PrePRint

• RF4DEL: A Random Forest approach for accurate deletion detection.
  Xavier R, Fiston-Lavier AS, Alves RCO*, Cherif E*. (* co-last author).
  https://doi.org/10.1101/2022.03.10.483419

In press

• TrEMOLO : Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
  Mohamed M*, Sabot F*, Varoqui M, Mugat B, Audouin K, , Pélisson A, Fiston-Lavier AS°, Chambeyron S°. (* co-first author; ° co-last author).
  https://doi.org/10.1101/2022.07.21.500944 (accepted in Genome Biology)

Published

• Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV).
  Nurul Novelia Fuandila, Anne-Sophie Gosselin-Grenet, Marie-Ka Tilak, Sven M Bergmann, Jean-Michel Escoubas, Sandro Klafack, Angela Mariana Lusiastuti, Munti Yuhana, Anna-Sophie Fiston-Lavier, Jean-Christophe Avarre, Emira Cherif.
  10.24072/pcjournal.154 – Peer Community Journal, Volume 2 (2022), article no. e44.
• Finding and Characterizing Repeats in Plant Genomes.
  Nicolas J., Tempel S., Fiston-Lavier AS., Cherif E. In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. 2022.
  https://doi.org/10.1007/978-1-0716-2067-0_18
• Involving Repetitive Regions in Scaffolding Improvement.
  Delorme Q, Costa R, Mansour Y, Fiston-Lavier AS, Chateau A. Journal of Bioinformatics and Computational Biology. Volume No., Issue No., Article No. 2140016, 2021.
  https://doi.org/10.1142/S0219720021400163
• Ten simple rules for switching from face-to-face to remote conference: an opportunity to estimate the reduction in GHG emissions.
  Guignon V, Breton C, Mariette J, Sabot F, Jumey J, Lefort V*, Fiston-Lavier AS* (*co-last author) PLoS Comp Biol. 2021.
  https://doi.org/10.1371/journal.pcbi.1009321
• PlasForest : a homology-based random forest classifier for plasmid detection in genomic datasets.
  Pradier L, Tissot T, Fiston-Lavier AS, Bedhomme S.  BMC Bioinformatics 22, 349. 2021.
  https://doi.org/10.1186/s12859-021-04270-w
• BREC: An R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes.
  Mansour Y, Chateau A, Fiston-Lavier AS. 2021. BMC Bioinformatics 22, 396 (2021).
  https://doi.org/10.1186/s12859-021-04233-1
  
• Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia.
  Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS,  Mariani J, Abyzov A, Petrov DA, Barres BA, Duncan L, Abyzov A, Vogel H, Brain Somatic Mosaicism Network, Moran, JV, Vaccarino FM, Tamminga CA,  Levinson DF, Urban AE. Nature Neuroscience. 2021.
  https://doi.org/10.1038/s41593-020-00767-4
  
• T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
  Bogaerts-Márquez M, Barrón MG, Fiston-Lavier AS, Vendrell-Mir P, Castanera R, Casacuberta JM, and González J. Bioinformatics, Volume 36, Issue 4, 15 February 2020, Pages 1191–1197.
  https://doi.org/10.1093/bioinformatics/btz727.
  
• Cyprinid herpesvirus 3 evolves in vitro through an assemblage of haplotypes that alternatively become dominant or under-represented.
  Klafack S, Fiston-Lavier AS, Bergmann S, Hammoumi S, Schroeder L, Fuchs W, Lusiastuti A, Lee P-Y,  Heredia SV, Student Consortium*, Gosselin-Grenet AS, Avarre JC. Viruses 2019, 11(8), 754.
  https://doi.org/10.3390/v1108075.
• Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.
  Rech GE, Bogaerts-Marquez M, Barron MG, Merenciano M, Villanueva-Canas JL, Horvath V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, Gonzalez J. PLoS Genetics 2019.
  https://doi.org/10.1371/journal.pgen.1007900.
  
• The somatic piRNA pathway controls germline transposition over generations.
  Barckmann B, El-Barouk M, Pélisson A, Mugat B, Li B, Franckhauser C, Fiston-Lavier AS, Mirouze M, Fablet M and Chambeyron S, 2018.  Nucleic Acids Research gky761.
• The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications.
  Assogba BS, Milesi P, Djogbénou LS, Berthomieu A, Makoundou P, Baba-Moussa LS, Fiston-Lavier AS, Belkhir K, Labbé P, Weill M. PLoS Biol. 2016 Dec 5;14(12):e2000618. doi: 10.1371/journal.pbio.2000618. eCollection 2016 Dec.
  
• A call for benchmarking transposable element annotation methods.
  Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. Mob DNA. 2015 Aug 4;6:13. doi: 10.1186/s13100-015-0044-6. eCollection 2015.
  
• Impact Of Transposable Elements On Insect Genomes And Biology.
  Fiston Lavier AS*,  Maumus F*, Quesneville H. Current Opinion in Insect Science 2015. https://doi.org/10.1016/j.cois.2015.01.001 (* co-first authors).
• T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
  Fiston-Lavier AS, Barrón MG, Petrov DA, González J. Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.
• Population genomics of transposable elements in Drosophila.
  Barrón MG, Fiston-Lavier AS, Petrov DA, González J. Annu Rev Genet. 2014;48:561-81. doi: 10.1146/annurev-genet-120213-092359. Epub 2014 Oct 1. Review.
  
• Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.
  McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA*, Fiston-Lavier AS*. PLoS One. 2014 Sep 4;9(9):e106689. doi: 10.1371/journal.pone.0106689. eCollection 2014. (co-last authors)
• Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.
  Kelley JL, Peyton JT, Fiston-Lavier AS, Teets NM, Yee MC, Johnston JS, Bustamante CD, Lee RE, Denlinger DL. Nat Commun. 2014 Aug 12;5:4611. doi: 10.1038/ncomms5611.
• Formation of plant metabolic gene clusters within dynamic chromosomal regions.
  Field B, Fiston-Lavier AS, Kemen A, Geisler K, Quesneville H, Osbourn AE. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):16116-21. doi: 10.1073/pnas.1109273108. Epub 2011 Aug 29.
• T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
  Fiston-Lavier AS, Carrigan M, Petrov DA, González J.Nucleic Acids Res. 2011 Mar;39(6):e36. doi: 10.1093/nar/gkq1291.
• Population genomics of transposable elements in Drosophila melanogaster.
  Petrov DA, Fiston-Lavier AS, Lipatov M, Lenkov K, González J. Mol Biol Evol. 2011 May;28(5):1633-44. doi: 10.1093/molbev/msq337. Epub 2010 Dec 16.
• Drosophila melanogaster recombination rate calculator.
  Fiston-Lavier AS, Singh ND, Lipatov M, Petrov DA. Gene. 2010 Sep 1;463(1-2):18-20. doi: 10.1016/j.gene.2010.04.015. Epub 2010 May 7.
• A model of segmental duplication formation in Drosophila melanogaster.
  Fiston-Lavier AS, Anxolabehere D, Quesneville H. Genome Res. 2007 Oct;17(10):1458-70. Epub 2007 Aug 28.
• Detection of transposable elements by their compositional bias.
  Andrieu O, Fiston AS, Anxolabéhère D, Quesneville H. BMC Bioinformatics. 2004. doi: 10.1186/1471-2105-5-94