UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

Gavranovic H, Tannier E (2010)
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces Cerevisiae, Pacific Symposium on Biocomputing, , vol. 15 pp.21-30

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

Van de Wiel MA, Picard F, Van Wieringen WN, Ylstra B (2010)
Preprocessing and downstream analysis of microarray DNA copy number profiles, Manuscripts submitted to Briefings in Bioinformatics, vol. pp.1-20

Acuna V, Marchetti-Spaccamela A, Sagot M-F, Stougie L (2009)
A Note on the Complexity of Finding and Enumerating Elementary Modes, BioSystems, vol. pp.1-5

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2009)
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes, Journal of Computational Biology, vol. 16(10) pp.1287-1309

Boussau B, Guéguen L, Gouy M (2009)
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies, Evolutionary Bioinformatics, vol. 5 pp.67-79

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 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 systéemique 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

Fertin G, Labarre A, Rusu I, Tannier E, Vialette S (2009)
Combinatorics of Genome Rearrangements, MIT press, 2009

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 Bioinformatics, 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)
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

Ouangraoua A, Boyer F, McPherson A, Tannier E, Chauve C (2009)
Prediction of Contiguous Regions in the Amniote Ancestral Genome, 5th International Symposium on Bioinformatics Research and Applications, Springer, Lecture Notes in Bioinformatics, vol. 5542 pp.173-185

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. pp.1-9

Tannier E (2009)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods, Proceedings of RECOMB Comparative Genomics, Springer, Lecture notes in Bioinformatics, vol. 5817 pp.1-12

Tannier E, Zheng C, Sankoff D (2009)
Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol. 10(120) pp.1-15

Acuna 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 pp.775-792

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2008)
Perfect DCJ Rearrangement, RECOMB-CG 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. 5267 pp.159-168

Boussau B, Guéguen L, Gouy M (2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evolutionary Biology, vol. 8 pp.272-272

Boyer F, Chauve C, Tannier E (2008)
Prédiction de synténies dans le génome ancestral des amniotes, , vol. pp.141-148

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

Chauve C, Tannier E (2008)
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes, PLoS Computational Biology, vol. 4 pp.391-410

Cottret L, Milreu P-V, Acuna 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

Daudin J-J, Picard F, Robin S (2008)
A mixture model for random graphs, Statistics and Computing, vol. 18 pp.173-183

Lacroix V (2008)
Identification de motifs dans les réseaux métaboliques, , 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, , 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

Lenne R, Solnon C, Stützle T, Tannier E, Birattari M (2008)
Reactive Stochastic Local Search Algorithms for the Genomic Median Problem, EvoCOP 2008, Springer Verlag, Lecture Notes in Computer Science, vol. 4972 pp.266-276

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. pp.1-8

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

Picard F, Daudin J -J, Koskas M, Schbath S, Robin S (2008)
Assessing the exceptionality of network motifs, Journal of Computational Biology, vol. 15 pp.1-20

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

Tannier E (2008)
Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot, article in: Encyclopedia of algorithms, Springer, pp.860-863

Tannier E, Zheng C, Sankoff D (2008)
Multichromosomal Genome Median and Halving Problems, Proceedings of WABI`08, Springer-Verlag, Lecture notes in Bioinformatics, vol. 5251 pp.1-13

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 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, International Symposium on Bioinformatics Research and Applications, 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

Dumas J-G, Roch J-L, Tannier E, Varrette S (2007)
Théorie des codes: compression cryptage correction, Dunod, 2007

Guedj M, Della-Chiesa E, Picard F, Nuel G (2007)
Computing power in case-control association studies through the use of quadratic approximations: application to meat-statistics, Annals of Human genetics, vol. pp.57-62

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

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

Picard F, Robin S, Lebarbier E, Daudin J -J (2007)
A segmentation/clustering model for the analysis of array CGH data, Biometrics, vol. 63 pp.758-766

Rezvoy C, Charif D, Guéguen L , Marais GAB (2007)
MareyMap: an R-based tool with graphical interface for estimating recombination rates, Bioinformatics, vol. 23 pp.2188-2189

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

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

Daudin JJ, Lacroix V, Mariadassou M, Miele V, Picard F, Robin S, Sagot M-F (2006)
Uncovering structure in biological networks, , vol. pp.471-483

Daudin JJ, Lacroix V, Picard F, S Robin, Sagot M-F (2006)
Uncovering structure in biological networks, , vol. pp.471-483

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

Lubrano-Berthelier C, Dubern B, Lacorte J-M, Picard F, Shapiro A, Zhang S, Bertrais S, Hercberg S, Basdevant A, Clement K, Vaisse C (2006)
Melanocortin-4 receptor mutations in a large cohort of severely obese adults: prevalence functional classification genotype-phenotype relationship and lack of association with binge eating, Journal of Clinical Endocrinology and Metabolism, vol. 91 pp.1811-1818

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, pp.353-364

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

Govaerts C, Srinivasan S , Shapiro A, Zhang S, Picard F, Clement K, Lubrano-Berthelier C, Vaisse C (2005)
Obesity-associated mutations in the melanocortin-4 receptor provide novel insights into its function, Peptides, vol. 26 pp.1909-1919

Guéguen L (2005)
Sarment: Python modules for HMM analysis and partitioning of sequences, Bioinformatics, vol. 21 pp.3427-3428

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

Picard F, Robin S, Lavielle M, Vaisse C, Daudin J -J (2005)
A statistical approach for array CGH data analysis, BMC Bioinformatics, vol. 6 pp.1-14

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

Sebo A, Tannier E (2004)
On Metric Generators of Graphs, Mathematics of Operations Research, vol. 29 pp.383-393

Srinivasan S, Lubrano-Berthelier C, Govaerts C, Picard F, Santiago P, Conklin B, Vaisse C (2004)
Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humans, Journal of Clinical Investigation, vol. 114 pp.1158-1164

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

Gravier S, Mhalla M, Tannier E (2003)
On a modular domination game, Theoretical Computer Science, vol. 306 pp.291-303

Lubrano-Berthelier C, Cavazos M, Dubern B, Shapiro A, Le Stunff C, Zhang SM, Picard F, Govaerts C, Froguel P, Bougneres P, Clement K, Vaisse C (2003)
Molecular genetics of human obesity-associated MC4R mutations, Annals of the New Yok Academy of Sciences, vol. 994 pp.49-57

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

Sebo A, Tannier E (2001)
Connected Joins in Graphs, Proceedings of IPCO`01, Springer Verlag, Lecture Notes in Computer Science, vol. 2081 pp.383-391

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

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