 |
 |
 |
|
Menu
- Présentation
- Equipes de recherche
- Production
- Logiciels et bases de données
- Animations scientifiques
- Enseignement
- Emplois/stages/thèses
- Pôles techniques
- Sécurité
- Liens
- PRABI
- Projets en cours
Rechercher
Equipe Baobab
Research
Software
Projects
Calls/Offers
Membres
- Baudet Christian CDD CNRS
- Birmelé Etienne chercheur invité INRIA
- Bouheddi Florence CDD INRIA
- Brilli Matteo post-doc INRIA
- Coimbra Klein Cécilia doctorant UCBL
- Donati Béatrice doctorant UCBL
- Farnier Pierre Antoine doctorant UCBL
- Gautier Christian PU émérite UCBL
- Higashi Susan doctorant UCBL
- Kielbassa Janice post-doc INRIA
- Lacroix Vincent MCU UCBL
- Sacomoto Gustavo doctorant UCBL
- Simões Patricia doctorant UCBL
- Sinaimeri Blerina post-doc INRIA
- Viari Alain DR INRIA
- Vieira-Milreu Paulo doctorant CNRS
+Anciens membres -Anciens membres
- Acuña Vicente CDD CNRS
- Ansel Juliette M2 UCBL
- Braga Marilia doctorant UCBL
- Canet Laurent doctorant UCBL
- Charlat Thomas M2 UCBL
- Cottret Ludovic doctorant UCBL
- Cp Da Silva Joao chercheur invité autre
- Crescenzi Pierluigi chercheur invité autre
- Da Silva Freire Alexandre doctorant UCBL
- Duquenne Lauranne CDD INRIA
- Elkaoutari Abdessamad M2 UCBL
- Fippo Fitime Louis M2 INRIA
- Gaye Bamba M2 UCBL
- Gonindard Christelle ATER UCBL
- Lemaitre Claire doctorant UCBL
- Marot Guillemette post-doc INRIA
- Marrakchi Emna M2 UCBL
- Mendes Nuno doctorant UCBL
- Navratil Vincent post-doc INRIA
- Nguyen My Phi Long doctorant UCBL
- Nor Igor post-doc CNRS
- Palmeira Leonor post-doc UCBL
- Pizzi Cinzia post-doc INRIA
- Prestat Emmanuel doctorant UCBL
- Soares Da Fonseca Paulo Gustavo post-doc UCBL
- Thebault Patricia post-doc INRIA
- Tworkowski Gaelle TCH INRIA
- Vasconcelos Ana Tereza chercheur invité autre
- Vellozo Augusto post-doc UCBL
- Véron Amélie post-doc CNRS
- Walter Costa Maria-Emilia chercheur invité autre
Ex PhD or postdoc students who remain collaborators
ADI Said Sadique - ALLALI Julien - BOYER Frédéric - C. B. DE MELO Jeane - CAVALLI Florence - GAMBIS Alexis - MARIS RODRIGUES Estela - MARSAN Laurent - MELO DE LIMA Christelle - NAVRATIL Vincent - PETERLONGO Pierre - PISANTI Nadia - PIZZI Cinzia - PROVENCHER Sébastien - TAVARES Raquel - THEBAULT Patricia - TOURNOUD Maud - TRUNTZER Caroline - VINGA SusanaStudents from another team/lab/country in collaboration or yet to arrive/return
CARVALHO Alexandra - NGUYEN Mi Phi Long - SAEYS Yvan+Publications -Publications
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T K, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn R D, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn A F, Rivoire C, Sangrador-Vegas A, Selengut J D, Sigrist C J A, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas P D, Wu C H, Yeats C, Yong S-Y (|2012|)
InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Research, vol. 40 pp.D306-D312
Berthoumieux S, Brilli M, de Jong H, Kahn D, Cinquemani E (|2011|)
Identification of metabolic network models from incomplete high-throughput datasets, Bioinformatics, vol. 27 pp.i186-i195
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
Kielbassa J, Charles S, Delignette-Muller M-L (|2011|)
The importance of incorporating age and sex when backcalculating length in bullhead Cottus gobio, Journal of Fish Biology, vol. 78 pp.1492-1507
Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L (|2011|)
Meiotic Recombination favors the spreading of deleterious mutations in human populations, Human Mutation, vol. 32 pp.198-206
Palmeira L, Penel S, Lotteau V, Rabourdin-Combe C, Gautier C (|2011|)
PhEVER: a database for the global exploration of virus-host evolutionary relationships, Nucleic Acids Research, vol. 39 pp.569-575
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
Acuña V (|2010|)
Models and algorithms for metabolic networks: elementary modes and precursor sets, , |2010|
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
Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi E (|2010|)
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis, BMC Systems Biology, vol. 4(52) pp.1-46
Brinza L, Calevro F, Duport G, Gaget K, Gautier C, Charles H (|2010|)
Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS, BMC Genomics, vol. 11(666) pp.1-16
Chun-Long C, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d`Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C (|2010|)
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes, Genome Research, vol. 20(4) pp.447-457
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
Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glémin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarroti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N (|2010|)
Evolution Moléculaire, article in: Biologie Evolutive, de Boeck, pp.114-173
Fondi M, Bacci G, Brilli M, Papaelo CM, Mengoni A, Vaneechoutte M, Dijkshoorn L, Fani R (|2010|)
Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome, BMC Evolutionary Biology, vol. 10(59) pp.1-41
Frandi A, Mengoni A, Brilli M (|2010|)
Comparative genomics of VirR regulons in Clostridium perfringens strains, BMC Evolutionary Biology, vol. pp.1-20
Kielbassa J (|2010|)
Mathematical modelling of temperature effects on the life-history traits and the population dynamics of bullhead textit(Cottus gobio), , |2010|
Kielbassa J, Delignette-Muller M-L, Pont D, Charles S (|2010|)
Application of a temperature-dependent von Bertalanffy growth model to bullhead Cottus gobio, Ecological Modelling, vol. 221 pp.2475-2481
Nor I, Hermelin D, Charlat S, Engelstadter J, Reuter M, Duron O, Sagot M-F (|2010|)
Mod/Resc Parsimony Inference, 21st Annual Symposium on Combinatorial Pattern Matching, , Lecture notes in Computer Science, vol. 6129 pp.202-213
Pellet J, Tafforeau L, Lucas-Hourani M, Navratil V, Meyniel L, Achaz G, Guironnet-Paquet A, Aublin-Gex A, Caignard G, Cassonnet P, Chaboud A, Chantier T, Deloire A, Demeret C, Le Breton M, Neveu G, Jacotot L, Vaglio P, Delmotte S, Gautier C, Combet S, Deleage G, Favre M, Tangy T, Jacob M, Andre P, Lotteau V, Rabourdin-Combe C, Vidalain PO (|2010|)
ViralORFeome: an integrated database to generate a versatile collection of viral ORFs, Nucleic Acids Research, vol. 38 pp.371-378
Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V (|2010|)
Identifying SNPs without a Reference Genome by Comparing Raw Reads, SPIRE, Springer, Lecture Notes in Computer Science, vol. 6393 pp.147-158
Vaillant C, Palmeira L, Chevereau G, Audit B, D`Aubenton-Carafa Y, Thermes C, Arneodo A (|2010|)
A novel strategy of transcription regulation by intra-genic nucleosome ordering, Genome Research, vol. 20 pp.59-67
Vieira-Milreu P, Acuña V, Birmelé E, Crescenzi P, Marchetti-Spaccamela A, Sagot M-F, Stougie L, Lacroix V (|2010|)
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
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 (|2009|)
BaobabLUNA: the solution space of sorting by reversals, Bioinformatics, vol. 25(14) pp.1833-1835
Braga M (|2009|)
L`espace de solutions du tri par inversions et son utilisation dans l`analyse de réarrangements de génomes, , |2009|
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
Chevereau G, Palmeira L, Thermes C, Arneodo A, Vaillant C (|2009|)
Thermodynamics of Intragenic Nucleosome Ordering, Physical review letters, vol. 103(18) pp.188-103
Cottret L (|2009|)
Analyse systémique de la symbiose intracellulaire : évolution et organisation du réseau métabolique des endocytobiotes, , |2009|
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
Deniélou Y-P, Boyer F, Viari A, Sagot M-F (|2009|)
Multiple Alignment of Biological Networks: A Flexible Approach, 20th Annual Symposium on Combinatorial Pattern Matching, , vol. 5577 pp.263-273
Guyonnet B, Marot G, Dacheux J-L, Mercat M-J, Schwob S, Jaffrézic F, Gatti J-L (|2009|)
The adult boar testicular and epididymal transcriptomes, BMC Genomics, vol. 10(369) pp.339-343
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
Marot G, Foulley J-L, Jaffrézic F (|2009|)
A structural mixed model to shrink covariance matrices for time-course differential gene expression studies, Computational Statistics & Data Analysis, vol. 53 pp.1630-1638
Marot G, Foulley J-L, Mayer C-D, Jaffrézic F (|2009|)
Moderated effect size and P-value combinations for microarray meta-analyses, Bioinformatics, vol. 25(20) pp.2692-2699
Marot G, Mayer C-D (|2009|)
Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis, Statistical Applications in Genetics and Molecular Biology, vol. 8(1) pp.1-35
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
Papaleo MC, Russo E, Fondi M, Emiliani G, Frandi A, Brilli M, Pastorelli R, Fani R (|2009|)
Structural evolutionary and genetic analysis of the histidine biosynthetic core in the genus Burkholderia, Gene, vol. 448(1) pp.16-28
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
Picard F, Miele V, Daudin JJ, Cottret L, Robin S (|2009|)
Deciphering the connectivity structure of biological networks using MixNet, BMC Bioinformatics, vol. 10 pp.1-11
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
Adi SS, Braga MDV, Fernandes CG, Ferreira CE, Martinez FV, Sagot M-F, Stefanes MA, Tjandraatmadja C, Wakabayashi Y (|2008|)
Repetition-free longest common subsequence, IV Latin-American Algorithms Graphs and Optimization Symposium, Electronic Notes in Discrete Mathematics, vol. 30 pp.243-248
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
Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Lio P, Fani R (|2008|)
Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network, BMC Bioinformatics, vol. 9(551) pp.1-13
Charles S, Subtil F, Kielbassa J, Pont D (|2008|)
An individual-based model to describe a bullhead population dynamics including temperature variations, Ecological Modelling, vol. 215 pp.377-392
Cottret L, Milreu P-V, Acuña V, Marchetti-Spaccamela A, Viduani-Martinez F, Sagot M-F, Stougie L (|2008|)
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network, WABI 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. LNBI 5251 pp.233-244
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist C, Thimma M, Thomas P, Valentin F, Wilson D, Wu C, Yeats C (|2008|)
InterPro: the integrative protein signature database, Nucleic Acids Research, vol. 37 pp.D211-D215
 | Lacroix V (|2008|) Identification de motifs dans les réseaux métaboliques, Edilivre, |2008| |
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
Lacroix V, Sammeth M, Guigo R, Bergeron A (|2008|)
Exact Transcriptome Reconstruction from Short Sequence Reads, Proceeding of WABI`08, Springer Verlag, Lecture Notes in Bioinformatics, vol. 5251 pp.50-63
Lemaitre C (|2008|)
Réarrangements chromosomiques dans les génomes de mammifères : caractérisation des points de cassure, , |2008|
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
Li P, Brilli M, Fani R (|2008|)
Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies, BIRD Study, vol. 13 pp.207-220
Melodelima C, Gautier C (|2008|)
The GC-heterogeneity of teleost fishes, BMC Genomics, vol. 9 pp.1-11
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, André P, Lotteau V, Rabourdin-Combe C (|2008|)
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks, Nucleic Acids Research, vol. 37 pp.661-668
Navratil V, Penel S, Delmotte S , Mouchiroud D, Gautier C, Aouacheria A (|2008|)
DigiPINS: A database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies, Biochimie, vol. 90 pp.563-569
Peterlongo P, Allali J, Sagot M-F (|2008|)
Indexing gapped-factors using a tree, , vol. 19-1 pp.79-87
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
Aouacheria A, Navratil V, Lopez-Perez R, Gutierrez N C, Churkin A, Barash D, Mouchiroud D, Gautier C (|2007|)
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions, BMC Genomics, vol. 8 pp.1-13
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
Braga MDV, Sagot M-F, Scornavacca C, Tannier E (|2007|)
The solution space of sorting by reversals, Proceedings of ISBRA`07, Lecture Notes in Bioinformatics, vol. 4463 pp.293-304
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
Carvalho A, Oliveira A, Sagot M-F (|2007|)
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
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
Jaffrézic F, Marot G, Degrelle S, Hué I, Foulley J-L (|2007|)
A structural mixed model for variances in differential gene expression studies, Genet. Res. Camb, vol. 89(1) pp.19-25
Kielbassa J, Bortfeldt R, Schuster S, Koch I (|2007|)
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets, Computational Biology and Chemistry, vol. 33(1) pp.46-61
Lacroix V (|2007|)
Identification de motifs dans les réseaux métaboliques Définitions algorithmes et application au métabolisme d’Escherichia coli, , |2007|
Melodelima C, Gautier C (|2007|)
Markovian approach for the segmentation of the chimpanzee genome, Proceeding of BIRD`07, , Lecture notes in Bioinformatics, vol. 4414 pp.251-262
Melodelima C, Gautier C, Piau D (|2007|)
A Markovian approach for the prediction of mouse isochore, Journal of Mathematical Biology, vol. 55 pp.353-364
Palmeira L (|2007|)
Analyse et modélisation des dépendances entre sites voisins dans l’évolution des séquences d’ADN, , |2007|
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
Truntzer C, Mercier C, Estève J, Gautier C, Roy P (|2007|)
Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data, BMC Bioinformatics, vol. 8 pp.1-12
Acuña V, Didier G, Maass A (|2006|)
Coding with variable block maps, Theoretical Computer Science, vol. 369 pp.396-405
Aouacheria A, Navratil V, Barthelaix A, Mouchiroud D, Gautier C (|2006|)
Bioinformatic sreening of human ESTs for differentially expressed genes in normal and tumor tissues, BMC Genomics, vol. 7 pp.1-11
Bourqui R, Auber D, Lacroix V, Jourdan F (|2006|)
Metabolic network visualization using constraint planar graph drawing algorithm, 10th conf. on Information Visualization, IEEE Computer Society pp.489-496
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
Melodelima C, Guéguen L, Gautier C, Piau D (|2006|)
A Markovian Approach for the Analysis of the Gene Structure, Proceedings of the Prague Stringology Conference, , vol. 19(1) pp.19-35
Melodelima C, Guéguen L, Piau D, Gautier C (|2006|)
A computational prediction of isochores based on hidden Markov models, Gene, vol. 385 pp.41-49
Palmeira L, Guéguen L, Lobry JR (|2006|)
UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes, Molecular Biology and Evolution, vol. 23 pp.2214-2219
Pisanti N, Carvalho A, Marsan L , Sagot M-F (|2006|)
RISOTTO: Fast extraction of motifs with mismatches, LATIN’06, Springer Verlag, Lecture Notes in Computer Science, vol. 3887 pp.757-768
Allali J, Sagot M-F (|2005|)
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison, SPIRE`05, , Lecture note in computer science, vol. 3772 pp.412-425
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
Aouacheria A, Navratil V, Wen W, Jiang M, Mouchiroud D, Gautier C, Gouy M, Zhang M (|2005|)
In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant, Oncogene, vol. 24 pp.6133-6142
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
Carvalho A, Freitas AT, Oliveira AL, Sagot M-F (|2005|)
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
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
Lacroix V, Fernandes CG, Sagot M-F (|2005|)
Reaction motifs in metabolic networks, Proceedings of WABI `05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3692 pp.178-191
Meunier J, Khelifi A, Navratil V, Duret L (|2005|)
Homology-dependent methylation in primate repetitive DNA, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.5471-5476
Peterlongo P, Pisanti N, Boyer F, Sagot M-F (|2005|)
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
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
Pisanti N, Crochemore M, Grossi R, Sagot M-F (|2005|)
A comparative study of bases for motif inference, article in: String algorithmics, King`s College Publications, pp.195-226
Pisanti N, Sagot M-F (|2005|)
Network expression inference, article in: Applications of Combinatorics on Words, Cambridge University Press, pp.227-250
Sagot M-F, Tannier E (|2005|)
Perfect sorting by reversals, Proceedings of COCOON`05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3595 pp.42-51
Allali J, Sagot M-F (|2004|)
Novel tree edit operations for RNA secondary structure comparison, WABI`04, Springer Verlag, Lecture Notes in BioInformatics, vol. 3240 pp.412-425
Carvalho A, Freitas AT, Oliveira AL, Sagot M-F (|2004|)
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 (|2004|)
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
Crochemore M, Giancarlo R, Sagot M-F (|2004|)
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 (|2004|)
Longest Repeated Motif with a Block Don`t Cares, LATIN`04, Springer Verlag, Lecture Notes in Computer Science, vol. 2976 pp.271-278
Crochemore M, Sagot M-F (|2004|)
Motifs in sequences: localization and extraction, article in: Handbook of Computational Chemistry, Marcel Dekker Inc, pp.47-97
Gautier C, Navratil V, Melodelima C (|2004|)
Genomic Information along the Genome: Modeling Statistical analysis and Evolutionary Implication, IFIP World Computer Congress (18th), pp.22-28
Tannier E, Sagot M-F (|2004|)
Sorting by reversals in subquadratic time, Proceedings of CPM`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3109 pp.1-13
Blayo P, Rouzé P, Sagot M-F (|2003|)
Orphan gene finding -- An exon assembly approach, Theoretical Computer Science, vol. 290 pp.1407-1431
Gautier C, Navratil V, Melodelima C (|2003|)
Genomic mapping and molecular processes, , vol. 2 pp.22-28
Pisanti N, Crochemore M, Grossi R, Sagot M-F (|2003|)
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
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
Sagot M-F, Wakabayashi Y (|2003|)
Pattern inference under many guises, article in: Recent advances in algorithms and combinatorics, Springer Verlag, pp.245-288
Bronner G, Spataro B, Gautier C (|2002|)
Cartographie génomique comparée chez les mammifères, Médecine Science, vol. 18 pp.767-774
Bronner G, Spataro B, Gautier C (|2002|)
Comparative genomic mapping in mammals, Medecine Science, vol. 18 pp.767-774
Bronner G, Spataro B, Page M, Gautier C, Rechenmann F (|2002|)
Modeling comparative mapping using objects and associations, Computers and Chemistry, vol. 26 pp.413-420
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
Mathé C, Schiex T, Rouzé P, Blayo P, Sagot M-F (|2002|)
Gene finding in eukaryotes, article in: Gene cloning and expression technologies, Eaton Publishing, pp.27-43
Piganeau G, Mouchiroud D, Duret L, Gautier C (|2002|)
Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores, Journal of Molecular Evolution, vol. 54 pp.129-133.
Pisanti N, Sagot M-F (|2002|)
Further thoughts on the syntenic distance between genomes, Algorithmica, vol. 34 pp.157-180
Piganeau G, Westrelin R, Tourancheau B, Gautier C (|2001|)
Multiplicative versus additive selection in relation to genome evolution: a simulation study, Genetical Research, vol. 78 pp.171-175
Rodrigues EM, Sagot M-F, Wakabayashi Y (|2001|)
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
Gautier C (|2000|)
Compositional bias in DNA, Current Opinion in Genetics and Development, vol. 10 pp.656-661
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
Fauvergue X, Fleury F, Lemaitre C, Allemand R (|1999|)
Parasitoid mating structures when hosts are patchily distributed: field and laboratory experiments with Leptophilina boulardi and L. Heterotoma, Oikos, vol. 86 pp.344-356
Matassi G, Sharp PM, Gautier C (|1999|)
Chromosomal location effects on gene sequence evolution in mammals, Current biology, vol. 9 pp.786-791
Vanet A, Marsan L, Sagot M-F (|1999|)
Promoter sequences and algorithmical methods for identifying them, Research in microbiology, vol. 150 pp.779-799
Laurent L, Casale P, Bradai MN, Godley BJ, Gerosa G, Broderick AC, Schroth W, Schierwater B, Levy AM, Freggi D, Abd El-Mawla EM, Hadoud DA, Gomati HE, Domingo M, Hadjichristophorou M, Kornaraky L, Demirayak F, Gautier C (|1998|)
Molecular resolution of marine turtle stock composition in fishery bycatch: a case study in the Mediterranean, Molecular Biology and Evolution, vol. 7 pp.1529-1542
Montrocher R, Verner M-C, Briolay J, Gautier C, Marmeisse R (|1998|)
Phylogenetic analysis of the Saccharomyces cerevisiae group based on polymorphisms of rDNA spacer sequences, International Journal of Systematic Bacteriology, vol. 48 pp.295-303
Robinson M, Gouy M, Gautier C, Mouchiroud D (|1998|)
Sensitivity of the relative-rate test to taxonomic sampling, Molecular Biology and Evolution, vol. 15 pp.1091-1098
Sagot M-F (|1998|)
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, Myers EW (|1998|)
Identifying satellites and periodic repetitions in biological sequences, Journal of Computational Biology, vol. 5 pp.539-554
Mouchiroud D, Robinson M, Gautier C (|1997|)
Impact of changes in GC content on the silent molecular clock in murids, Gene, vol. 205 pp.317-322
Robinson M, Gautier C, Mouchiroud D (|1997|)
Evolution of isochores in rodents, Molecular Biology and Evolution, vol. 14 pp.823-828
Sagot M-F, Viari A (|1997|)
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
Galtier N, Gouy M, Gautier C (|1996|)
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol. 12 pp.543-548
Sagot M-F, Viari A (|1996|)
A Double Combinatorial Approach to Discovering Patterns in Biological Sequences, , vol. 1075 pp.186-208
Brun C, Julien N, Jacobzone M, Gautier C, Massod R (|1995|)
SARS ARSS and A T-rich regions evidenced by restriction mapping on an 835-kb DNA fragment from drosophila, Experimental Cell Research, vol. 220 pp.338-347
Duret L, Mouchiroud D, Gautier C (|1995|)
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores, Journal of Molecular Evolution, vol. 40 pp.308-317
Mouchiroud D, Gautier C, Bernardi G (|1995|)
Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions, Journal of Molecular Evolution, vol. 40 pp.107-113
Sagot M-F, Escalier V, Viari A, Soldano H (|1995|)
Searching for repeated words in a text allowing for mismatches and gaps, Second South American Workshop on String Processing, pp.87-100
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
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
Biémont C, Lemeunier F, Gautier C, Guerreiro MG, Aulard S, Pasyukova EG (|1994|)
High rate of movement of one (mdg3) out of four transposable elements in a natural population of Drosophila melanogaster, Comptes Rendus de l`Académie des Sciences - Séries III - Sciences de la Vie, vol. 317 pp.213-216
Biémont C, Lemeunier F, Guerreiro MPG, Brookfield JF, Gautier C, Aulard S, Pasyukova EG (|1994|)
Population dynamics of the copia mdg1 mdg3 gypsy and P transposable elements in a natural population of Drosophila melanogaster, Genetical Research, vol. 63 pp.197-212
Lobry JR, Gautier C (|1994|)
Hydrophobicity expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes, Nucleic Acids Research, vol. 22 pp.3174-3180
Bernardi G, Mouchiroud D, Gautier C (|1993|)
Silent substitutions in mammalian genomes and their evolutionary implications, Journal of Molecular Evolution, vol. 37 pp.583-589
Duret L, Dorkeld F, Gautier C (|1993|)
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression, Nucleic Acids Research, vol. 21 pp.2315-2322
Perrière G, Dorkeld F, Rechenmann F, Gautier C (|1993|)
Object-oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes, In Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, vol. 1 pp.319-327
Perrière G, Gautier C (|1993|)
ColiGene: object-centered representation for the study of E coli gene expressivity by sequence analysis, Biochimie, vol. 75 pp.415-422
Schmeltzer O, Medigue C, Uvietta P, Rechenmann F, Dorkeld F, Perrière G, Gautier C (|1993|)
Building large knowledge bases in molecular biology, In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, vol. 1 pp.345-353
Aissani B, D`Onofrio G, Mouchiroud D, Gardiner K, Gautier C, Bernardi G (|1991|)
The compositional properties of human genes, Journal of Molecular Evolution, vol. 32 pp.493-503
D`Onofrio G, Mouchiroud D, Aissani B, Gautier C, Bernardi G (|1991|)
Correlations between the compositional properties of human genes codon usage and amino acid composition of proteins, Journal of Molecular Evolution, vol. 32 pp.504-510
Mouchiroud D, D`Onofrio G, Aissani B, Macaya G, Gautier C, Bernardi G (|1991|)
The distribution of genes in the human genome, Gene, vol. 100 pp.181-187
Biémont C, Ronsseray S, Anxolabéhère D, Izaabel H, Gautier C (|1990|)
Localization of P elements copy number regulation and cytotype determination in Drosophila melanogaster, Genetical Research, vol. 56 pp.3-14
Mouchiroud D, Gautier C (|1990|)
Codon usage changes and sequence dissimilarity between human and rat, Journal of Molecular Evolution, vol. 31 pp.81-91
Biémont C, Aouar A, Gautier C (|1989|)
Hybrid viability is correlated with the i-mobile and P-mobile element copy numbers of the maternal inbred line in Drosophila melanogaster, Heredity, vol. 62 pp.301-305
Cortay J C, Bleicher F, Duclos B, Cenatiempo Y, Gautier C, Prato J-L, Cozzone A J (|1989|)
Utilization of acetate in Escherichia coli: structural organization and differential expression of the ace operon, Biochimie, vol. 71 pp.1043-1049
Gautier C, Bernstein C (|1989|)
Computer-science and biology, Impact of Science on Society, vol. 39 pp.281-289
Bernardi G, Mouchiroud D, Gautier C (|1988|)
Compositional patterns in vertebrate genomes: conservation and change in evolution, Journal of Molecular Evolution, vol. 28 pp.7-18
Biémont C, Gautier C (|1988|)
Localization polymorphism of mdg-1 copia I-mobile-element and P-mobile-element in genome of Drosophila-melanogaster, Heredity, vol. 60 pp.335-346
Biémont C, Gautier C, Heizmann A (|1988|)
Independent regulation of mobile element copy nimber in Drosophila-melanogaster inbred lines, Chromosoma, vol. 96 pp.291-294
Fichant G, Quentin Y, Gautier C (|1988|)
(G+C) variation along eukaryotic genomic sequences and chromatine organization, Molecular and Cellular Biology, vol. 7 pp.49-56
Mouchiroud D, Gautier C (|1988|)
High codon-usage changes in mammalian genes, Molecular Biology and Evolution, vol. 5 pp.192-194
Mouchiroud D, Gautier C, Bernardi G (|1988|)
The compositional distribution of coding sequences and DNA molecules in humans and murids, Journal of Molecular Evolution, vol. 27 pp.311-320
Biémont C, Gautier C, Heizmann A (|1987|)
Independent regulation of mobile element copy nimber in Drosophila-melanogaster, Heredity, vol. 58 pp.167-172
Fichant G, Gautier C (|1987|)
Statistical method for predicting protein coding regions in nucleic acid sequences, Computer Applications in the Biosciences, vol. 3 pp.287-295
Gautier C (|1987|)
Codon usage changes during evolution - animal mitochondria example, Comptes Rendus de l`Académie des Sciences - Séries III - Sciences de la Vie, vol. 304 pp.123-123
Gautier C, Gouy M, Louail S (|1985|)
Non-parametric statistics for nucleic acid sequence study, Biochimie, vol. 67 pp.449-453
Gouy M, Gautier C, Attimonelli M, Lanave C, di Paola G (|1985|)
ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage, Bioinformatics, vol. 1 pp.167-172
Gouy M, Gautier C, Milleret F (|1985|)
System analysis and nucleic acid sequence banks, Biochimie, vol. 67 pp.433-436
Grantham R, Greenland T, Louail S, Mouchiroud D, Prato J-L, Gouy M, Gautier C (|1985|)
Molecular evolution of viruses as seen by nucleic acid sequence study, Bulletin de l’Institut Pasteur, vol. 83 pp.95-148
Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (|1984|)
ACNUC: a nucleic acid sequence data base and analysis system, Nucleic Acids Research, vol. 12 pp.121-127
Biémont C, Gautier C (|1983|)
An inbreeding-incompatibility genetic system in Drosophila melanogaster and its frequency in natural populations, Genetica, vol. 61 pp.191-195
Gouy M, Gautier C (|1982|)
Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Research, vol. 10 pp.7055-7074
 | Gautier C, Gouy M, Jacobzone M, Grantham R (|1981|) Nucleic acid sequences handbook, Praeger, |1981| |
Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (|1981|)
Codon catalog usage is a genome strategy modulated for gene expressivity, Nucleic Acids Research, vol. 9 pp.R43-R74
Grantham R, Gautier C (|1980|)
Genetic distances from mRNA sequences, Naturwissenschaften, vol. 67 pp.93-94
Grantham R, Gautier C, Gouy M (|1980|)
Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type, Nucleic Acids Research, vol. 8 pp.1893-1912
Grantham R, Gautier C, Gouy M, Mercier R, Pave A (|1980|)
Codon catalog usage and the genome hypothesis, Nucleic Acids Research, vol. 8 pp.R49-R62
Gautier C (|1979|)
Analysis of presence-absence grids monospecific and multispecific cases, Oecologia Plantarum, vol. 14 pp.251-251
Cheruy A, Gautier C, Pavé A (|1978|)
Analyse des systèmes biologiques: certains aspects méthodologiques liés à la modélisation, ATP Analyse des Systèmes, vol. pp.1-71
Chessel D, Gautier C (|1977|)
Des statistiques non paramétriques pour l`analyse des données binaires, Revue de statistique appliquée, vol. 25 pp.57-73
Gautier C (|1977|)
Directional mutation-rates measure of protein evolution, Année Biologique, vol. 16 pp.1-39
Gautier C (|1976|)
Average proteins and the genetic code, Science, vol. 194 pp.642-643
