Marie-France Sagot

According to our database1, Marie-France Sagot authored at least 112 papers between 1995 and 2020.

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Bibliography

2020
Lazy listing of equivalence classes - A paper on dynamic programming and tropical circuits.
CoRR, 2020

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering.
BMC Bioinform., 2020

Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions.
Bioinform., 2020

MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network.
Bioinform., 2020

On Bubble Generators in Directed Graphs.
Algorithmica, 2020

A Family of Tree-Based Generators for Bubbles in Directed Graphs.
Proceedings of the Combinatorial Algorithms - 31st International Workshop, 2020

2019
Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

2018
Computing and Listing st-Paths in Public Transportation Networks.
Theory Comput. Syst., 2018

Geometric medians in reconciliation spaces of phylogenetic trees.
Inf. Process. Lett., 2018

Algorithmic Enumeration: Output-sensitive, Input-Sensitive, Parameterized, Approximativ (Dagstuhl Seminar 18421).
Dagstuhl Reports, 2018

2017
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.
Algorithms Mol. Biol., 2017

Extracting Few Representative Reconciliations with Host Switches.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2017

2016
Tackling Big Data in the Life Sciences - Introduction to the Special Theme.
ERCIM News, 2016

DegreeCox - a network-based regularization method for survival analysis.
BMC Bioinform., 2016

Enumeration of minimal stoichiometric precursor sets in metabolic networks.
Algorithms Mol. Biol., 2016

On Maximal Chain Subgraphs and Covers of Bipartite Graphs.
Proceedings of the 17th Italian Conference on Theoretical Computer Science, 2016

Computing and Listing st-Paths in Public Transportation Networks.
Proceedings of the Computer Science - Theory and Applications, 2016

Robustness of the Parsimonious Reconciliation Method in Cophylogeny.
Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data.
BMC Bioinform., 2015

MeDuSa: a multi-draft based scaffolder.
Bioinform., 2015

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs.
Algorithms Mol. Biol., 2015

EUCALYPT: efficient tree reconciliation enumerator.
Algorithms Mol. Biol., 2015

Incremental Complexity of a Bi-objective Hypergraph Transversal Problem.
Proceedings of the Fundamentals of Computation Theory - 20th International Symposium, 2015

2014
Rime: Repeat identification.
Discret. Appl. Math., 2014

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.
Bioinform., 2014

Navigating in a Sea of Repeats in RNA-seq without Drowning.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Efficiently Listing Bounded Length st-Paths.
Proceedings of the Combinatorial Algorithms - 25th International Workshop, 2014

Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs.
Proceedings of the Algorithms - ESA 2014, 2014

2013
Telling Stories Fast.
Proceedings of the Experimental Algorithms, 12th International Symposium, 2013

A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets.
Theor. Comput. Sci., 2012

EIC Editorial.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Mod/Resc Parsimony Inference: Theory and application.
Inf. Comput., 2012

Optimal Listing of Cycles and st-Paths in Undirected Graphs
CoRR, 2012

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinform., 2012

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.
Bioinform., 2012

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.
Bioinform., 2012

Sampling solution traces for the problem of sorting permutations by signed reversals.
Algorithms Mol. Biol., 2012

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.
Adv. Bioinformatics, 2012

Efficient Bubble Enumeration in Directed Graphs.
Proceedings of the String Processing and Information Retrieval, 2012

Minimum Ratio Cover of Matrix Columns by Extreme Rays of Its Induced Cone.
Proceedings of the Combinatorial Optimization - Second International Symposium, 2012

2011
Bacterial syntenies: an exact approach with gene quorum.
BMC Bioinform., 2011

CycADS: an annotation database system to ease the development and update of BioCyc databases.
Database J. Biol. Databases Curation, 2011

Finding Long and Multiple Repeats with Edit Distance.
Proceedings of the Prague Stringology Conference 2011, 2011

2010
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, <i>Baumannia cicadellinicola</i> and <i>Sulcia muelleri</i>, with Their Insect Host, <i>Homalodisca coagulata</i>.
PLoS Comput. Biol., 2010

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.
Nucleic Acids Res., 2010

A note on the complexity of finding and enumerating elementary modes.
Biosyst., 2010

Cassis: detection of genomic rearrangement breakpoints.
Bioinform., 2010

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Identifying SNPs without a Reference Genome by Comparing Raw Reads.
Proceedings of the String Processing and Information Retrieval, 2010

Mod/Resc Parsimony Inference.
Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

2009
EIC Editorial: Introducing New Associate Editors.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

New EIC Editorial.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Assessing the Exceptionality of Coloured Motifs in Networks.
EURASIP J. Bioinform. Syst. Biol., 2009

Modes and cuts in metabolic networks: Complexity and algorithms.
Biosyst., 2009

ISMB/ECCB 2009 Stockholm.
Bioinform., 2009

Lossless filter for multiple repeats with bounded edit distance.
Algorithms Mol. Biol., 2009

An asymmetric approach to preserve common intervals while sorting by reversals.
Algorithms Mol. Biol., 2009

Multiple Alignment of Biological Networks: A Flexible Approach.
Proceedings of the Combinatorial Pattern Matching, 20th Annual Symposium, 2009

2008
A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints.
Theor. Comput. Sci., 2008

An Introduction to Metabolic Networks and Their Structural Analysis.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

A multiple layer model to compare RNA secondary structures.
Softw. Pract. Exp., 2008

Lossless filter for multiple repetitions with Hamming distance.
J. Discrete Algorithms, 2008

Editorial.
J. Discrete Algorithms, 2008

Indexing Gapped-Factors Using a Tree.
Int. J. Found. Comput. Sci., 2008

Repetition-free longest common subsequence.
Electron. Notes Discret. Math., 2008

Precise detection of rearrangement breakpoints in mammalian chromosomes.
BMC Bioinform., 2008

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Efficient representation and <i>P</i>-value computation for high-order Markov motifs.
Proceedings of the ECCB'08 Proceedings, 2008

2007
The maximum agreement forest problem: Approximation algorithms and computational experiments.
Theor. Comput. Sci., 2007

Evolution under Reversals: Parsimony and Conservation of Common Intervals.
IEEE ACM Trans. Comput. Biol. Bioinform., 2007

All maximal-pairs in step-leap representation of melodic sequence.
Inf. Sci., 2007

Advances on sorting by reversals.
Discret. Appl. Math., 2007

Metabolic network visualization eliminating node redundance and preserving metabolic pathways.
BMC Syst. Biol., 2007

The Solution Space of Sorting by Reversals.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

Efficient Learning of Bayesian Network Classifiers.
Proceedings of the AI 2007: Advances in Artificial Intelligence, 2007

2006
Longest repeats with a block of <i>k</i> don't cares.
Theor. Comput. Sci., 2006

Motif Search in Graphs: Application to Metabolic Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

The gapped-factor tree.
Proceedings of the Prague Stringology Conference, 2006

RISOTTO: Fast Extraction of Motifs with Mismatches.
Proceedings of the LATIN 2006: Theoretical Informatics, 2006

2005
Bases of Motifs for Generating Repeated Patterns with Wild Cards.
IEEE ACM Trans. Comput. Biol. Bioinform., 2005

A New Distance for High Level RNA Secondary Structure Comparison.
IEEE ACM Trans. Comput. Biol. Bioinform., 2005

A first approach to finding common motifs with gaps.
Int. J. Found. Comput. Sci., 2005

Reaction Motifs in Metabolic Networks.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array.
Proceedings of the String Processing and Information Retrieval, 2005

A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison.
Proceedings of the String Processing and Information Retrieval, 2005

A Pattern Extraction Algorithm for Abstract Melodic Representations that Allow Partial Overlapping of Intervallic Categories.
Proceedings of the ISMIR 2005, 2005

Perfect Sorting by Reversals.
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

A highly scalable algorithm for the extraction of CIS-regulatory regions.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004
Novel Tree Edit Operations for RNA Secondary Structure Comparison.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Longest Motifs with a Functionally Equivalent Central Block.
Proceedings of the String Processing and Information Retrieval, 2004

Efficient Extraction of Structured Motifs Using Box-Links.
Proceedings of the String Processing and Information Retrieval, 2004

A parallel algorithm for the extraction of structured motifs.
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004

Longest Repeats with a Block of Don't Cares.
Proceedings of the LATIN 2004: Theoretical Informatics, 2004

Sorting by Reversals in Subquadratic Time.
Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

2003
Orphan gene finding - an exon assembly approach.
Theor. Comput. Sci., 2003

A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum.
Proceedings of the Mathematical Foundations of Computer Science 2003, 2003

2002
Occurrence Probability of Structured Motifs in Random Sequences.
J. Comput. Biol., 2002

Further Thoughts on the Syntenic Distance between Genomes.
Algorithmica, 2002

2001
Some Approximation Results for the Maximum Agreement Forest Problem.
Proceedings of the Approximation, 2001

2000
Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification.
J. Comput. Biol., 2000

Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1998
Identifying Satellites and Periodic Repetitions in Biological Sequences.
J. Comput. Biol., 1998

Identifying satellites in nucleic acid sequences.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

Spelling Approximate Repeated or Common Motifs Using a Suffix Tree.
Proceedings of the LATIN '98: Theoretical Informatics, 1998

1997
Multiple Sequence Comparison - A Peptide Matching Approach.
Theor. Comput. Sci., 1997

Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices.
Proceedings of the Combinatorial Pattern Matching, 8th Annual Symposium, 1997

1996
A Double Combinatorial Approach to Discovering Patterns in Biological Sequences.
Proceedings of the Combinatorial Pattern Matching, 7th Annual Symposium, 1996

1995
Finding flexible patterns in a text: an application to three-dimensional molecular matching.
Comput. Appl. Biosci., 1995

A Distance-Based Block Searching Algorithm.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995


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