Publications des membres de l'ABI

(depuis 2016)

Journaux internationaux


  • L. Caputi, Q. Carradec,D. Eveillard, A. Kirilovsky, E. Pelletier, J.J. Pierella Karlusich, … M. Boccara ,... et al. (2019). Community‐level responses to iron availability in open ocean planktonic ecosystems. Global Biogeochemical Cycles , 33
  • J Auvinet, P. Graça, L. Ghigliotti, E. Pisano, A. Dettaï, C. Ozouf-Costaz, and D. Higuet. 2019. Insertion Hot Spots of DIRS1 Retrotransposon and Chromosomal Diversifications among the Antarctic Teleosts Nototheniidae. Int. J. Mol. Sci. 20:701.
  • 2018

    • B. Charrier, H. Rabillé, B. Billoud, Gazing at Cell Wall Expansion under a Golden Light. Trends in plant science 2018-11 (2018) DOI: 10.1016/j.tplants.2018.10.013 PMID: 30472067
    • H. Rabillé, B. Billoud, É Rolland, B. Charrier, Dynamic and microscale mapping of cell growth: Case of Ectocarpus filament cells. in: Protocols for Macroalgae Research (B. Charrier, T. Wichard, C. R. K. Reddy Eds.), pp. 349--364 (2018) isbn 978-1-4987-9642-2, https://www.kriso.ee/db/9781498796422.html
    • R. Lagadec, M. Lanoizelet, N. Sánchez-Farías, F. Hérard, A. Menuet, H. Mayeur, B. Billoud, I. Rodriguez-Moldes, E. Candal, D. Mazan, Neurogenetic asymmetries in the catshark developing habenulae: mechanistic and evolutionary implications. Scientific Reports 8(1):4616 (2018) doi: 10.1038/s41598-018-22851-3 PMID: 29545638
    • T Nogueira, PHC David, J Pothier Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach Drug Development Research 10-2018 doi:10.1002/ddr.21466
    • F El Sayed, G Sapriel , N Fawal, A Gruber, T Bauer, B Heym, C Dupont, HJ Garchon, JL Gaillard, M Rottman, SLe Hello. In-Host Adaptation of Salmonella enterica Serotype Dublin during Prosthetic Hip Joint Infection. Emerg Infect Dis. 2018 Dec;24(12):2360-2363. doi: 10.3201/eid2412.180214.
    • L Ferretti, A Klassman, AM Ferrer, E Raineri, T Wiehe, S Ramos-Onsins and G Achaz. The neutral frequency spectrum of linked sites. Theoretical Population Biology (2018), 123:70-79.
    • G Achaz, A Lambert and E Schertzer. The sequential loss of the allelic diversity. Journal of Applied Probability. (2018), 50(A):13-29
    • L Ferretti, D Weinreich, F Tajima and G Achaz Evolutionary constraints in fitness landscapes. Heredity. (2018), 121:466-481.
    • G Achaz, S Gangloff and B. Arcangioli. The quiescent X, the replicative Y and the Autosomes. bioRxiv 351288, ver 3 peer-reviewed and recommended by PCI Evol Biol (2019). DOI: 10.1101/351288
    • G Achaz. Which model(s) explain(s) biodiversity. In: Evolution & Biodiversity (2018), ISTE Editions, in press.
    • S Shanthirabalan, J Chomilier J, M Carpentier. Structural effects of point mutations in proteins. Proteins. 2018 Mar 22. doi: 10.1002/prot.25499
    • Z Landoulsi, F Laatar, E Noé, S Mrabet, M Ben Djebara, G Achaz, C Nava, S Baulac, I Kacem, A Gargori-Berrechidi, R Gouider, E Leguern. Clinical and genetic study of Tunisian families with Genetic Generalized Epilepsy: contribution of CACNA1H and MAST4 genes. Neurogenetics. (2018), in press
    • S Baldassari, F Picard, ..., G Achaz, ... and S Baulac [87 co-authors] The landscape of epilepsy-related GATOR1 variants. Genetics in Medicine (2018)
    • 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 (2018), 35(3):631-645.
    • S Bridel, AB Olsen, H Nilsen, J-F Bernardet, G Achaz, R Avendan ̃o-Herrera and E Duchaud. Comparative genomics of Tenacibaculum dicentrarchi and “Tenacibaculum finnmarkense” highlights intricate evolution of fish-pathogenic species. Genom Biol Evol (2018), 10 (2), 452-457.
    • S Matuszewski, ME Hildebrandt, G Achaz and JD Jensen. Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography, Genetics. 2018 Jan;208(1):323-338. doi: 10.1534/genetics.117.300499.


    • S Gangloff *, G Achaz *, S Miled, C Denis A Villain and B Arcangioli. Quiescence: the unforseen mutations, eLife, doi: 10.7554/eLife.27469
    • 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)


    • 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.

    Actes de conférences internationales avec comité de lecture (Informatique)


  • LM Veillon, G Bourgne, H Soldano Better Collective Learning with Consistency Guarantees - Lecture Notes in Computer Science vol 11224:671–679
  • H Soldano, G Santini, D Bouthinon, S Bary, E Lazega - Bi-Pattern Mining of Two Mode and Directed Networks 2018 WWW Companion Volume 1287--1294
  • H Soldano, S Bary, G Santini, D Bouthinon - Core Stratification of Two-Mode - Studies in Computational Intelligence 2018 vol 812:130--142
  • 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.


    • 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.