Mathieu Blanchette

According to our database1, Mathieu Blanchette authored at least 64 papers between 1997 and 2020.

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Bibliography

2020
Mycorrhiza: genotype assignment using phylogenetic networks.
Bioinformatics, 2020

2019
Prediction of mRNA subcellular localization using deep recurrent neural networks.
Bioinformatics, 2019

Large-scale mammalian genome rearrangements coincide with chromatin interactions.
Bioinformatics, 2019

2018
Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches.
Proceedings of the 18th IEEE International Conference on Bioinformatics and Bioengineering, 2018

RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment.
Proceedings of the 18th IEEE International Conference on Bioinformatics and Bioengineering, 2018

2017
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.
Bioinformatics, 2017

Lessons from an Online Massive Genomics Computer Game.
Proceedings of the Fifth AAAI Conference on Human Computation and Crowdsourcing, 2017

2016
Substring Parsimony.
Encyclopedia of Algorithms, 2016

Models and algorithms for genome rearrangement with positional constraints.
Algorithms for Molecular Biology, 2016

Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015
BigDataScript: a scripting language for data pipelines.
Bioinformatics, 2015

Models and Algorithms for Genome Rearrangement with Positional Constraints.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics.
Proceedings of the Seconf AAAI Conference on Human Computation and Crowdsourcing, 2014

2013
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.
Nucleic Acids Research, 2013

2012
A flexible ancestral genome reconstruction method based on gapped adjacencies.
BMC Bioinformatics, 2012

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.
BMC Bioinformatics, 2012

Clique Cover on Sparse Networks.
Proceedings of the 14th Meeting on Algorithm Engineering & Experiments, 2012

2011
An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny.
Journal of Computational Biology, 2011

A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels.
Journal of Computational Biology, 2011

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.
BMC Bioinformatics, 2011

Predicting site-specific human selective pressure using evolutionary signatures.
Bioinformatics [ISMB/ECCB], 2011

2010
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human.
PLoS Computational Biology, 2010

Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks.
Journal of Computational Biology, 2010

Ancestors 1.0: a web server for ancestral sequence reconstruction.
Bioinformatics, 2010

Predicting direct protein interactions from affinity purification mass spectrometry data.
Algorithms for Molecular Biology, 2010

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics.
Proceedings of the Comparative Genomics - International Workshop, 2010

A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses.
Journal of Computational Biology, 2009

Genetic Map Refinement Using a Comparative Genomic Approach.
Journal of Computational Biology, 2009

2008
Substring Parsimony.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.
BMC Bioinformatics, 2008

Seeder: discriminative seeding DNA motif discovery.
Bioinformatics, 2008

A Phylogenetic Approach to Genetic Map Refinement.
Proceedings of the Comparative Genomics, International Workshop, 2008

An Evolutionary Study of the Human Papillomavirus Genomes.
Proceedings of the Comparative Genomics, International Workshop, 2008

2007
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
Nucleic Acids Research, 2007

Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem.
Journal of Computational Biology, 2007

Gene Maps Linearization Using Genomic Rearrangement Distances.
Journal of Computational Biology, 2007

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees.
BMC Bioinformatics, 2007

2006
A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model.
Proceedings of the Data Science and Classification, 2006

FootPrinter3: phylogenetic footprinting in partially alignable sequences.
Nucleic Acids Research, 2006

On the Inference of Parsimonious Indel Evolutionary Scenarios.
J. Bioinformatics and Computational Biology, 2006

Ordering Partially Assembled Genomes Using Gene Arrangements.
Proceedings of the Comparative Genomics, 2006

Finding Maximum Likelihood Indel Scenarios.
Proceedings of the Comparative Genomics, 2006

Inferring Gene Orders from Gene Maps Using the Breakpoint Distance.
Proceedings of the Comparative Genomics, 2006

Common Substrings in Random Strings.
Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2004
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences.
BMC Bioinformatics, 2004

Reconstructing Ancestral Gene Orders Using Conserved Intervals.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Motif Discovery in Heterogeneous Sequence Data.
Proceedings of the Biocomputing 2004, 2004

Into the heart of darkness: large-scale clustering of human non-coding DNA.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003
FootPrinter: a program designed for phylogenetic footprinting.
Nucleic Acids Research, 2003

A comparative analysis method for detecting binding sites in coding regions.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

An Empirical Comparison of Tools for Phylogenetic Footprinting.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

2002
Algorithms for Phylogenetic Footprinting.
Journal of Computational Biology, 2002

2001
Algorithms for phylogenetic footprinting.
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

Separating real motifs from their artifacts.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Evolutionary Puzzles: An Introduction to Genome Rearrangement.
Proceedings of the Computational Science - ICCS 2001, 2001

2000
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999
Phylogenetic Invariants for Genome Rearrangements.
Journal of Computational Biology, 1999

Probability models for genome rearrangement and linear invariants for phylogenetic inference.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998
Multiple Genome Rearrangement and Breakpoint Phylogeny.
Journal of Computational Biology, 1998

Multiple genome rearrangements.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997
The Median Problem for Breakpoints in Comparative Genomics.
Proceedings of the Computing and Combinatorics, Third Annual International Conference, 1997


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