Jean-François Flot's publications list

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last update: 2017-07-31

PhD dissertation

Flot J-F (2007) Vers une taxonomie moléculaire des coraux du genre Pocillopora. (=Towards a molecular taxonomy of corals of the genus Pocillopora) PhD thesis, Muséum national d'Histoire naturelle, Paris

Articles in international peer-reviewed journals

1 - Flot J-F, Tillier A, Samadi S, Tillier S (2006) Phase determination from direct sequencing of length-variable DNA regions. Molecular Ecology Notes 6:627-630

2 - Flot J-F (2007) Champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Molecular Ecology Notes 7:974-977

3 - Flot J-F, Tillier S (2007) The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function. Gene 401:80-87

4 - Magalon H, Flot J-F, Baudry E (2007) Molecular identification of symbiotic dinoflagellates in Pacific corals in the genus Pocillopora. Coral Reefs 26:551-558

5 - Flot J-F, Magalon H, Cruaud C, Couloux A, Tillier S (2008) Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. Comptes Rendus Biologies 331:239-247

6 - Flot J-F, Licuanan W, Nakano Y, Payri C, Cruaud C, Tillier S (2008) Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region. Coral Reefs 27:789-794

7 - Flot J-F (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Molecular Ecology Resources 10:162-166

8 - Flot J-F, Wörheide G, Dattagupta S. (2010) Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy. BMC Evolutionary Biology 10:171

9 - Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton. BMC Evolutionary Biology 10:372

10 - Flot J-F, Blanchot J, Charpy L, Cruaud C, Licuanan W, Nakano Y, Payri C, Tillier S (2011) Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecology 11:22

11 - Figueiredo J, Baird A, Cohen M, Flot J-F, Kamiki T, Meziane T, Tsuchiya M, Yamasaki H (2012) Ontogenetic change in the lipid and fatty acid composition of scleractinian coral larvae. Coral Reefs 31:613-619

12 - Flot J-F, Dahl M, André C (2013) Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Research Notes 6:144

13 - Flot J-F, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, Hejnol A, Henrissat B, Koszul R, Aury J-M, Barbe V, Barthélémy R-M, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K (2013) Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500:453-457
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14 - GIGA Community of Scientists (2014) The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. Journal of Heredity 105:1-18

15 - Flot J-F, Bauermeister J, Brad T, Hillebrand-Voiculescu A, Sarbu SM, Dattagupta S (2014) Niphargus-Thiothrix associations may be widespread in sulfidic groundwater ecosystems: evidence from southeastern Romania. Molecular Ecology 23:1405-1417

16 - Adjeroud M, Guérécheau A, Vidal-Dupiol J, Flot J-F, Arnaud-Haond S, Bonhomme F (2014) Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system. Marine Biology 161:531-541

17 - Marie-Nelly H, Marbouty M, Cournac A, Flot J-F, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R (2014) High-quality genome (re)assembly using chromosomal contact data. Nature Communications 5:5695

18 - Marbouty M, Cournac A, Flot J-F, Marie-Nelly H, Mozziconacci J, Koszul R (2014) Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3:e03318

19 - Dellicour S, Flot J-F (2015) Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC. Systematic Biology 64:900-908

20 - Fontaneto D, Flot J-F, Tang CQ (2015) Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity 45:433-451

21 - Fišer C, Luštrik R, Sarbu S, Flot J-F, Trontelj P (2015) Morphological evolution of coexisting amphipod species pairs from sulfidic caves suggests competitive interactions and character displacement, but no environmental filtering and convergence. PLoS ONE 10:e0123535

22 - Flot J-F, Marie-Nelly H, Koszul R (2015) Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Letters 598:2966-2974

23 - Hespeels B, Li X, Flot J-F, Pigneur L-M, Malaisse J, Da Silva C, Van Doninck K (2015) Against all odds: trehalose-6-phosphate synthase and trehalase genes in the bdelloid rotifer Adineta vaga were acquired by horizontal gene transfer and are upregulated during desiccation. PLoS ONE 10:e0131313

24 - Flot J-F (2015) Species delimitations's coming of age. Systematic Biology 64:897-899

25 - Brad T, Fišer C, Flot J-F, Sarbu SM (2015) Niphargus dancaui sp. nov. (Amphipoda, Niphargidae) – a new species thriving in sulfidic groundwaters in southeastern Romania. European Journal of Taxonomy 164:1-28

26 - Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang CQ, Flot J-F, Van Doninck K (2016) Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex. Current Biology 26:723-732

27 - Flot J-F, Debortoli N, Hallet B, Van Doninck K (2016) Response to Signorovitch et al. Current Biology 26:R755

28 - Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot J-F, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė, Irma, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J (2016) DNAqua-Net: developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes 2:e11321

29 - Eme D, Zagmajster M, Delić T, Fišer C, Flot J-F, Konecny-Dupré L, Pálsson S, Stoch F, Zakšek V, Douady CJ, Malard F (2017) Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants. Ecography

30 - Voolstra CR, Adamski M, Agrawa S, Antunes A, Aranda M, Baxevanis A, Blaxter M, Bosch T, Bracken-Grissom H, Coddington J, Collins T, Crandall K, Dahl M, Distel D, Dunn C, Eitel M, Flot J-F, Giribet G, Ghiselli F, Haddock SHD, Kocot K, Liew YJ, Majeske A, Misof B, Mungal C, O'Brien SJ, Ravasi T, Rebelo MdF, Riesgo A, Schnitzler C, Schulze A, Swalla B, Tagu D, Toonen R, Uliano M, Vargas S, Zhou X, Wörheide G, Lopez JV (2017) Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA). Invertebrate Systematics 31:1-7

31 - Blanc-Mathieu R, Perfus-Barbeoch L, Aury J-M, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Bailly-Bechet M, Castagnone-Sereno P, Flot J-F, Kozlowski DK, Cazareth J, Couloux A, Da Silva C, Guy J, Kim-Jo Y-J, Rancurel C, Schiex T, Abad P, Wincker P, Danchin EGJ (2017) Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics 13:e1006777

32 - Johnston EC, Forsman ZH, Flot J-F, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ (2017) A genomic glance through the fog of plasticity and diversification in Pocillopora. Scientific Reports 7:5991

33 - Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic N-M, Flot J-F, Posnien N, Richards S, McGregor AP (2017) The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biology 15:62

Other journal articles

1 - Flot J-F (2010) Vers une taxonomie moléculaire des amphipodes du genre Niphargus : exemples d'utilisation de séquences d'ADN pour l'identification des espèces. (=Toward a molecular taxonomy of the amphipod genus Niphargus: examples of use of DNA sequences for species identification) Bulletin de la Société des Sciences Naturelles de l'Ouest de la France 32:62-68

2 - Flot J-F, Weber D (2013) Amphipods from caves of the Grand Duchy of Luxembourg. Ferrantia. Travaux scientifiques du Musée national d'histoire naturelle Luxembourg 69:186-192

Preprints

1 - Blanc-Mathieu R, Perfus-Babeoch L, Aury J-M, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Castagnone-Sereno P, Flot J-F, Kozlowski D, Cazareth J, Couloux A, Da Silva C, Guy J, Rancurel C, Schiex T, Abad P, Wincker P, Danchin E (2016) Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis. bioRxiv:046805

2 - Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Qu J, Ronshaugen M, Schomburg C, Schoenauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren J, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic N-M, Flot J-F, Posnien N, Richards S, McGregor AP (2017) The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. bioRxiv:1063855

Book chapters

1 - Flot J-F, Adjeroud M (2009) Les coraux. In: Charpy L (ed) Clipperton, environnement et biodiversité d'un microcosme océanique (Patrimoines Naturels 68). Muséum national d'Histoire naturelle, Paris & IRD, Marseille, pp155-162

2 - Danchin EGJ, Flot J-F, Perfus-Barbeoch L, Van Doninck K (2011) Genomic perspectives on the long-term absence of sexual reproduction in animals. In: Pontarotti P (ed) Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution. Springer, Berlin Heidelberg, pp223-242

3 - Hespeels B, Flot J-F, Derzelle A, Van Doninck K (2014) Evidence for ancient horizontal gene acquisitions in bdelloid rotifers of the genus Adineta. In: Pontarotti P (ed.) Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Springer International Publishing, pp207-225

Peer-reviewed conference proceedings

1 - Flot J-F, Ozouf-Costaz C, Tsuchiya M, van Woesik R (2006) Comparative coral cytogenetics. Proceedings of the 10th International Coral Reef Symposium 1:4-8

2 - Flot J-F, Tillier S (2006) Molecular phylogeny and systematics of the scleractinian coral genus Pocillopora in Hawaii. Proceedings of the 10th International Coral Reef Symposium 1:24-29

Other conference proceedings

1 - Flot J-F, Cady SL (2002) Microbial silicification trends in alkaline hot springs, Yellowstone National Park, USA. In: Lacoste H (ed) Proceedings of the Second European Workshop on Exo-Astrobiology, Graz, Austria, 16-19 September 2002 (ESA SP-518, November 2002). ESA Publications Division, Noordwijk, Netherlands, pp453-454

2 - Flot J-F, Cady SL (2003) Formation of thermophilic streamer biosignatures, Yellowstone National Park, USA. In: Celnikier LM, Tran Thanh Van J (eds) Frontiers of Life. Proceedings of the XIIth Rencontres de Blois. The Gioi, Hanoi, pp133-135

Selected conference presentations

1 - Flot J-F (2011) Haplowebs: a graphical method for species delimitation. Poster presented at the 22nd Pacific Science Congress in Kuala Lumpur (Malaysia), 14-17 June 2011

2 - Flot J-F, Van Doninck K (2011) Genomic consequences of long-term asexuality in the bdelloid rotifer Adineta vaga. Poster presented at the 13th Congress of the European Society for Evolutionary Biology, Tübingen (Germany), 20-25 August 2011

Resources and teaching materials

1 - Flot J-F (2016) Haplowebs: delimiting species using heterozygosity.

2 - Flot J-F (2017) (Meta)genome assembly: a primer.