UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

Bourg S, Jacob L, Menu F, Rajon E (2019)
Hormonal pleiotropy and the evolution of allocation trade-offs, Evolution, vol. 73 pp.661-674.

Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C (2019)
Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes, BMC Genomics, vol. 20 pp.56-56.

Smid M, Wilting SM, Uhr K, Rodriguez-Gonzalez FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A, Martin S, Davies HR, Staaf J, van de Vijver MJ, Richardson AL, MacGrogan G, Salgado R, van den Eynden GGGM, Purdie CA, Thompson AM, Caldas C, Span P N, Sweep FFCGJ, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Paradiso A, Eyfjord J, Broeks A, Vincent-Salomon A, Futreal A P, Knappskog S, King T, Viari A, Borresen-Dale AL, Stunnenberg HG, Stratton M, Foekens JA, Sieuwerts AM, Martens JWM (2019)
The circular RNome of primary breast cancer, Genome research, vol. 29 pp.356-366.

Tonon L, Fromont G, Boyault S, Thomas E, Ferrari A, Sertier AS, Kielbassa J, Le Texier V, Kamoun A, Elarouci N, Irani J, Multigner L, Gut I G, Gut M, Blanchet P, De Reynies A, Cancel-Tassin G, Viari A, Cussenot O (2019)
Mutational Profile of Aggressive Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men, European urology, vol. 75 pp.11-15.

Benoit-Pilven C, Marchet C, Chautard E, Lima L, Lambert MP, Sacomoto G, Rey A, Cologne A, Terrone S, Dulaurier L, Claude JB, Bourgeois CF, Auboeuf D, Lacroix V (2018)
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data, Scientific reports, vol. 8 pp.4307-4307.

Di Genova A, Ruz GA, Sagot MF, Maass A (2018)
Fast-SG: an alignment-free algorithm for hybrid assembly, GigaScience, vol. 7 pp.1-15.

Drouet Y, Treilleux I, Viari A, Leon S, Devouassoux-Shisheboran M, Voirin N, de la Fouchardiere C, Manship B, Puisieux A, Lasset C, Moyret-Lalle C (2018)
Integrated analysis highlights APC11 protein expression as a likely new independent predictive marker for colorectal cancer, Scientific reports, vol. 8 pp.7386-7386.

Galvao Ferrarini M, Mucha SG, Parrot D, Meiffrein G, Ruggiero Bachega JF, Comte G, Zaha A, Sagot MF (2018)
Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae, Molecular microbiology, vol. 108 pp.683-696.

Huber KT, Moulton V, Sagot MF, Sinaimeri B (2018)
Geometric medians in reconciliation spaces of phylogenetic trees, Information Processing Letters, vol. 136 pp.96-101.

Huet S, Tesson B, Jais JP, Feldman AL, Magnano L, Thomas E, Traverse-Glehen A, Albaud B, Carrère M, Xerri L, Ansell SM, Baseggio L, Reyes C, Tarte K, Boyault S, Haioun C, Link BK, Feugier P, Lopez-Guillermo A, Tilly H, Brice P, Hayette S, Jardin F, Offner F, Sujobert P, Gentien D, Viari A, Campo E, Cerhan JR, Salles G (2018)
A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts, Lancet Oncology, vol. 19 pp.549-561.

Jacob L, Speed TP (2018)
The healthy ageing gene expression signature for Alzheimer`s disease diagnosis: a random sampling perspective, Genome biology, vol. 19 pp.1-3.

Jaillard M, Lima L, Tournoud M, Mahé P, van Belkum A, Lacroix V, Jacob L (2018)
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events, PLoS genetics, vol. 14 pp.e1007758-e1007758.

Kyrkou I, Pusa T, Ellegaard-Jensen L, Sagot MF, Hansen LH (2018)
Pierce`s Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model, Frontiers in microbiology, vol. 9 pp.2141-2141.

Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard J C, Couloux A, Cottret L, Aury J M, Szécsi J, Latrasse D, Madoui MA, Francois L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M (2018)
The Rosa genome provides new insights into the domestication of modern roses, Nature genetics, vol. 50 pp.772-777.

Acuna V, Grossi R, Italiano GF, Lima L, Rizzi R, Sacomoto G, Sagot MF, Sinaimeri B (2017)
On Bubble Generators in Directed Graphs, Lecture Notes in Bioinformatics, vol. 10520 pp.18-31.

Bailly-Bechet M, Martins-Simoes P, Szollosi GJ, Mialdea G, Sagot MF, Charlat S (2017)
How Long Does Wolbachia Remain on Board?, Molecular Biology and Evolution, vol. 34 pp.1183-1193.

Beaudou L, Mary A, Nourine L (2017)
Algorithms for k-meet-semidistributive lattices, Theoretical Computer Science, vol. 658 pp.391-398.

Cheynel L, Lemaitre JF, Gaillard JM, Rey B, Bourgoin G, Ferte H, Jego M, Débias F, Pellerin M, Jacob L, Gilot-Fromont E (2017)
Immunosenescence patterns differ between populations but not between sexes in a long-lived mammal, Scientific reports, vol. 7 pp.13700-13700.

Davies H, Glodzik D, Morganella S, Yates L R, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts A M, Simpson P T, King T A, Raine K, Eyfjord J E, Kong G, Borg A, Birney E, Stunnenberg H G, van de Vijver M J, Borresen-Dale A L, Martens J W, Span P N, Lakhani S R, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson A M, Van Laere S, Richardson A L, Viari A, Campbell P J, Stratton M R, Nik-Zainal S (2017)
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures, Nature medicine, vol. 23 pp.517-525.

Davies H, Morganella S, Purdie C A, Jang S J, Borgen E, Russnes H, Glodzik D, Zou X, Viari A, Richardson AL, Borresen-Dale AL, Thompson A, Eyfjord JE, Kong G, Stratton MR, Nik-Zainal S (2017)
Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency, Cancer research, vol. 77 pp.4755-4762.

Douhard F, Gaillard JM, Pellerin M, Jacob L, Lemaitre JF (2017)
The cost of growing large: costs of post-weaning growth on body mass senescence in a wild mammal, Oikos, vol. 126 pp.1329-1338.

Dudnik A, Almeida AF, Andrade R, Avila B, Bañados P, Barbay D, Bassard JE, Benkoulouche M, Bott M, Braga A, Breitel D, Brennan R, Bulteau L, Chanforan C, Costa I, Costa RS, Doostmohammadi M, Faria N, Feng C, Fernandes A, Ferreira P, Ferro R, Foito A, Freitag S, Garcia G, Gaspar P, Godinho-Pereira J, Hamberger B, Hartmann A, Heider H, Jardim C, Julien-Laferriere A, Kallscheuer N, Kerbe W, Kuipers OP, Li S, Love N, Marchetti-Spaccamela A, Marienhagen J, Martin C, Mary A, Mazurek V, Meinhart C, Sevillano DM, Menezes R, Naesby M, Nørholm MHH, Okkels FT, Oliveira J, Ottens M, Parrot D, Pei L, Rocha I, Rosado-Ramos R, Rousseau C, Sagot MF, dos Santos CN, Schmidt M , Shelenga T, Shepherd L, Silva AR, da Silva MH, Simon O, Stahlhut SG, Solopova A, Sorokin A, Stewart D, Stougie L, Su S, Thole V, Tikhonova O, Trick M, Vain P, Veríssimo A, Vila-Santa A, Vinga S, Vogt M, Wang L, Wang L, Wei W, Youssef S, Neves AR, Forster J (2017)
BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits, Phytochemistry Reviews, vol. 17 pp.291-326.

Foy JP, Bazire L, Ortiz-Cuaran S, Deneuve S, Kielbassa J, Thomas E, Viari A, Puisieux A, Goudot P, Bertolus C, Foray N, Kirova Y, Verrelle P, Saintigny P (2017)
A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes, BMC medicine, vol. 15 pp.165-165.

Foy JP, Bertolus C, Michallet MC, Deneuve S, Incitti R, Bendriss-Vermare N, Albaret MA, Ortiz-Cuaran S, Thomas E, Colombe A, Py C, Gadot N, Michot JP, Fayette J, Viari A, Van den Eynde B, Goudot P, Devouassoux-Shisheboran M, Puisieux A, Caux C, Zrounba P, Lantuejoul S, Saintigny P (2017)
The immune microenvironment of HPV-negative oral squamous cell carcinoma from never-smokers and never-drinkers patients suggests higher clinical benefit of IDO1 and PD1/PD-L1 blockade, Annals of oncology, vol. 28 pp.1934-1941.

Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye I H, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S (2017)
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers, Nature genetics, vol. 49 pp.341-348.

Hartmann A, Vila-Santa A, Kallscheuer N, Vogt M, Julien-Laferriere A, Sagot MF, Marienhagen J, Vinga S (2017)
OptPipe - a pipeline for optimizing metabolic engineering targets, BMC systems biology, vol. 11 pp.143-143.

Huet S, Szafer-Glusman E, Tesson B, Xerri L, Fairbrother W J, Mukhyala K, Bolen C, Punnoose E, Tonon L, Chassagne-Clément C, Feugier P, Viari A, Jardin F, Salles G, Sujobert P (2017)
BCL2 mutations do not confer adverse prognosis in follicular lymphoma patients treated with rituximab, American journal of hematology, vol. 92 pp.515-519.

Huet S, Xerri L, Tesson B, Mareschal S, Taix S, Mescam-Mancini L, Sohier E, Carrere M, Lazarovici J, Casasnovas O, Tonon L, Boyault S, Hayette S, Haioun C, Fabiani B, Viari A, Jardin F, Salles G (2017)
EZH2 alterations in follicular lymphoma: biological and clinical correlations, Blood cancer journal, vol. 7 pp.e555-e555.

Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O`Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg A, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van `t Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjord JE, Borresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR (2017)
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo, Nature, vol. 543 pp.714-718.

Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V (2017)
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads, Algorithms for Molecular Biology, vol. 12 pp.2-2.

Lopez-Maestre H, Carnelossi EA, Lacroix V, Burlet N, Mugat B, Chambeyron S, Carareto CM, Vieira C (2017)
Identification of misexpressed genetic elements in hybrids between Drosophila-related species, Scientific reports, vol. 7 pp.40618-40618.

Saintigny P, Foy JP, Ferrari A, Cassier P, Viari A, Puisieux A (2017)
Apport et défis des Big Data en cancérologie, Bulletin du Cancer, vol. 104 pp.281-287.

Siberchicot A, Julien-Laferrière A, Dufour AB, Thioulouse J, Dray S (2017)
adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data, R Journal, vol. 9 pp.198-212.

Urbini L (2017)
Models and algorithms to study the common evolutionary history of hosts and symbionts .

Andrade R, Wannagat M, Klein CC, Acuna V, Marchetti-Spaccamela A, Milreu P V, Stougie L, Sagot MF (2016)
Enumeration of minimal stoichiometric precursor sets in metabolic networks, Algorithms for Molecular Biology, vol. 11 pp.25-25.

Bulteau L, Fertin G, Tannier E (2016)
Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinformatics, vol. 17 pp.225-231.

Calamoneri T, Sinaimeri B (2016)
Pairwise Compatibility Graphs: A Survey, SIAM Review, vol. 58 pp.445-460.

Ferrari A, Vincent-Salomon A, Pivot X, Sertier A S, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanche H, Deleuze J F, Jacquemier J, Mathieu M C, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga J Y, Tredan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero J M, Tarpin C, Bouteille C, Calvo F, Gut I G, Gut M, Martin S, Nik-Zainal S, Stratton M R, Pauporte I, Saintigny P, Birnbaum D, Viari A, Thomas G (2016)
A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers, Nature Communications, vol. 7 pp.12222-12222.

Ferrarini MG, Siqueira FM, Mucha SG, Palama TL, Jobard E, Elena-Herrmann B, R Vasconcelos AT, Tardy F, Schrank IS, Zaha A, Sagot MF (2016)
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling, BMC Genomics, vol. 17 pp.353-353.

Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B, Day JW, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee KY, Swanson MS, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi MP, Charlet-Berguerand N (2016)
Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, Nature communications, vol. 7 pp.11067-11067.

Jacob L, Gagnon-Bartsch JA, Speed TP (2016)
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed, Biostatistics, vol. 17 pp.16-28.

Julien-Laferrière A (2016)
Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia .

Julien-Laferriere A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF (2016)
A Combinatorial Algorithm for Microbial Consortia Synthetic Design, Scientific reports, vol. 6 pp.29182-29182.

Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals E, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P (2016)
Colib`read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads, GigaScience, vol. 5 pp.9-9.

Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, El Filali A, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V (2016)
SNP calling from RNA-seq data without a reference genome: identification quantification differential analysis and impact on the protein sequence, Nucleic Acids Research, vol. 44 pp.e148-e148.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR (2016)
Landscape of somatic mutations in 560 breast cancer whole-genome sequences, Nature, vol. 534 pp.47-54.

Sessegolo C, Burlet N, Haudry A (2016)
Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies, Biology Letters, vol. 12 pp.20160407-20160407.

Siqueira FM, de Morais GL, Higashi S, Beier LS, Breyer GM, de Sa Godinho CP, Sagot MF, Schrank IS, Zaha A, de Vasconcelos AT (2016)
Mycoplasma non-coding RNA: identification of small RNAs and targets, BMC Genomics, vol. 17 pp.327-335.

Smid M, Rodriguez-Gonzalez FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringner M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerod A, Borresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW (2016)
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration, Nature communications, vol. 7 pp.12910-12910.

Urbini L, Sinaimeri B, Matias C, Sagot MF (2016)
Robustness of the Parsimonious Reconciliation Method in Cophylogeny, Lecture Notes in Computer Science, vol. 9702 pp.119-130.

Verissimo A, Oliveira AL, Sagot MF, Vinga S (2016)
DegreeCox - a network-based regularization method for survival analysis, BMC Bioinformatics, vol. 17 pp.449-449.

Wannagat M (2016)
Study of the evolution of symbiosis at the metabolic level using models from game theory and economics .

Baudet C, Dias U, Dias Z (2015)
Sorting by weighted inversions considering length and symmetry, BMC Bioinformatics, vol. 16 pp.1-11.

Baudet C, Donati B, Sinaimeri B, Crescenzi P, Gautier C, Matias C, Sagot MF (2015)
Cophylogeny Reconstruction via an Approximate Bayesian Computation, Systematic biology, vol. 64 pp.416-431.

Bernard E, Jacob L, Mairal J, Viara E, Vert J P (2015)
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples, BMC Bioinformatics, vol. 16 pp.262-262.

Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lio P, Crescenzi P, Fani R, Fondi M (2015)
MeDuSa: a multi-draft based scaffolder, Bioinformatics, vol. 31 pp.2443-51.

Bulteau L, Chen J, Faliszewski P, Niedermeier R, Talmon N (2015)
Combinatorial Voter Control in Elections, Theoretical Computer Science, vol. 589 pp.99-120.

Bulteau L, Sacomoto G, Sinaimeri B (2015)
Computing an Evolutionary Ordering is Hard, Electronic Notes in Discrete Mathematics, vol. 50 pp.255-260.

Campan-Fournier A, Oger C, Ginevra C, Navratil V, Ranc AG, Perrière G, Jarraud S (2015)
Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d`identifier les déterminants de la pathogénicité, JOBIM, pp.89-89.

David J, Lhote L, Mary A, Rioult F (2015)
An average study of hypergraphs and their minimal transversals, Theoretical Computer Science, vol. 596 pp.124-141.

Donati B, Baudet C, Sinaimeri B, Crescenzi P, Sagot MF (2015)
EUCALYPT: efficient tree reconciliation enumerator, Algorithms for Molecular Biology, vol. 10 pp.3-3.

Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens A L, Henri H, Vavre F, Aury J M, Fournier P, Kergoat G J, d`Alencon E (2015)
Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?, Genetica, vol. 143 pp.305-16.

Galvao Ferrarini M (2015)
Metabolic investigation of the mycoplasmas from the swine respiratory tract .

Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF (2015)
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data, BMC Bioinformatics, vol. 16 pp.179-179.

Livera AM, Sysi-Aho M, Jacob L, Gagnon-Bartsch JA, Castillo S, Simpson JA, Speed TP (2015)
Statistical methods for handling unwanted variation in metabolomics data, Analytical chemistry, vol. 87 pp.3606-15.

Rao Q, Rollat-Farnier PA, Zhu D T, Santos-Garcia D, Silva FJ, Moya A, Latorre A, Klein CC, Vavre F, Sagot MF, Liu SS, Mouton L, Wang XW (2015)
Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci, BMC Genomics, vol. 16 pp.226-226.

Rollat-Farnier P A, Santos-Garcia D, Rao Q, Sagot MF, Silva F J, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu S S, Wang X W, Vavre F, Mouton L (2015)
Two Host Clades Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts, Genome Biology and Evolution, vol. 7 pp.839-55.

Sacomoto G, Lacroix V, Sagot MF (2015)
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs, Algorithms for Molecular Biology, vol. 10 pp.20-20.

Baudet C, Dias U, Dias Z (2014)
Length and Symmetry on the Sorting by Weighted Inversions Problem, Lecture Notes in Computer Science, vol. 8826 pp.99-106.

Bernard E, Jacob L, Mairal J, Vert JP (2014)
Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows, Bioinformatics, vol. 30 pp.2447-2455.

Donati B (2014)
Graph models and algorithms in (co-)evolutionary contexts .

Duvoisin G, Fischer C, Maucort-Boulch D, Giannoni E (2014)
Reduction in the use of diagnostic tests in infants with risk factors for early-onset neonatal sepsis does not delay antibiotic treatment, Swiss medical weekly, vol. 144 pp.w13981-w13981.

Farnier PA (2014)
Évolution des génomes des endosymbiotes chez les insectes phloémophages : le cas d`Hamiltonella defensa en interaction avec ses différents partenaires .

Federico M, Peterlongo P, Pisanti N, Sagot MF (2014)
Rime: Repeat identification, Discrete Applied Mathematics, vol. 163 pp.275-286.

Ferreira R, Grossi R, Rizzi R, Sacomoto G, Sagot MF (2014)
Amortized Õ(V)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs, Lecture Notes in Computer Science, vol. 8737 pp.418-429.

Higashi S (2014)
MiRNA and co: Methodologically exploring the world of small RNAs .

Kanté MM, Limouzy V, Mary A, Nourine L (2014)
On the Enumeration of Minimal Dominating Sets and Related Notions, SIAM Journal on Discrete Mathematics, vol. 28 pp.1916-1929.

Kim S Y, Jacob L, Speed T P (2014)
Combining calls from multiple somatic mutation-callers, BMC Bioinformatics, vol. 15 pp.154-154.

Mallinjoud P, Villemin J P, Mortada H, Polay Espinoza M, Desmet F O, Samaan S, Chautard E, Tranchevent L C, Auboeuf D (2014)
Endothelial epithelial and fibroblast cells exhibit specific splicing programs independently of their tissue of origin, Genome research, vol. 24 pp.511-21.

Milreu PV, Klein C C, Cottret L, Acuna V, Birmele E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF (2014)
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure, Bioinformatics, vol. 30 pp.61-70.

Sacomoto G (2014)
Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNAseq Data .

Sacomoto G, Sinaimeri B, Marchet C, Miele V, Sagot MF, Lacroix V (2014)
Navigating in a Sea of Repeats in RNA-seq without Drowning, Lecture Notes in Computer Science, vol. 8701 pp.82-96.

Salikhov K, Sacomoto G, Kucherov G (2014)
Using cascading Bloom filters to improve the memory usage for de Brujin graphs, Algorithms for Molecular Biology, vol. 9 pp.2-2.

Santos-Garcia D, Rollat-Farnier PA, Beitia F, Zchori-Fein E, Vavre F, Mouton L, Moya A, Latorre A, Silva FJ (2014)
The genome of Cardinium cBtQ1 provides insights into genome reduction symbiont motility and its settlement in Bemisia tabaci, Genome Biology and Evolution, vol. 6 pp.1013-30.

Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P (2014)
Reference-free detection of isolated SNPs, Nucleic Acids Research, vol. 43 pp.e11-e11.

Alves J, Klein C, Maia Da Silva F, Costa-Martins AG, Serrano MG, Buck GA, Vasconcelos AT, Sagot MF, Teixeira M, Motta MC, Camargo EP (2013)
Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers, BMC Evolutionary Biology, vol. 13 pp.190-190.

Berthoumieux S, Brilli M, Kahn D, de Jong H, Cinquemani E (2013)
On the identifiability of metabolic network models, Journal of mathematical biology, vol. 67 pp.1795-832.

Brilli M, Lio P, Lacroix V, Sagot MF (2013)
Short and long-term genome stability analysis of prokaryotic genomes, BMC Genomics, vol. 14 pp.309-309.

Brinza L, Calevro F, Charles H (2013)
Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera, BMC Genomics, vol. 14 pp.73-73.

Coimbra Klein C (2013)
Bioinformatic study of the metabolic dialog between a non-pathogenic trypanosomatid and its endosymbiont with evolutionary and functional goals .

Dias U, Baudet C, Dias Z (2013)
Greedy Randomized Search Procedure to Sort Genomes using Symmetric Almost-Symmetric and Unitary Inversions, ACM Conference on Bioinformatics Computational Biology and Biomedical Informatics, pp.181-190.

Duong V, Henn M R, Simmons C, Ngan C, Y B, Gavotte L, Viari A, Ong S, Huy R, Lennon N J, Ly S, Vong S, Birren B W, Farrar J J, Deubel V, Frutos R, Buchy P (2013)
Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters, Infection Genetics and Evolution, vol. 15 pp.77-86.

Duong V, Simmons C, Gavotte L, Viari A, Ong S, Chantha N, Lennon N J, Birren B W, Vong S, Farrar J J, Henn M R, Deubel V, Frutos R, Buchy P (2013)
Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia, Infection Genetics and Evolution, vol. 15 pp.59-68.

Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A (2013)
ChiTaRS: a database of human mouse and fruit fly chimeric transcripts and RNA-sequencing data, Nucleic Acids Research, vol. 41 pp.D142-51.

Giacofci M, Lambert-Lacroix S, Marot G, Picard F (2013)
Wavelet-based clustering for mixed-effects functional models in high dimension, Biometrics, vol. 69 pp.31-40.

Gutierrez R A, Viari A, Godelle B, Frutos R, Buchy P (2013)
Biased mutational pattern and quasispecies hypothesis in H5N1 virus, Infection Genetics and Evolution, vol. 15 pp.69-76.

Julien-Laferrière A, Sacomoto G, Chikhi R, Scaon E, Parsons D , Sagot MF, Peterlongo P, Miele V, Lacroix V (2013)
New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data, JOBIM, pp.1-6.

Kanté MM, Limouzy V, Mary A, Nourine L, Uno T (2013)
On the Enumeration and Counting of Minimal Dominating sets in Interval and Permutation Graphs, Algorithms and Computation - 24th International Symposium ISAAC 2013, , Lecture Notes in Computer Science, vol. 8283 pp.339-349.

Klein C, Alves J M, Serrano M G, Buck G A, Vasconcelos A T, Sagot MF, Teixeira M M, Camargo E P, Motta M C (2013)
Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses, PLoS one, vol. 8 pp.e79786-e79786.

Motta M C, Martins A C, de Souza S S, Catta-Preta C M, Silva R, Klein C C, de Almeida L G, de Lima Cunha O, Ciapina L P, Brocchi M, Colabardini A C, de Araujo Lima B, Machado C R, de Almeida Soares C M, Probst C M, de Menezes C B, Thompson C E, Bartholomeu D C, Gradia D F, Pavoni D P, Grisard E C, Fantinatti-Garboggini F, Marchini F K, Rodrigues-Luiz G F, Wagner G, Goldman G H, Fietto J L, Elias M C, Goldman M H, Sagot MF, Pereira M, Stoco P H, de Mendonca-Neto R P, Teixeira S M, Maciel T E, de Oliveira Mendes T A, Urmenyi T P, de Souza W, Schenkman S, de Vasconcelos A T (2013)
Predicting the proteins of Angomonas deanei Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family, PLoS one, vol. 8 pp.e60209-e60209.

Nor I, Engelstadter J, Duron O, Reuter M, Sagot MF, Charlat S (2013)
On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data, The American Naturalist, vol. 182 pp.E15-E24.

Prestat E, de Morais S R, Vendrell J A, Thollet A, Gautier C, Cohen P A, Aussem A (2013)
Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours, Computers in biology and medicine, vol. 43 pp.334-41.

Sorn S, Sok T, Ly S, Rith S, Tung N, Viari A, Gavotte L, Holl D, Seng H, Asgari N, Richner B, Laurent D, Chea N, Duong V, Toyoda T, Yasuda C Y, Kitsutani P, Zhou P, Bing S, Deubel V, Donis R, Frutos R, Buchy P (2013)
Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade, Infection Genetics and Evolution, vol. 15 pp.87-94.

Acuna V, Birmelé E, Cottret L, Crescenzi P, Jourdan F, Lacroix V, Marchetti-Spaccamela A, Marino A, Vieira Milreu P, Sagot M-F, Stougie L (2012)
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets, Theoretical Computer Science, vol. 457 pp.1-9.

Acuna V, Milreu P V, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF (2012)
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks, Bioinformatics, vol. 28 pp.2474-83.

Allali J, Saule C, Chauve C, d`Aubenton-Carafa Y, Denise A, Drevet C, Ferraro P, Gautheret D, Herrbach C, Leclerc F, de Monte A, Ouangraoua A, Sagot MF, Termier M, Thermes C, Touzet H (2012)
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms, Advances Bioinformatics, vol. 2012 pp.893048-893048.

Baudet C, Dias Z, Sagot MF (2012)
Sampling solution traces for the problem of sorting permutations by signed reversals, Algorithms for Molecular Biology, vol. 7 pp.18-18.

Birmelé E, Crescenzi P, Ferreira R, Grossi R, Lacroix V, Marino A, Pisanti N, Sacomoto G, Sagot MF (2012)
Efficient Bubble Enumeration in Directed Graphs, SPIRE 2012, pp.1505-1515.

Coimbra Klein C, Cottret L, Keilbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF (2012)
Exploration of the core metabolism of symbiotic bacteria, BMC Genomics, vol. 13 pp.438-438.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge J M, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray R R, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress M L, Gelpi J L, Orozco M, Valencia A, van Berkum N L, Lajoie B R, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis S E, Guigo R, Gingeras T R (2012)
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells, PLoS one, vol. 7 pp.e28213-e28213.

Freire AS, Acuna V, Crescenzi P, Ferreira CE, Lacroix V, Milreu PV, Moreno E, Sagot M-F (2012)
Minimum ratio cover of matrix colums by extreme rays of its induced cone, International Symposium on Combinatorial Optimization, pp.1-12.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, del Pozo A, Tress M, Johnson R, Guigo R, Valencia A (2012)
Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts, Genome Research, vol. 22 pp.1231-1242.

Griebel T, Zacher B, Ribera P, Raineri E, Lacroix V, Guigo R, Sammeth M (2012)
Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Research, vol. 40 pp.10073-10083.

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.

Jacob L, Neuvial P, Dudoit S (2012)
More Power via Graph-Structured Tests for Differential Expression of Gene Networks, Annals of applied statistics, vol. 6 pp.561-600.

Kanté MM, Limouzy V, Mary A, Nourine L (2012)
On the Neighbourhood Helly of Some Graph Classes and Applications to the Enumeration of Minimal Dominating Sets, Algorithms and Computation - 23rd International Symposium ISAAC 2012, , Lecture Notes in Computer Science, vol. 7676 pp.289-298.

Klein C, Marino A, Sagot MF, Vieira Milreu P, Brilli M (2012)
Structural and dynamical analysis of biological networks, Briefings In Functional Genomics, vol. 11 pp.420-33.

Luauté J, Cotton F, Lemaire J-J, Tell L, Iwaz J, Fischer C, André-Obadia N (2012)
Let live or let die after traumatic coma, Neurology Clinical Practice, vol. 2 pp.24-32.

Mendes N D, Heyne S, Freitas A T, Sagot MF, Backofen R (2012)
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches, Bioinformatics, vol. 28 pp.3034-41.

Morgat A, Coissac E, Coudert E, Axelsen K B, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A (2012)
UniPathway: a resource for the exploration and annotation of metabolic pathways, Nucleic Acids Research, vol. 40 pp.D761-D769.

Nor I, Hermelin D, Charlat S, Engelstadter J, Reuter M, Duron O, Sagot MF (2012)
Mod/Resc Parsimony Inference: Theory and application, Information and Computation, vol. 213 pp.23-32.

Popa A, Samollow P, Gautier C, Mouchiroud D (2012)
The sex-specific impact of meiotic recombination on nucleotide composition, Genome Biology and Evolution, vol. 4 pp.412-422.

Ribeca P, Lacroix V, Sammeth M, Guigo R (2012)
Analysis of RNA Transcripts by High-Throughput RNA Sequencing
in: Alternative pre-mRNA Splicing, Wiley-VCH Verlag GmbH & Co. KGaA, pp.544-554.

Sacomoto G, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot M-F, Peterlongo P, Lacroix V (2012)
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC Bioinformatics, vol. 13 pp.S5-S5.

Servant N, Bollet M A, Halfwerk H, Bleakley K, Kreike B, Jacob L, Sie D, Kerkhoven R M, Hupe P, Hadhri R, Fourquet A, Bartelink H, Barillot E, Sigal-Zafrani B, van de Vijver M J (2012)
Search for a gene expression signature of breast cancer local recurrence in young women, Clinical cancer research, vol. 18 pp.1704-15.

Simões P (2012)
Diversity and dynamics of Wolbachia-host associations in arthropods from the Society archipelago French Polynesia .

Smith A A, Belda E, Viari A, Medigue C, Vallenet D (2012)
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes, PLoS computational biology, vol. 8 pp.e1002540-e1002540.

Tolon V, Martin J, Dray S, Loison A, Fischer C, Baudet E (2012)
Predator–prey spatial game as a tool to understand the effects of protected areas on harvester–wildlife interactions, Ecological Applications, vol. 22 pp.648-657.

Amos C I, Wang Li-E, Lee J E, Gershenwald J E, Chen W V, Fang S, Kosoy R, Zhang M, Quershi A A, Vattathil S, Schacherer C W, Gardner J M, Wang Y, Bishop D T, Barrett J H, GenoMEL Investigators, MacGregor S, Hayward N K, Martin N G, Duffy D L, Q-Mega Investigators, Mann G J, Cust A, Hopper J, AMFS Investigators, Brown K M (2011)
Genome-wide association study identifies novel loci predisposing to cutaneous melanoma, Human Molecular Genetics, vol. 20 pp.5012-5023.

Baudet C, Dias Z (2011)
Partial Enumeration of Solutions Traces for the Problem of Sorting by Signed Reversals, ACM Conference on Bioinformatics Computational Biology and Biomedicine, pp.505-507.

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 pp.1-15.

Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng J F, Goodwin L, Pitluck S, Land M, Hauser L, Woyke T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi E G (2011)
Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti, BMC Genomics, vol. 12 pp.235-235.

Jacob L (2011)
Regularized learning in bioinformatics, Journal de la Société Française de Statistique, vol. 152 pp.51-76.

Kanté MM, Limouzy V, Mary A, Nourine L (2011)
Enumeration of Minimal Dominating Sets and Variants, Fundamentals of Computation Theory - 18th International Symposium FCT 2011, pp.298-309.

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.

Lopes ME, Jacob L, Wainwright MJ (2011)
A More Powerful Two-Sample Test in High Dimensions using Random Projection, Advances in Neural Information Processing Systems 24, pp.12-21.

Mendes N (2011)
Efficient algorithms for the identification of miRNA motifs in DNA sequences .

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.

Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011)
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis, Nucleic Acids Research, vol. 39 pp.e145-e145.

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 MF, Charles H, Colella S (2011)
CycADS: an annotation database system to ease the development and update of BioCyc databases, Database, vol. 2011 pp.bar008-bar008.

Veron AS, Lemaitre C, Gautier C, Lacroix V, Sagot MF (2011)
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC Genomics, vol. 12 pp.303-303.

Acuña V (2010)
Models and algorithms for metabolic networks: elementary modes and precursor sets .

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, Dias Z (2010)
Chronological order of reversal events on Rickettsia genus, International Symposium on Biocomputing, pp.1-5.

Baudet C, Dias Z (2010)
An Improved Algorithm to Enumerate All Traces that Sort a Signed Permutation by Reversals, ACM Symposium on Applied Computing, pp.1521-1525.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF (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 pp.52-52.

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.

Consortium The International Aphid Genomics, Sagot MF (2010)
Genome Sequence of the Pea Aphid Acyrthosiphon pisum, PLOS Biology, vol. 8 pp.E1000313-E1000313.

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 pp.e1000904-e1000904.

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

Degletagne C, Keime C, Rey B, de Dinechin M, Forcheron F, Chuchana P, Jouventin P, Gautier C, Duchamp C (2010)
Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays, BMC Genomics, vol. 11(344) pp.1-9.

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
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 pp.59-59.

Frandi A, Mengoni A, Brilli M (2010)
Comparative genomics of VirR regulons in Clostridium perfringens strains, BMC Evolutionary Biology, vol. 10 pp.65-65.

Kielbassa J (2010)
Mathematical modelling of temperature effects on the life-history traits and the population dynamics of bullhead textit(Cottus gobio) .

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.

Mendes N D, Freitas A T, Vasconcelos A T, Sagot MF (2010)
Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi, BMC Genomics, vol. 11 pp.529-529.

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 .

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 pp.1-22.

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, Comptes Rendus 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 .

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.95-108.

Horard B, Eymery A, Fourel G, Vassetzky N, Puechberty J, Roizes G, Lebrigand K, Barbry P, Laugraud A, Gautier C, Bensimon E, Devaux F, Magdinier F, Vourc`h C, Gilson E (2009)
Global analysis of DNA methylation and transcription of human repetitive sequences, Epigenetics, vol. 4 pp.339-350.

Jacob L, Bach F, Vert JP (2009)
Clustered Multi-Task Learning: a Convex Formulation, Neural Information Processing Systems 21, pp.1-8.

Jacob L, Obozinski G, Vert JP (2009)
Group Lasso with Overlap and Graph Lasso, International Conférence on Machine Learning 26, pp.1-8.

Lemaitre C, Braga Marilia D V , Gautier C, Sagot MF, 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 MF, 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 G, do Lago AP, Pisanti N, Sagot M-F (2009)
Lossless filter for multiple repeats with bounded edit distance, Algorithms for Molecular Biology, vol. 4 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.s17-s17.

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.619234-619234.

Tolon V, Dray S, Loison A, Zeileis A, Fischer C, Baubet E (2009)
Responding to spatial and temporal variations in predation risk: space use of a game species in a changing landsape of fear, Canadian journal of zoology, vol. 87 pp.1129-1137.

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 MF, 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.

Jacob L, Hoffmann B, Stoven V, Vert J P (2008)
Virtual screening of GPCRs: an in silico chemogenomics approach, BMC Bioinformatics, vol. 9 pp.363-363.

Jacob L, Vert JP (2008)
Efficient peptide-MHC-I binding prediction for alleles with few known binders, Bioinformatics, vol. 24 pp.358-66.

Jacob L, Vert JP (2008)
Protein-ligand interaction prediction: an improved chemogenomics approach, Bioinformatics, vol. 24 pp.2149-56.

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 .

Lemaitre C, Sagot MF (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 MF (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.

Vert JP, Jacob L (2008)
Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies, Combinatorial Chemistry & High Throughput Screening, vol. 11 pp.677-685.

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.2-2.

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 .

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.

Montavont A, Demarquay G, Ryvlin P, Rabilloud M, Guénot M, Ostrowsky K, Isnard J, Fischer C, Mauguière F (2007)
Efficacité de la stimulation intermittente du nerf vague dans les épilepsies pharmaco-résistantes non chirurgicales de l`adolescent et de l`adulte, Revue Neurologique, vol. 163(12) pp.1169-1177.

Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR (2007)
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography, Genome Research, vol. pp.7-15.

Palmeira L (2007)
Analyse et modélisation des dépendances entre sites voisins dans l’évolution des séquences d’ADN .

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.90-90.

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.94-94.

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 MF (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.

Fischer C, Luaute J, Nemoz C, Morlet D, Kirkorian G, Mauguiere F (2006)
Editorial response: Evoked potentials can be used as a prognosis factor for awakening, Critical Care Medicine, vol. 34 pp.2025-2025.

Fischer C, Luaute J, Nemoz C, Morlet D, Kirkorian G , Mauguiere F (2006)
Improved prediction of awakening or nonawakening from severe anoxic coma using tree-based classification analysis, Critical Care Medicine, vol. 34 pp.1520-1524.

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 MF (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.

Barna A, Baudet M, Cambou J-P, Chatellier G, Cucherat M, Dallongeville J, Durlach V, Giral P, Gueyffier F, Kownator S, Lang T, Léonard D, Pace E, Paillard F, Vallée J-P, Vergès B, Aquino J-P , Aulanier S, Balarac N, Beucler I, Bobrie G, Caporossi L, Dénolle T, D`Ivernois C, Dumarcet N, Erpeldinger S, Farnier M, Ferrières J, Fischer C, Friocourt P, Girerd X, Godin M, Halimi S, Jean T, Lièvre M, Loirat P, Lucas C, Marechaud R, Marre M, Ménard J, Mimran A, Moulin P, Picard S, Poncelet P, Pouchain D, Scarabin P-Y, Seux M-L, Senechal M, Sicard D, Turpin G, Vaisse B, Vallée J (2005)
Methods for evaluation of total cardiovascular risk, Médecine thérapeutique, vol. 11 pp.233-236.

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 MF (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 MF (2005)
Reaction motifs in metabolic networks, Proceedings of WABI `05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3692 pp.178-191.

Luauté J, Fischer C, Adeleine P, Morlet D, Tell L, Boisson D (2005)
Late auditory and event-related potentials can be useful to predict good functional outcome after coma, Archives of physical medicine and rehabilitation, vol. 86 pp.917-923.

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 MF (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 MF (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
in: String algorithmics, King`s College Publications, pp.195-226.

Pisanti N, Sagot M-F (2005)
Network expression inference
in: Applications of Combinatorics on Words, Cambridge University Press, pp.227-250.

Sagot MF, 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 MF (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 MF (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 MF (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 MF (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 MF (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 MF (2004)
Motifs in sequences: localization and extraction
in: Handbook of Computational Chemistry, Marcel Dekker Inc, pp.47-97.

Fischer C, Luaute J, Adeleine P, Morlet D (2004)
Predictive value of sensory and cognitive evoked potentials for awakening from coma, Neurology, vol. 63 pp.669-673.

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.

Jaillon O, Aury J-M, Brunet F, Petit J L, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander E S, Weissenbach J, Roest Crollius H (2004)
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol. 431 pp.946-957.

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 MF (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 MF (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 MF, Schbath S (2003)
Occurrence probability of structured motifs in random sequences, Journal of Computational Biology, vol. 9 pp.761-773.

Sagot MF, Wakabayashi Y (2003)
Pattern inference under many guises
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 MF, 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 MF (2002)
Gene finding in eukaryotes
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 MF (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 MF, 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 MF (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 MF (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 MF (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 MF (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 MF, 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 MF, 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 MF, Viari A (1996)
A Double Combinatorial Approach to Discovering Patterns in Biological Sequences, Lecture Notes in Computer Science, 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 MF, 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 MF, 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 MF, 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 MF, 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.