ABI


Publications des membres de l'ABI

(depuis 2014)

Journaux internationaux

2017

  • S Gangloff *, G Achaz *, S Miled, C Denis A Villain and B Arcangioli. Quiescence: the unforseen mutations, eLife, in press [* equal contribution].
  • N Vakirlis, AS Hebert, DA Opulente, G Achaz, CT Hittinger, G Fischer, JJ Coon, and I Lafontaine. A Molecular Portrait Of De Novo Genes, Mol Biol Evol, in press
  • S Matuszewski, ME Hildebrandt, G Achaz and JD Jensen. Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography, Genetics, in press.
  • FX Weill, D Domman, E Njamkepo, C Tarr,J Rauzier, N Fawal, KH Keddy, H Salje, S Moore, AK Mukhopadhyay, R Bercion, FJ Luquero, A Ngandjio, M Dosso, E Monakhova, B Garin, C Bouchier, C Pazzani, A Mutreja, R Grunow , F Sidikou, L Bonte, S Breurec, M Damian, BM Njanpop-Lafourcade, G Sapriel, AL Page, M Hamze, M Henkens, G Chowdhury, M Mengel, JL Koeck, JM Fournier, G Dougan, PAD Grimont, J Parkhill, KE Holt, R Piarroux, T Ramamurthy, ML Quilici, and NR Thomson. Genomic history of the seventh pandemic of cholera in Africa. Science. 2017 Nov 10;358(6364):785-789. doi: 10.1126/science.aad5901.
  • F Jia, M Ben Amar, B Billoud, B Charrier (2017). Morphoelasticity in the development of brown alga Ectocarpus siliculosus: from cell rounding to branching. J. R. Soc. Interface 14: 20160596.
  • P Brézellec, MA Petit, S Pasek, I Vallet-Gely, C Possoz, and JL Ferat. Domestication of Lambda Phage Genes into a Putative Third Type of Replicative Helicase Matchmaker. Genome Biol Evol. 2017 Jun 1;9(6):1561-1566.
  • L Ferretti, A Ledda, T Wiehe, G Achaz, S Ramos-Onsins. Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests. Genetics (2017), 207(1):229-240.
  • M Lapierre, A Lambert, G Achaz. Accuracy of demographic inferences from Site Frequency Spectrum: The case of the Yoruba population. Genetics 2017, 206(1):439:449
  • C Roose-Amsaleg, Y Fedala, C Vénien-Bryan, J Garnier, AC Boccara, M Boccara. Utilization of interferometric light microscopy for the rapid analysis of virus abundance in a river. Res Microbiol. 2017 168(5):413-418.
  • M Boccara, A Sarazin, B Billoud, A Bulski, L Chapell, D Baulcombe, V Colot. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays (DOI: 10.1007/978-1-4899-7708-3_11 In book: Plant Epigenetics, pp.127-139)

2016

  • M Lescot, P Hingamp, KK Kojima, E Villar, S Romac, A Veluchamy, M Boccara, O Jaillon, D Ludicone, C Bowler, P Wincker, JM Claverie, H Ogata. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME J. 2016 May;10(5):1134-46. doi: 10.1038/ismej.2015.192.
  • M Boccara, Y Fedala, CV Bryan, M Bailly-Bechet, C Bowler, AC Boccara. Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans. Biomed Opt Express. 2016 7(9):3736-3746.
  • 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
  • H Soldano, G Santini, D Bouthinon. Motifs abstraits et sous-communautés dans les réseaux attribués. Revue d’intelligence artificielle – n° 4/2016, 443-471, Lavoisier.
  • N Vakirlis, V Sarilar, G Drillon, N Agier, JP Meyniel, L Blanpain, A Carbone, H Devillers, K Dubois, A Fleiss, A Gillet Markowska, S Graziani, HV Nguyen, M Poirel, C Reisser, J Schott, J Schacherer, I Lafontaine, B Llorente, C Neuvéglise, G Fischer. 2016 Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Research 26: 918–932.
  • M Lapierre, C Blin, A Lambert, G Achaz, EP Rocha. 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.
  • L Ferretti, B Schmiegelt, D Weinreich, A Yamauchi, Y Kobayashi, F Tajima, G Achaz. 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
  • A Behdenna, J Pothier, SS Abby, A Lambert, G Achaz.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
  • E Dumas, EC Boritsch, M Vandenbogaert, R C Rodríguez de la Vega, JM Thiberge, V Caro, JL Gaillard, B Heym, F Girard-Misguich, R Brosch, and G 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.
  • J Konjek, S Souded, Y Guerardel, X Trivelli, A Bernut, L Kremer, B Welte B,M Joyeux, S Dubrou, JP Euzeby, JL Gaillard , G Sapriel, 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.
  • G Sapriel, J Konjek, M Orgeur, L Bouri, L Frézal, AL Roux, E Dumas, R Brosch, C Bouchier, S Brisse, M Vandenbogaert, JM Thiberge, V Caro, YF Ngeow, JL Tan, JL Herrmann, JL Gaillard, B Heym, T Wirth. 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.
  • A Bernut, A Viljoen, C Dupont, G Sapriel, M Blaise, C Bouchier, R Brosch, C de Chastellier, JL Herrmann, L Kremer. 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

  • R Avendaño-Herrera, R Irgang, C Sandoval, P Moreno-Lira, A Houel, E Duchaud, M Poblete-Morales, P Nicolas, P Ilardi. 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]
  • E Gómez, B Álvarez, E Duchaud, JA Guijarro. 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.
  • D Saint-Marcoux, B Billoud, JA Langdale and B 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
  • B Billoud, E Jouanno, Z Nehr, B Carton, E Rolland, S henivesse and B 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
  • M Lescot, P Hingamp, KK Kojima, E Villar, S Romac, A Veluchamy, M Boccara, O Jaillon, D Iudicone, C Bowler, P Wincker, JM Claverie, H Ogata. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME J. 2015 Nov 27.
  • M Banach, N Prudhomme, M Carpentier, E Duprat, N Papandreou, B Kalinowska, J Chomilier , I 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)
  • A Thierry, V Khanna V, S Créno S, I Lafontaine, L Ma, C Bouchier and B Dujon. (2015). Formation of macrotene chromosomes, insights to a new mechanism of high order gene amplification in eukaryotes. Nature Communications, 6. doi :10.1038/ncomms7154.

2014

  • M Boccara, A Sarazin, O Thiébeauld, F Jay, O Voinnet, L Navarro, V Colot. The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes. PLoS Pathog. 2014;10(1):e1003883.
  • 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
  • A Hovhannisyan, TH Pham, D Bouvier, A Piroyan, L Dufau, L Qin, Y Cheng, G Melikyan, M Reboud-Ravaux and M Bouvier-Durand. 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
  • A Gillet-Markowska, H Richard, G Fischer and I Lafontaine. (2014) Ulysses: Accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Bioinformatics, 31 :801-808.
  • G Kunze, C Gaillardin, M Czernicka,P Durrens, T Martin, E Böer, T Gabaldón, JA Cruz, E Talla, C Marck, A Goffeau, V Barbe, P Baret, K Baronian, S Beier, C Bleykasten, R Bode, S Casaregola, L Despons, C Fairhead, M Giersberg, PP Gierski, U Hähnel, A Hartmann, D Jankowska, C Jubin, P Jung, I Lafontaine, V Leh-Louis, M Lemaire, M Marcet-Houben, M Mascher, G Morel, GF Richard, J Riechen, C Sacerdot, A Sarkar, G Savel, J Schacherer, DJ Sherman, N Stein, ML Straub, A Thierry, A Trautwein-Schult, B Vacherie, E Westhof, S Worch, B Dujon, JL Souciet, P Wincker, U Scholz, and C Neuvéglise (2014). The complete genome of Blastobotrys (Arxula) adeninivorans LS3 – a yeast of biotechnological interest. Biotechnology for Biofuels, 7:66


Actes de conférences internationales avec comité de lecture (Informatique)

2017

  • H Soldano, G Santini, and D Bouthinon. Formal Concept Analysis in Social Network Analysis. edited by Rokia Missaoui, Sergei Obiedkov, and Sergei Kuznetsov, 143–70. Lecture Notes in Social Network. Springer, 2017.
  • H Soldano, G Santini, and D Bouthinon. Motifs Abstraits et Sous-Communautés Dans Les Réseaux Attribués. Revue d’Intelligence Artificielle 30, no. 4 (2016): 441–68. https://doi.org/10.3166/ria.30.441-468.
  • H Soldano, Guillaume Santini, Dominique Bouthinon, and Emmanuel Lazega. Hub-Authority Cores and Attributed Directed Network Mining. In IEEE 29th International Conference on Tools with Artificial Intelligence (ICTAI), To appear. Boston, MA, USA: IEEE Computer Society, 2017.
  • L-M Veillon, G Bourgne, and H Soldano. Effect of Network Topology on Neighbourhood-Aided Collective Learning. In 9th International Conference on Computational Collective Intelligence (ICCCI), Nicosia, Cyprus, 202–11. Lecture Notes in Artificial Intelligence. Springer, 2017.
  • L-M Veillon, G Bourgne, and H Soldano. Waves : A Model of Collective Learning. In 2017 IEEE/WIC/ACM International Conference on Web Intelligence (WI’17), Leipzig, Germany, 314–21. ACM, 2017.

2016

  • Michaelis, Stefan, Nico Piatkowski, and Marco Stolpe, eds. Solving Large Scale Learning Tasks. Challenges and Algorithms - Essays Dedicated to Katharina Morik on the Occasion of Her 60th Birthday. Vol. 9580. Lecture Notes in Computer Science. Springer, 2016. http://dx.doi.org/10.1007/978-3-319-41706-6.
  • C Rodrigues, H Soldano, G Bourgne, and C Rouveirol. “Collaborative Decision in Multi-Agent Learning of Action Models.” In 2016 IEEE 28th International Conference on Tools with Artificial Intelligence (ICTAI), 640–47. Los Alamitos, CA, USA: IEEE Computer Society, 2016. https://doi.org/doi.ieeecomputersociety.org/10.1109/ICTAI.2016.0103.
  • C Rodrigues, H Soldano, G Bourgne, and C Rouveirol. “Collaborative Online Learning of an Action Model.” In Solving Large Scale Learning Tasks. Challenges and Algorithms - Essays Dedicated to Katharina Morik on the Occasion of Her 60th Birthday, 300–319, 2016. https://doi.org/10.1007/978-3-319-41706-6_16.

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).