico. (2004) (158)
Parametric genome rearrangement. (1996) (149)
A Newly Uncovered Group of Distantly Related Lysine Methyltransferases Preferentially Interact with Molecular Chaperones to Regulate Their Activity (2013) (143)
The three-dimensional architecture of Hox cluster silencing (2010) (143)
Evolutionarily conserved sequence elements that positively regulate IFN-γ expression in T cells (2004) (138)
The Median Problem for Breakpoints in Comparative Genomics (1997) (129)
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora (2014) (117)
Chromatin conformation signatures of cellular differentiation (2009) (115)
BH3‐ligand regulates access of MCL‐1 to its E3 ligase (2005) (111)
A critical assessment of topologically associating domain prediction tools (2017) (99)
PReMod: a database of genome-wide mammalian cis-regulatory module predictions (2006) (96)
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* (2010) (94)
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. (2009) (88)
RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions (2019) (85)
Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation (2015) (84)
A call for benchmarking transposable element annotation methods (2015) (76)
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. (2004) (75)
Into the heart of darkness: large-scale clustering of human non-coding DNA (2004) (74)
Motif Discovery in Heterogeneous Sequence Data (2003) (67)
Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis (2020) (61)
Separating real motifs from their artifacts (2001) (61)
CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells (2018) (58)
Computational prediction of the localization of microRNAs within their pre-miRNA (2013) (57)
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species (2000) (55)
Reconstructing Ancestral Gene Orders Using Conserved Intervals (2004) (53)
Seeder: discriminative seeding DNA motif discovery (2008) (52)
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species (2019) (50)
A flexible ancestral genome reconstruction method based on gapped adjacencies (2012) (49)
Computation and analysis of genomic multi-sequence alignments. (2007) (46)
Hox in motion: tracking HoxA cluster conformation during differentiation (2013) (45)
Modeling contaminants in AP-MS/MS experiments. (2011) (45)
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2 (2013) (44)
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem (2007) (41)
PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing (2015) (41)
Ancestors 1.0: a web server for ancestral sequence reconstruction (2010) (39)
Detecting non-coding selective pressure in coding regions (2007) (38)
Phylogenetic Invariants for Genome Rearrangements (1999) (36)
Prediction of mRNA subcellular localization using deep recurrent neural networks (2019) (36)
Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin. (2014) (36)
Probability models for genome rearrangement and linear invariants for phylogenetic inference (1999) (35)
BigDataScript: a scripting language for data pipelines (2014) (33)
Classifying leukemia types with chromatin conformation data (2014) (31)
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human (2010) (31)
On the Inference of Parsimonious Indel Evolutionary Scenarios (2006) (29)
A probabilistic approach for SNP discovery in high-throughput human resequencing data. (2009) (29)
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment (2013) (28)
Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences (2016) (28)
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions (2020) (27)
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania (2008) (26)
FootPrinter3: phylogenetic footprinting in partially alignable sequences (2006) (24)
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. (2013) (24)
Computing chromosome conformation. (2010) (23)
Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements (2016) (23)
Upstream ORF-encoded ASDURF is a novel prefoldin-like subunit of the PAQosome. (2019) (23)
Long-range regulation is a major driving force in maintaining genome integrity (2009) (22)
Genome-Wide Mouse Mutagenesis Reveals CD45-Mediated T Cell Function as Critical in Protective Immunity to HSV-1 (2013) (21)
An N-Ethyl-N-Nitrosourea (ENU)-Induced Dominant Negative Mutation in the JAK3 Kinase Protects against Cerebral Malaria (2012) (21)
Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila. (2020) (21)
Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss (2010) (21)
Predicting direct protein interactions from affinity purification mass spectrometry data (2010) (19)
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees (2007) (19)
Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes (2019) (18)
Combining Computational Prediction of Cis-Regulatory Elements with a New Enhancer Assay to Efficiently Label Neuronal Structures in the Medaka Fish (2011) (18)
Models and algorithms for genome rearrangement with positional constraints (2015) (18)
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks (2009) (17)
Clique Cover on Sparse Networks (2012) (17)
Multiple genome rearrangements (1998) (17)
HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution (2020) (17)
Gene Maps Linearization Using Genomic Rearrangement Distances (2007) (15)
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences (2013) (15)
A comparative analysis method for detecting binding sites in coding regions (2003) (13)
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels (2011) (13)
Ordering Partially Assembled Genomes Using Gene Arrangements (2006) (13)
Overview of the First Phylogenomics Conference (2007) (12)
Specific Dysregulation of IFNγ Production by Natural Killer Cells Confers Susceptibility to Viral Infection (2014) (12)
Comparative Genomics Via Phylogenetic Invariants For Jukes-Cantor Semigroups (2003) (11)
Leishmania parasites exchange drug-resistance genes through extracellular vesicles. (2022) (11)
An empirical comparison of tools for phylogenetic footprinting (2003) (10)
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data (2015) (10)
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes (2017) (10)
Double-Stranded Biotinylated Donor Enhances Homology-Directed Repair in Combination with Cas9 Monoavidin in Mammalian Cells. (2018) (9)
Finding Maximum Likelihood Indel Scenarios (2006) (9)
Lessons from an Online Massive Genomics Computer Game (2017) (9)
Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks (2017) (8)
RobusTAD: A Tool for Robust Annotation of Topologically Associating Domain Boundaries (2018) (8)
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas (2022) (8)
HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution (2018) (8)
Predicting site-specific human selective pressure using evolutionary signatures (2011) (8)
An analytic approach for interpretable predictive models in high‐dimensional data in the presence of interactions with exposures (2018) (7)
EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM (2020) (7)
Genetic Map Refinement Using a Comparative Genomic Approach (2009) (6)
A Phylogenetic Approach to Genetic Map Refinement (2008) (6)
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses (2009) (6)
RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment (2018) (6)
Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny (2011) (5)
StructMiner: a tool for alignment and detection of conserved secondary structure. (2004) (5)
A Human-Computation Platform for Multi-Scale Genome Analysis (2017) (5)
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). (2008) (5)
Multiple genome rearrangement (2007) (5)
Mycorrhiza: genotype assignment using phylogenetic networks (2019) (4)
Positional Mapping and Candidate Gene Analysis of the Mouse Ccs3 Locus That Regulates Differential Susceptibility to Carcinogen-Induced Colorectal Cancer (2013) (4)
ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells (2021) (3)
Reconstruction of full-length LINE-1 progenitors from ancestral genomes (2022) (3)
Operations on Sets of Conserved Intervals (2004) (3)
An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss (2011) (3)
Evolutionary Puzzles: An Introduction to Genome Rearrangement (2001) (3)
Inferring Gene Orders from Gene Maps Using the Breakpoint Distance (2006) (3)
Large-scale mammalian genome rearrangements coincide with chromatin interactions (2019) (3)
Efficient Homology Directed Repair by Cas9:DNA Localization and Cationic Polymeric Transfection in Mammalian Cells (2018) (3)
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing (2019) (3)
Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites (2020) (2)
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites (2012) (2)
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts (2014) (2)
LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads (2020) (2)
Supervised learning on phylogenetically distributed data. (2020) (2)
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2021) (2)
Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells (2018) (2)
Common Substrings in Random Strings (2006) (2)
3D genome mapping and analysis methods. (2018) (2)
A flexible ancestral genome reconstruction method based on gapped adjacencies (2012) (1)
Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions (2020) (1)
Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization. (2019) (1)
An EM algorithm for mapping short reads in multiple RNA structure probing experiments (2017) (1)
Classification of the Human Papilloma Viruses (2011) (1)
Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics (2010) (1)
Nuclear import of RNA polymerase II requires the conserved GPN‐loop GTPase XAB1/GPN1 (2010) (1)
3DGV: Immersive Exploration of 3D Genome Structures using Virtual Reality (2019) (1)
ISMB 2014 Proceedings Papers Committee (2014) (1)
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics (2014) (1)
An Evolutionary Study of the Human Papillomavirus Genomes (2008) (1)
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment (2013) (1)
Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data (2022) (1)
Classifying leukemia types with chromatin conformation data (2014) (1)
SACSANN: identifying sequence-based determinants of chromosomal compartments (2020) (1)
3 DGB : A Low-Latency , Big Database System and Browser for Storage , Querying and Visualization of 3 D Genomic Data (2017) (0)
Additional Paper for " Multiple Sequence Alignment " Paper Reference (0)
ISMB 2010 Organization (2010) (0)
Models and algorithms for genome rearrangement with positional constraints (2016) (0)
Mapping and Visualizing Spatial Genome Organization (2016) (0)
Substring Parsimony (2008) (0)
Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy (2016) (0)
Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation (2015) (0)
A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error (2010) (0)
Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP. (2021) (0)
2011 Reviewers List (2012) (0)
[Regular Paper] Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches (2018) (0)
Evolution by whole genome duplication (2011) (0)
A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model (2006) (0)
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing (2019) (0)
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information (2022) (0)
An analytic approach for interpretable predictive models in high dimensional data, in the presence of interactions with exposures (2017) (0)
EPCO-38. TYPE B ULTRA LONG-RANGE INTERACTIONS IN PFAS (TULIPS) ARE RECURRENT EPIGENOMIC FEATURES OF PFA EPENDYMOMA (2022) (0)
The Difficulty In Computing Ancestral DNA Sequences: Using Computational Analysis To Reconstruct DNA Sequences (2006) (0)
A call for benchmarking transposable element annotation methods (2015) (0)
Neural representation and generation for RNA secondary structures (2021) (0)
silico Reconstructing large regions of an ancestral mammalian genome in data (2004) (0)
Supplementary Material : Description of database implementation (2015) (0)
Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions (2021) (0)
Reference panel guided topological structure annotation of Hi-C data (2022) (0)
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2022) (0)
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites (2012) (0)
High‐precision mapping of the protein interaction network for the human transcription machinery reveals a novel class of cellular regulatory factors (2008) (0)
Reconstructing Domain Compositions of Ancestral Multi-domain Proteins Behshad Behzadi and Martin Vingron Domain Architecture in Homolog Identification (2006) (0)
Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches. (2018) (0)
OP-CBIO190349 117..126 (2019) (0)
G RAPH NEURAL REPRESENTATIONAL LEARNING OF RNA SECONDARY STRUCTURES FOR PREDICTING RNA- PROTEIN INTERACTIONS (2020) (0)
Prediction of complete Hi-C contact maps from genomic sequence alone (2018) (0)
Multiple, Nonintegrated Systems (1997) (0)
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? (2023) (0)
Leveraging Structure Between Environments: Phylogenetic Regularization Incentivizes Disentangled Representations (2022) (0)
Aligner Aligning Multiple Genomic Sequences With the Threaded Blockset data (2004) (0)
LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads (2020) (0)
A Model for Interpretable High Dimensional Interactions (2010) (0)
Histone-mutant interneuron progenitors co-opt PDGFRA for gliomagenesis (2020) (0)
Integrated pretraining with evolutionary information to improve RNA secondary structure prediction (2022) (0)

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