UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

article :
Deniélou Y-P, Sagot M-F, Boyer F, Viari A (2011)
Bacterial syntenies: an exact approach with gene quorum, BMC Bioinformatics, vol. 12(193) pp.1-15

Simoes P, Mialdea G, Reiss D, Sagot M-F, Charlat S (2011)
Wolbachia detection: an assessment of standard PCR Protocols, Molecular Ecology Resources, vol. 11 pp.567-572

Vellozo AF, Véron A, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldon T, Sagot M-F, Charles H, Colella S (2011)
CycADS: an annotation database system to ease the development and update of BioCyc databases, Database, vol. 2011 pp.1-11

Veron AS, Lemaitre C, Gautier C, Lacroix V, Sagot M-F (2011)
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC Genomics, vol. 12(1) pp.1-38

Adi SS, Braga M, Fernandes CG, Ferreira CE, Martinez FV, Sagot M-F, Stefanes MA, Tjandraatmadja C, Wakabayashi Y (2010)
Repetition-free longest common subsequence, Discrete Applied Mathematics, vol. 158(12) pp.1315-1324

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot M-F (2010)
Cassis: detection of genomic rearrangement breakpoints, Bioinformatics, vol. 26(15) pp.1897-1898

Cottret L, Milreu P-V, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot M-F (2010)
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts Baumannia cicadellinicola and Sulcia muelleri with Their Insect Host Homalodisca coagulata, PLos Computational Biology, vol. 6(9) pp.307-316

Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot M-F, Jourdan F (2010)
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic Acids Research, vol. 38 pp.132-137

Acuña V, Marchetti-Spaccamela A, Sagot M-F, Stougie L (2009)
A Note on the Complexity of Finding and Enumerating Elementary Modes, BioSystems, vol. 99 pp.210-214

Braga M, Gautier C, Sagot M-F (2009)
An asymmetric approach to preserve common intervals while sorting by reversals, Algorithms for Molecular Biology, vol. 4(16) pp.1833-1835

Braga MDV, Gautier C, Sagot M-F (2009)
An asymmetric approach to preserve common intervals while sorting by reversals, Algorithms for Molecular Biology, vol. 4(16) pp.1833-1835

Brinza L, Vinuelas J, Cottret L, Calevro F, Rahbé Y, Febvay G, Duport G, Colella S, Rabatel A, Gautier C, Fayard J-M, Sagot M-F, Charles H (2009)
Systemic analysis of the symbiotic function of Buchnera aphidicola the primary endosymbiont of the pea aphid Acyrthosiphon pisum, C.R. Biologies, vol. 332(11) pp.1034-1049

Deloger M, Cavalli FMG, Lerat E, Biémont C, Sagot M-F, Vieira C (2009)
Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster, Gene, vol. 439 pp.55-62

Lemaitre C, Braga Marilia D V , Gautier C, Sagot M-F, Tannier E, Marais GAB (2009)
Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes, Genome Biology and Evolution, vol. 1(1) pp.56-66

Lemaitre C, Zaghloul L, Sagot M-F, Gautier C, Arneodo A, Tannier E, Audit B (2009)
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation, BMC Genomics, vol. 10:335 pp.1-12

Mendes ND, Freitas AT, Sagot M-F (2009)
Current tools for the identification of miRNA genes and their targets, Nucleic Acids Research, vol. 2009 pp.2419-2433

Peterlongo P, Sacomoto GAT, do Lago AP, Pisanti N, Sagot M-F (2009)
Lossless filter for multiple repeats with bounded edit distance, Algorithms for Molecular Biology, vol. 4(3) pp.1-20

Schbath S, Lacroix V, Sagot M-F (2009)
Assessing the exceptionality of coloured motifs in networks, Eurasip Journal on Bioinformatics and Systems Biology, vol. 2009 pp.1-9

Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot M-F, Stougie L (2008)
Modes and Cuts in Metabolic Networks:Complexity and Algorithms, BioSystems, vol. 95 - n°1 pp.51-60

Allali J, Sagot M-F (2008)
A multiple layer model to compare RNA secondary structures, Software-practice and experience, vol. 38(8) pp.775-792

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2008)
Exploring the Solution Space of Sorting by Reversals with Experiments and an Application to Evolution, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 5 - n°3 pp.348-356

Lacroix V, Cottret L, Thébault P, Sagot M-F (2008)
An Introduction to Metabolic Networks and Their Structural Analysis, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 5 - n°4 pp.1-24

Lemaitre C, Sagot M-F (2008)
A small trip in the untranquil world of genomes a survey on the detection and analysis of genome rearrangement breakpoints, Theoretical Computer Science, vol. 395 pp.171-192

Lemaitre C, Tannier E, Gautier C, Sagot M-F (2008)
Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol. 9 pp.286-322

Peterlongo P, Pisanti N, Boyer Fr, Do Lago P, Sagot M-F (2008)
Lossless filter for multiple repetitions with Hamming distance, Journal of Discrete Algorithms, vol. 6 pp.124-135

Soares da Fonseca P, Gautier C, Guimarães Ks, Sagot M-F (2008)
Efficient representation and P-value computation for high-order Markov motifs, Bioinformatics, vol. 24 pp.i160-i166

Bourqui R, Cottret L, Lacroix V, Auber D, Mary P, Sagot M-F, Jourdan F (2007)
Metabolic network visualization eliminating node redundance and preserving metabolic pathways, BMC Systems Biology, vol. 1 - n°29 pp.1-19

Cambouropoulos E, Crochemore M, Lliopoulos CS, Mohamed M, Sagot M-F (2007)
All maximal-pairs in step–leap representation of melodic sequence, Information Sciences, vol. 177 pp.1954-1962

Diekmann Y, Sagot M-F, Tannier E (2007)
Evolution under Reversals: Parsimony and Conservation of Common Intervals, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 4 pp.301-309

Rodrigues E , Sagot M-F, Wakabayashi Y (2007)
The maximum agreement forest problem: Approximation algorithms and computational experiments, Theoretical Computer Science, vol. 374 pp.91-110

Tannier E, Bergeron A, Sagot M-F (2007)
Advances on sorting by reversals, Discrete Applied Mathematics, vol. 155 pp.881-888

Carvalho AM, Freitas AT, Oliveira AL, Sagot M-F (2006)
An efficient algorithm for the identification of structured motifs in DNA promoter sequences, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 3 pp.126-140

Crochemore M, Lliopoulos CS, Mohamed M, Sagot M-F (2006)
Longest repeats with a block of k don’t cares, Theoretical Computer Science, vol. 362 pp.248-254

Lacroix V, Fernandes CG, Sagot M-F (2006)
Motif search in graphs: application to metabolic networks., IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 3 - n°4 pp.360-368

Allali J, Sagot M-F (2005)
A new distance for high level RNA secondary structure comparison, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 2 pp.3-14

Iliopoulos CS, McHugh J, Peterlongo P, Pisanti N, Rytter W, Sagot M-F (2005)
A first approach to finding common motifs with gaps, International Journal of Foundations of Computer Science, vol. 16 pp.1145-1154

Pisanti N, Crochemore M, Grossi R, Sagot M-F (2005)
Bases of motifs for generating repeated patterns with wild cards, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 2 pp.40-50

Blayo P, Rouzé P, Sagot M-F (2003)
Orphan gene finding -- An exon assembly approach, Theoretical Computer Science, vol. 290 pp.1407-1431

Robin S, Daudin JJ, Richard H, Sagot M-F, Schbath S (2003)
Occurrence probability of structured motifs in random sequences, Journal of Computational Biology, vol. 9 pp.761-773

Mathé C, Sagot M-F, Schiex T, Rouzé P (2002)
Current methods of gene prediction their strengths and weaknesses, Nucleic Acids Research, vol. 30 pp.4103-4117

Pisanti N, Sagot M-F (2002)
Further thoughts on the syntenic distance between genomes, Algorithmica, vol. 34 pp.157-180

Marsan L, Sagot M-F (2000)
Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification, Journal of Computational Biology, vol. 7 pp.345-360

Vanet A, Marsan L, Labigne A, Sagot M-F (2000)
Inferring regulatory elements from a whole genome. An application to the analysis of the genome of Helicobacter pylori sigma 80 family of promoter signals, Journal of Molecular Biology, vol. 297 pp.335-353

Vanet A, Marsan L, Sagot M-F (1999)
Promoter sequences and algorithmical methods for identifying them, Research in microbiology, vol. 150 pp.779-799

Sagot M-F, Myers EW (1998)
Identifying satellites and periodic repetitions in biological sequences, Journal of Computational Biology, vol. 5 pp.539-554

Sagot M-F, Viari A (1996)
A Double Combinatorial Approach to Discovering Patterns in Biological Sequences, , vol. 1075 pp.186-208

Sagot M-F, Viari A, Pothier J, Soldano H (1995)
Finding flexible patterns in a text - An application to 3D matching, Computer Applications in the Biosciences, vol. 11 pp.59-70

inbook :
Pisanti N, Crochemore M, Grossi R, Sagot M-F (2005)
A comparative study of bases for motif inference, , vol. pp.195-226

Pisanti N, Sagot M-F (2005)
Network expression inference, , vol. pp.227-250

Crochemore M, Sagot M-F (2004)
Motifs in sequences: localization and extraction, , vol. pp.47-97

Sagot M-F, Wakabayashi Y (2003)
Pattern inference under many guises, , vol. pp.245-288

Mathé C, Schiex T, Rouzé P, Blayo P, Sagot M-F (2002)
Gene finding in eukaryotes, , vol. pp.27-43

inproceedings :
Adi SS, Braga MDV, Fernandes CG, Ferreira CE, Martinez FV, Sagot M-F, Stefanes MA, Tjandraatmadja C, Wakabayashi Y (2010)
Repetition-free longest common subsequence, IV Latin-American Algorithms Graphs and Optimization Symposium, Electronic Notes in Discrete Mathematics, vol. 30 pp.243-248

Cottret L, Milreu P-V, Acuña V, Marchetti-Spaccamela A, Viduani-Martinez F, Sagot M-F, Stougie L (2010)
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network, WABI 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. LNBI 5251 pp.233-244

Deniélou Y-P, Boyer F, Viari A, Sagot M-F (2010)
Multiple Alignment of Biological Networks: A Flexible Approach, 20th Annual Symposium on Combinatorial Pattern Matching, , vol. 5577 pp.263-273

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2009)
The solution space of sorting by reversals, Proceedings of ISBRA`07, Lecture Notes in Bioinformatics, vol. 4463 pp.293-304

Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V (2009)
Identifying SNPs without a Reference Genome by Comparing Raw Reads, SPIRE, Springer, Lecture Notes in Computer Science, vol. 6393 pp.147-158

Pisanti N, Carvalho A, Marsan L , Sagot M-F (2009)
RISOTTO: Fast extraction of motifs with mismatches, LATIN’06, Springer Verlag, Lecture Notes in Computer Science, vol. 3887 pp.757-768

Pisanti N, Crochemore M, Grossi R, Sagot M-F (2009)
A basis of tiling motifs for generating repeated patterns and its complexity for higher quorum, 28th International Symposium on Mathematical Foundations of Computer Science, Springer Verlag, Lecture Notes in Computer Science, vol. 2747 pp.622-632

Sagot M-F (2009)
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree, 3rd Latin American Symposium on Theoretical Informatics (LATIN 98), , vol. 1380 pp.374-390

Sagot M-F, Escalier V, Viari A, Soldano H (2009)
Searching for repeated words in a text allowing for mismatches and gaps, Second South American Workshop on String Processing, pp.87-100

Lacroix V, Fernandes CG, Sagot M-F (2008)
Reaction motifs in metabolic networks, Proceedings of WABI `05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3692 pp.178-191

Peterlongo P, Pisanti N, Boyer F, Sagot M-F (2008)
Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure the Bi-Factor Array, SPIRE`05, Springer Verlag, Lecture note in computer science, vol. 3772 pp.124-135

Rodrigues EM, Sagot M-F, Wakabayashi Y (2007)
Some approximation results for the maximum agreement forest problem, Approximation Randomization and Combinatorial Optimization: Algorithms and Techniques (APPROX & RANDOM 2001), Springer Verlag, Lecture Notes in Computer Science, vol. 2129 pp.159-169

Tannier E, Sagot M-F (2007)
Sorting by reversals in subquadratic time, Proceedings of CPM`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3109 pp.1-13

Crochemore M, Giancarlo R, Sagot M-F (2006)
Longest motifs with a functionally equivalent block, SPIRE`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3246 pp.298-299

Crochemore M, Iliopoulos C, Mohamed M, Sagot M-F (2006)
Longest Repeated Motif with a Block Don`t Cares, LATIN`04, Springer Verlag, Lecture Notes in Computer Science, vol. 2976 pp.271-278

Cambouropoulos E, Crochemore M, Lliopoulos C, Mohamed M, Sagot M-F (2005)
A pattern extraction algorithm for abstract melodic representations that allow partial overlapping of intervallic categories, The 6th International Conference on Music Information Retrieval ISMIR`05, pp.167-174

Allali J, Sagot M-F (2003)
Novel tree edit operations for RNA secondary structure comparison, WABI`04, Springer Verlag, Lecture Notes in BioInformatics, vol. 3240 pp.412-425

Allali J, Sagot M-F (2003)
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison, SPIRE`05, , Lecture note in computer science, vol. 3772 pp.412-425

Nor I, Hermelin D, Charlat S, Engelstadter J, Reuter M, Duron O, Sagot M-F (2003)
Mod/Resc Parsimony Inference, 21st Annual Symposium on Combinatorial Pattern Matching, , Lecture notes in Computer Science, vol. 6129 pp.202-213

Vieira-Milreu P, Acuña V, Birmelé E, Crescenzi P, Marchetti-Spaccamela A, Sagot M-F, Stougie L, Lacroix V (2000)
Enumerating Chemical Organisations in consistent metabolic networks: complexity and algorithms, WABI` 2010, Springer-Verlag Berlin, Lecture notes in computer science, vol. 6293 pp.226-237

Sagot M-F, Tannier E (1998)
Perfect sorting by reversals, Proceedings of COCOON`05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3595 pp.42-51

Sagot M-F, Viari A (1996)
Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes Mirror Repeats Pseudoknots and Triple Helices, Proceeding in CPM`97, Springer Verlag, Lecture notes in computer science, vol. 1264 pp.224-246

Sagot M-F, Viari A, Soldano H (1995)
A Distance-based block searching algorithm, Third International Symposium on Intelligent Systems for Molecular Biology, AAAI Press pp.322-331

Sagot M-F, Viari A, Soldano H (1995)
Multiple Sequence Comparison:A Peptide Matching Approach, Proceeding CPM`95, Springer-Verlag, Lecture notes in computer science, vol. 937 pp.366-385

Carvalho A, Freitas AT, Oliveira AL, Sagot M-F (1991)
Efficient Extraction of Structured Motifs Using Box-links, SPIRE`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3246 pp.267-268

Carvalho A, Freitas AT, Oliveira AL, Sagot M-F (1991)
A parallel algorithm for the extraction of structured motifs, ACM Symposium on Applied Computing (SAC`04), ACM Press, Lecture Notes in Computer Science pp.147-153

Carvalho A, Freitas AT, Oliveira AL, Sagot M-F (1991)
A highly scalable algorithm for the extraction of cis-regulatory regions, Proceedings of 3rd Asia-Pacific Bioinformatics Conference (APBC`05), Imperial College Press, Advances in Bioinformatics and Computational Biology pp.273-282

Carvalho A, Oliveira A, Sagot M-F (1991)
Efficient learning of Bayesian network classifiers:An extension to the TAN classifie, 20th Australian Joint Conference on Artificial Intelligence, , Lecture notes in computer science, vol. 4830 pp.16-25

misc :
Peterlongo P, Allali J, Sagot M-F (2008)
Indexing gapped-factors using a tree, , vol. 19-1 pp.79-87