ABI


Publications des membres de l'ABI

Journaux internationaux

2016

  • IR Gonçalves, S Brouillet, MC Soulié, S Gribaldo, C Sirven, N Charron, M Boccara and M Choquer. Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. BMC Evol Biol. 2016 Nov 24;16(1):252 doi:10.1186/s12862-016-0815-9
  • Henry Soldano, Guillaume Santini1, Dominique Bouthinon Motifs abstraits et sous-communautés dans les réseaux attribués.Revue d’intelligence artificielle – n° 4/2016, 443-471, Lavoisier.
  • Martine Boccara,Yasmina Fedala,Catherine Venien Bryan, Marc Bailly-Bechet, Chris Bowler and Albert Claude Boccara .Full-field interferometry for counting and differentiating aquatic biotic nanoparticles:from laboratory to Tara Oceans Vol. 7, No. 9 | 1 Sep 2016 | BIOMEDICAL OPTICS EXPRESS 3736
  • Vakirlis N, Sarilar V, Drillon G, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Fleiss A, Gillet Markowska A, Graziani S, Nguyen HV, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. 2016 Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Research 26: 918–932.
  • Lapierre M, Blin C, Lambert A, Achaz G, Rocha EP. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol. 2016 Jul;33(7):1711-25. doi: 10.1093/molbev/msw048. Epub 2016 Mar 1.
  • Ferretti L, Schmiegelt B, Weinreich D, Yamauchi A, Kobayashi Y, Tajima F, Achaz G. Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations. J Theor Biol. 2016 May 7;396:132-43. doi: 10.1016/j.jtbi.2016.01.037. Epub 2016 Feb 20
  • Behdenna A, Pothier J, Abby SS, Lambert A, Achaz G.Testing for Independence between Evolutionary Processes. Syst Biol. 2016 Sep;65(5):812-23. doi: 10.1093/sysbio/syw004. Epub 2016 May 21.
  • C Delaporte, G Achaz and A Lambert. Mutational pattern of a sample from a critical branching population. J Math Biol. 2016 Sep;73(3):627-64. doi: 10.1007/s00285-015-0964-2. Epub 2016 Jan 9.
  • M Suez, A Behdenna, S Brouillet, P Graça, D Higuet, G Achaz MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads Molecular Ecology Resources Volume 16, Issue 2 March 2016 Pages 524–533
  • Emilie Dumas, Eva Christina Boritsch, Mathias Vandenbogaert, Ricardo C Rodríguez de la Vega, Jean-Michel Thiberge, Valerie Caro, Jean-Louis Gaillard, Beate Heym, Fabienne Girard-Misguich, Roland Brosch, and Guillaume Sapriel Mycobacterial pan-genome analysis suggests important role of plasmids in the radiation of type VII secretion systems Genome Biol Evol published online January 8, 2016, : evw001v1-evw001.
  • Konjek J, Souded S, Guerardel Y, Trivelli X, Bernut A, Kremer L, Welte B, Joyeux M, Dubrou S, Euzeby JP, Gaillard JL, Sapriel G, Heym B. Mycobacterium lutetiense sp. nov., Mycobacterium montmartrense sp. nov. and Mycobacterium arcueilense sp. nov., members of a new group of non-pigmented rapidly growing mycobacteria recovered from the Paris water distribution system. Int J Syst Evol Microbiol. 2016 Jun 30. doi: 10.1099/ijsem.0.001253. [Epub ahead of print] PubMed PMID: 27375118.
  • Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics. 2016 Feb 17;17:118. doi: 10.1186/s12864-016-2448-1. PubMed PMID: 26884275; PubMed Central PMCID: PMC4756508.
  • Bernut A, Viljoen A, Dupont C, Sapriel G, Blaise M, Bouchier C, Brosch R, de Chastellier C, Herrmann JL, Kremer L. Insights into the smooth-to-rough transitioning in Mycobacterium bolletii unravels a functional Tyr residue conserved in all mycobacterial MmpL family members. Mol Microbiol. 2016 Mar;99(5):866-83. doi: 10.1111/mmi.13283. Epub 2015 Dec 18. PubMed PMID: 26585558.

2015

  • Avendaño-Herrera R, Irgang R, Sandoval C, Moreno-Lira P, Houel A, Duchaud E, Poblete-Morales M, Nicolas P, Ilardi P. Isolation, Characterization and Virulence Potential of Tenacibaculum dicentrarchi in Salmonid Cultures in Chile. Transbound Emerg Dis. 2016 Jan 8.doi: 10.1111/tbed.12464. [Epub ahead of print]
  • Gómez E, Álvarez B, Duchaud E, Guijarro JA. Development of a markerless deletion system for the fish-pathogenic bacterium Flavobacterium psychrophilum.PLoS One. 2015 Feb 18;10(2):e0117969. doi: 10.1371/journal.pone.0117969. eCollection 2015.
  • Denis Saint-Marcoux, Bernard Billoud, Jane A. Langdale and Bénédicte Charrier. Laser capture microdissection in Ectocarpus siliculosus: the pathway to cell-specific transcriptomics in brown algae Front. Plant Sci., 10 February 2015 | http://dx.doi.org/10.3389/fpls.2015.00054
  • Bernard Billoud, Émilie Jouanno, Zofia Nehr, Baptiste Carton, Élodie Rolland, Sabine Chenivesse and Bénédicte Charrier. Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches Front. Plant Sci., 19 February 2015 | http://dx.doi.org/10.3389/fpls.2015.00068
  • Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME J. 2015 Nov 27.
  • Mateusz Banach, Nicolas Prudhomme, Mathilde Carpentier, Elodie Duprat, Nikolaos Papandreou, Barbara Kalinowska, Jacques Chomilier , Irena Roterman Contribution to the Prediction of the Fold Code: Application to Immunoglobulin and Flavodoxin Cases PLOS ONE April 27, 2015 DOI: 10.1371/journal.pone.0125098
  • C Régnier, G Achaz, A Lambert, RH Cowie, P Bouchet, B Fontaine Mass extinction in poorly known taxa Proceedings of the National Academy of Sciences 112 (25), 7761-7766,4(2015)

2014

  • F Blanquart, G Achaz, T Bataillon and O Tenaillon Properties of selected mutations and genotypic landscapes under Fisher’s Geometric Model. Evolution, (2014).
  • M Bailly-Bechet, A Haudry and E Lerat ”One code to find them all”: a perl tool to conveniently parse RepeatMasker output files. Mobile DNA (2014), 5:13
  • X Zhang, B Mozeleski, S Lemoine, E D ériaud, A Lim, D Zhivaki, E Azria, C Le Ray, G Roguet, O Launay, A Vanet, C Leclerc, R Lo-Man CD4 T cells with effector memory phenotype and function develop in the sterile environment of the fetus Sci Transl Med. (2014), 6(238):238ra72
  • M PetitJean, A Vanet. VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations Bioinformatics (2014), 30(4):578-80
  • Hovhannisyan A, Pham TH, Bouvier D, Piroyan A, Dufau L, Qin L, Cheng Y, Me- likyan G, Reboud-Ravaux M and Bouvier-Durand M. New C(4)- and C(1)-derivatives of furo[3,4-c]pyridine-3-ones and related compounds: evidence for site-specific inhibi- tion of the constitutive proteasome and its immunoisoform. Bioorg Med Chem Lett. (2014), 24(6):1571-80
  • G Achaz, A Rodriguez-Verdugo, BS Gaut and O Tenaillon. The reproducibility of adap- tation in the light of experimental evolution with whole genome sequencing. Adv Exp Med Biol (2014), 781:211-31

2013

  • Dubrou S, Konjek J, Macheras E, Welté B, Guidicelli L, Chignon E, Joyeux M, Gail- lard JL, Heym B, Tully T and G Sapriel. Diversity, community composition, and dy- namics of nonpigmented and late-pigmenting rapidly growing mycobacteria in an urban tap water production and distribution system. Appl Environ Microbiol (2013), 79(18):5498-508
  • Bobay LM, Touchon M and Rocha EP. Manipulating or superseding host recombina- tion functions: a dilemma that shapes phage evolvability. PLoS Genet. (2013), 9(9):e1003825
  • Pawlik A1, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, Sapriel G, Roux AL, Conlon K, Honoré N, Dillies MA, Ma L, Bouchier C, Coppée JY, Gaillard JL, Gordon SV, Loftus B, Brosch R, Herrmann JL. Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus. Mol Microbiol. 2013 ;90(3):612-29.
  • H Magellan, M Boccara, T Drujon, MC Soulié, C Guillou, J Dubois and HF Becker. Discovery of two new inhibitors of Botrytis cinerea chitin synthase by a chemical library screening. Bioorg Med Chem. (2013). 21(17):4997-5003
  • S Ishida, F Picard, G Rudolf, E No é, G Achaz, P Thomas, P Genton, E Mundwiller, M Wolff, C Marescaux, R Mieles, M Baulac, E Hirsch, E Leguern and S Baulac. Mutations 4 of DEPDC5 cause autosomal dominant focal epilepsies. Nature Genetics (2013), 45(5):552-5
  • E Loire, D Higuet, P Netter and G Achaz. Evolution of coding microsatellites in primate genomes. Genome Biology and Evolution (2013), 5(2):283-295.

2012

  • G Santini, H Soldano and Pothier J. Automatic classification of protein structures re- lying on similarities between alignments BMC Bioinformatics (2012), 13:233
  • TH Pham, Hovhannisyan A, Bouvier D, Tian L, Reboud-Ravaux M, Melikyan G, Bouvier-Durand M. A new series of N5 derivatives of the 1,1,5-trimethyl furo[3,4- c]pyridine-3,4-dione (cerpegin) selectively inhibits the post-acid activity of mammalian 20S proteasomes. Bioorg Med Chem Lett (2012), 22(11):3822-7
  • A Detai, C Gallut, S Brouillet, J Pothier, G Lecointre and R Debruyne. Conveniently pre-tagged and pre-packaged: extended molecular identification and metagenomics using complete metazoan mitochondrial genomes PLoSOne (2012), 7(12):e51263
  • N Puillandre, A Lambert, S Brouillet and G Achaz. ABGD, Automatic Barcode Gap Discovery for Primary Species Delimitation. Molecular Ecology (2012), 21(8), 1864- 1877.

2011

  • M Piednoël, IR Gonçalves, D Higuet and E Bonnivard. Eukaryote DIRS1-like retro- transposons: an overview. BMC Genomics. (2011), 12:621.
  • JD Glasner et al. [xx co-authors including M Boccara and M Carpentier]. Genome se- quence of the plant-pathogenic bacterium Dickeya dadantii 3937. J Bacteriol. (2011), 193(8):2076-7.
  • Y Kobayashi, G Achaz and A Telschow. Effect of Parasitic Sex Ratio Distorters on Host Gene Frequencies in a Mainland-Island Context. Journal if Evolutionary Biology (2011), 24(8):1695-705.
  • E Loire, D Higuet, P Netter and G Achaz. Evolution of coding microsatellites in primate genomes. Genome Biology and Evolution (2013), 5(2):283-295.


Actes de conférences internationales avec comité de lecture (Informatique)

2015

  • H. Soldano, G. Santini, and D. Bouthinon. Local knowledge discovery in attributed graphs. In A. Es- posito, editor, 27th IEEE International Conference on Tools with Artificial Intelligence, ICTAI, Vietri sul Mare, Italy, pages 250–257. IEEE Computer Society, November 9-11 2015.
  • H. Soldano, G. Santini, and D. Bouthinon. Abstract and local rule learning in attributed networks. In F. Esposito, M.-S. Hacid, O. Pivert, and Z. Ras, editors, Foundations of Intelligent Systems 22nd International Symposium, ISMIS, volume 9384 of LNAI, pages 313–323, Lyon, France, October 21-23 2015. Springer.
  • H. Soldano. Extensional confluences and local closure operators. In J. Baixeries, C. Sacarea, and M. Ojeda-Aciego, editors, Formal Concept Analysis - 13th International Conference, ICFCA 2015, Nerja, Spain, June 23-26, 2015, Proceedings, volume 9113 of Lecture Notes in Computer Science, pages 128–144. Springer, 2015.
  • H. Soldano, G. Santini, and D. Bouthinon. Local rules associated to k-communities in an attributed graph. In MANEM at ASONAM 15 First International workshop on Multiplex and Attributed Network Mining, pages 1340–1347, Paris, August 25-28 2015. ACM Press

2014

  • C Rodrigues, H Soldano and G Bourgne and C Rouveirol. A Consistency Based ap- proach on Action Model Learning in a Community of Agents. International Confer- ence on Autonomous Agents and Multiagent Systems (AAMAS’14). (2014).
  • C Rodrigues, H Soldano and G Bourgne and C Rouveirol. Multi-agent learning of relational action models. European Conference in Artificial Intelligence (ECAI). (2014).
  • H Soldano. Closed patterns and abstraction beyond lattices. International Confer- ence on Formal Concept Analysis (ICFCA). (2014).
  • H Soldano and G Santini. Graph abstraction for closed pattern mining in attributed network. European Conference in Artificial Intelligence (ECAI). (2014).

2013

  • S. Bannour, L. Audibert and H Soldano. Ontology-based semantic annotation: an auto- matic hybrid rule-based method. Proceedings of the BioNLP Shared Task (2013)

2012

  • C Rodrigues, P Gérard, C Rouveirol and H Soldano Active learning of relational action models. Lecture Notes in Computer Science (2011)

2011

  • H Soldano and V Ventos. Abstract Concept Lattices. International Conference on Formal Concept Analysis. ICFCA 2011 (2011)
  • H Soldano A modal view on abstract learning and reasoning. Symposium on Ab- straction, Reformulation, and Approximation. SARA 2011 (2011)