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Florian Maumus

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Publications

The era of reference genomes in conservation genomics

Florian Maumus , Giulio Formenti , Kathrin Theissinger , Carlos Fernandes , Iliana Bista et al.
Trends in Ecology & Evolution, 2022, ⟨10.1016/j.tree.2021.11.008⟩
Journal articles hal-03542391v1
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CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes

Héléna Vassilieff , Sana Haddad , Véronique Jamilloux , Nathalie Choisne , Vikas Sharma et al.
Mobile DNA, 2022, 13, pp.31. ⟨10.1186/s13100-022-00288-w⟩
Journal articles hal-03883611v1
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Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci

Clément Gilbert , Florian Maumus
Genome Biology and Evolution, 2022, 14 (10), ⟨10.1093/gbe/evac141⟩
Journal articles hal-03846467v1

Gene-rich UV sex chromosomes harbor conserved regulators of sexual development

Sarah Carey , Jerry Jenkins , John Lovell , Florian Maumus , Avinash Sreedasyam et al.
Science Advances , 2021, 7 (27), pp.eabh2488. ⟨10.1126/sciadv.abh2488⟩
Journal articles hal-03283299v1

Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

Noe Fernandez‐pozo , Timo Metz , Jake Chandler , Lydia Gramzow , Zsuzsanna Mérai et al.
Plant Journal, 2021, ⟨10.1111/tpj.15161⟩
Journal articles hal-03135342v1
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Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah Farhat , Phuong Le , Ehsan Kayal , Benjamin Noel , Estelle Bigeard et al.
BMC Biology, 2021, 19 (1), ⟨10.1186/s12915-020-00927-9⟩
Journal articles hal-03114990v1

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Michael Alonge , Xingang Wang , Matthias Benoit , Sebastian Soyk , Lara Pereira et al.
Cell, 2020, 182 (1), pp.145-161.e23. ⟨10.1016/j.cell.2020.05.021⟩
Journal articles hal-02927024v1
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Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants

Vikas Sharma , Pierre Lefeuvre , Philippe Roumagnac , Denis Filloux , Pierre-Yves Teycheney et al.
Virus Evolution, 2020, 6 (2), ⟨10.1093/ve/veaa071⟩
Journal articles hal-02946712v1
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Current status of the multinational Arabidopsis community

Keith Adams , Wagner Araújo , Sebastien Aubourg , Sacha Baginsky , Erica Bakker et al.
Plant Direct, 2020, 4 (7), pp.e00248. ⟨10.1002/pld3.248⟩
Journal articles hal-02927028v1

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Michael Sparks , Raman Bansal , Joshua Benoit , Michael Blackburn , Hsu Chao et al.
BMC Genomics, 2020, 21 (1), ⟨10.1186/s12864-020-6510-7⟩
Journal articles hal-02927020v1
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Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Sylvain Legrand , Thibault Caron , Florian Maumus , Sol Schvartzman , Leandro Quadrana et al.
Mobile DNA, 2019, 10 (1), pp.1-17. ⟨10.1186/s13100-019-0171-6⟩
Journal articles hal-02265374v1
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RepetDB: a unified resource for transposable element references

Joëlle Amselem , Guillaume Cornut , Nathalie Choisne , Michael Alaux , Françoise Alfama Depauw et al.
Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩
Journal articles hal-02625212v1

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Daniel Lang , Kristian Ullrich , Florent Murat , Jörg Fuchs , Jerry Jenkins et al.
Plant Journal, 2018, 93 (3), pp.515 - 533. ⟨10.1111/tpj.13801⟩
Journal articles hal-01760352v1

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

Shira Corem , Adi Doron Faigenboim , Ophélie Jouffroy , Florian Maumus , Tzahi Arazi et al.
The Plant cell, 2018, 30 (7), pp.1628-1644. ⟨10.1105/tpc.18.00167⟩
Journal articles hal-02628646v1

The Chara genome

Tomoaki Nishiyama , Hidetoshi Sakayama , Jan de Vries , Henrik Buschmann , Denis Saint-Marcoux et al.
Cell, 2018, 174 (2), pp.448-464.e24. ⟨10.1016/j.cell.2018.06.033⟩
Journal articles hal-02624417v1
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Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat et al.
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
Journal articles hal-01820559v1
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Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae

Seydina Issa Diop , Andrew D. W. Geering , Françoise Alfama-Depauw , Mikaël Loaec , Pierre-Yves Teycheney et al.
Scientific Reports, 2018, 8, pp.1-9. ⟨10.1038/s41598-017-16399-x⟩
Journal articles hal-02626005v1
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Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

Achal Rastogi , Uma Maheswari , Richard Dorrell , Fabio Rocha Jimenez Vieira , Florian Maumus et al.
Scientific Reports, 2018, 8 (1), pp.1-14. ⟨10.1038/s41598-018-23106-x⟩
Journal articles hal-02366536v1
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Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.
Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩
Journal articles hal-01500475v1

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Thomas Mock , Robert P Otillar , Jan Strauss , Mark Mcmullan , Pirita Paajanen et al.
Nature, 2017, 541, pp.536-540. ⟨10.1038/nature20803⟩
Journal articles hal-01587937v1
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De novo assembly of a new Solanum pennellii accession using nanopore sequencing

Maximilian H.-W. Schmidt , Alexander Vogel , Alisandra K. Denton , Benjamin Istace , Alexandra Wormit et al.
The Plant cell, 2017, 29, pp.2336-2348. ⟨10.1105/tpc.17.00521⟩
Journal articles hal-02625700v1
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Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury et al.
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Journal articles hal-01633879v1
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Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.
Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩
Journal articles hal-01588181v1
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Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Swaraj Basu , Shrikant Patil , Daniel Mapleson , Monia Teresa Russo , Laura Vitale et al.
New Phytologist, 2017, 215 (1), pp.140-156. ⟨10.1111/nph.14557⟩
Journal articles hal-01607004v1
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Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015)

Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero , Richard Cooke et al.
Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩
Journal articles hal-02630062v1
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Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

Ophélie Jouffroy , Surya Saha , Lukas Mueller , Hadi Quesneville , Florian Maumus et al.
BMC Genomics, 2016, 17 (1), pp.1-15. ⟨10.1186/s12864-016-2980-z⟩
Journal articles hal-02631886v1
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Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of Amoeba-infecting viruses

Florian Maumus , Guillaume Blanc
Genome Biology and Evolution, 2016, 8 (11), pp.3351-3363. ⟨10.1093/gbe/evw260⟩
Journal articles hal-01604735v1

Impact and insights from ancient repetitive elements in plant genomes

Florian Maumus , Hadi Quesneville
Current Opinion in Plant Biology, 2016, 30, pp.41-46. ⟨10.1016/j.pbi.2016.01.003⟩
Journal articles hal-02638420v1
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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Jeanine L. Olsen , Pierre Rouzé , Bram Verhelst , Yao-Cheng Y.-C. Lin , Till Bayer et al.
Nature, 2016, 530 (7590), pp.331-335. ⟨10.1038/nature16548⟩
Journal articles hal-01289099v1

Giant viruses at the core of microscopic wars with global impacts

Adrien Villain , Lucie Gallot-Lavallee , Guillaume Blanc , Florian Maumus
Current Opinion in Virology, 2016, 17, pp.130-137. ⟨10.1016/j.coviro.2016.03.007⟩
Journal articles hal-02639930v1
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Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses

Guillaume Blanc , Lucie Gallot-Lavallee , Florian Maumus
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (38), pp.E5318-E5326. ⟨10.1073/pnas.1506469112⟩
Journal articles hal-02639645v1
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A new approach for annotation of transposable elements using small RNA mapping.

Moaine El Baidouri , Kyung Do Kim , Brian Abernathy , Siwaret Arikit , Florian Maumus et al.
Nucleic Acids Research, 2015, 43 (13), pp.e84. ⟨10.1093/nar/gkv257⟩
Journal articles hal-01215276v1

Impact of transposable elements on insect genomes and biology

Florian Maumus , Anna-Sophie Fiston-Lavier , Hadi Quesneville
Current Opinion in Insect Science, 2015, 7, pp.30-36. ⟨10.1016/j.cois.2015.01.001⟩
Journal articles hal-02640108v1

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Eva-Maria Willing , Vimal Rawat , Terezie Mandáková , Florian Maumus , Geo Velikkakam James et al.
Nature Plants, 2015, 1 (2), pp.14023-14028. ⟨10.1038/nplants.2014.23⟩
Journal articles hal-01179557v1
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Understanding Brassicaceae evolution through ancestral genome reconstruction

Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero Villanueva , Richard Cooke et al.
Genome Biology, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩
Journal articles hal-01281832v1
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Plant genomes enclose footprints of past infections by giant virus relatives

Florian Maumus , Aline Epert , Fabien Nogué , Guillaume Blanc
Nature Communications, 2014, 5, ⟨10.1038/ncomms5268⟩
Journal articles hal-01204072v1
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Global discovery and characterization of small non-coding RNAs in marine microalgae

Sara López-Gomollón , Matthew Beckers , Tina Rathjen , Simon Moxon , Florian Maumus et al.
BMC Genomics, 2014, 15, ⟨10.1186/1471-2164-15-697⟩
Journal articles hal-02640460v1
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Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter

Florian Maumus , Hadi Quesneville
PLoS ONE, 2014, 9 (4), ⟨10.1371/journal.pone.0094101⟩
Journal articles hal-02636753v1
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Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

Florian Maumus , Hadi Quesneville
Nature Communications, 2014, 5, 9 p. ⟨10.1038/ncomms5104⟩
Journal articles hal-02633174v1
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A call for benchmarking transposable element annotation methods.

Douglas R Hoen , Glenn Hickey , Guillaume Bourque , Josep Casacuberta , Richard Cordaux et al.
Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩
Journal articles hal-01204840v1
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Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Andrew D W Geering , Florian Maumus , Dario Copetti , Nathalie Choisne , Derrick J Zwickl et al.
Nature Communications, 2014, 5, ⟨10.1038/ncomms6269⟩
Journal articles hal-02631214v1

The genome of the stress-tolerant wild tomato species Solanum pennellii

Anthony Bolger , Federico Scossa , Marie E Bolger , Christa Lanz , Florian Maumus et al.
Nature Genetics, 2014, 46 (9), pp.1034-1038. ⟨10.1038/ng.3046⟩
Journal articles hal-01204066v1
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Pan genome of the phytoplankton Emiliania underpins its global distribution

Betsy A Read , Jessica Kegel , Mary J Klute , Alan Kuo , Stephane C Lefebvre et al.
Nature, 2013, 499 (7457), pp.209-213. ⟨10.1038/nature12221⟩
Journal articles hal-01074841v1
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Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Alaguraj Veluchamy , Xin Lin , Florian Maumus , Maximo Rivarola , Jaysheel Bhavsar et al.
Nature Communications, 2013, 4, pp.2091. ⟨10.1038/ncomms3091⟩
Journal articles hal-01545322v1

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Tanja Slotte , Khaled M Hazzouri , J Arvid Agren , Daniel Koenig , Florian Maumus et al.
Nature Genetics, 2013, 45 (7), pp.831-835. ⟨10.1038/ng.2669⟩
Journal articles hal-02650401v1

Highly Dynamic Exon Shuffling in Candidate Pathogen Receptors ... What if Brown Algae Were Capable of Adaptive Immunity?

Antonios Zambounis , Marek Elias , Lieven Sterck , Florian Maumus , Claire M. M. Gachon et al.
Molecular Biology and Evolution, 2012, 29 (4), pp.1263 - 1276. ⟨10.1093/molbev/msr296⟩
Journal articles hal-02647640v1

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias et al.
Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩
Journal articles hal-02649287v1
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Stemming epigenetics in marine stramenopiles

Florian Maumus , Pablo Rabinowicz , Chris Bowler , Máximo Rivarola
Current Genomics, 2011, 12 (5), pp.357-370
Journal articles hal-02644011v1
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The gypsy database (GyDB) of mobile genetic elements: release 2.0

Carlos Llorens , Ricardo Futami , Laura Covelli , Laura Dominguez-Escriba , Jose M. Viu et al.
Nucleic Acids Research, 2011, 39 (S1), pp.D70-D74. ⟨10.1093/nar/gkq1061⟩
Journal articles hal-02648997v1
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The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen et al.
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
Journal articles cea-00906990v1
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The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

Chris Bowler , Andrew E. Allen , Jonathan H. Badger , Jane Grimwood , Kamel Jabbari et al.
Nature, 2008, 456 (7410), pp.239-244. ⟨10.1038/nature07410⟩
Journal articles cea-00910244v1

Exploring the role of Florendovirus in plant biology

Saad Serfraz , V. Sharma , Andrew Geering , Florian Maumus , Pierre-Yves Teycheney et al.
Caribbean Science and Innovation Meeting 2019, Oct 2019, Pointe-à-Pitre (Guadeloupe), France
Conference papers hal-02575469v1

Nature, nurture and the structure of macroalgal genomes

J. Mark Cock , Jonas Collen , Lieven Sterck , Pierre Rouzé , Delphine Scornet et al.
5. European Phycological Congress, Sep 2011, Rhodes, Greece
Conference papers hal-02749757v1

Haslea ostrearia-like Diatoms: Biodiversity out of the Blue

Romain Gastineau , Nikolai Davidovich , Gert Hansen , Jan Rines , Angela Wulff et al.
Sea Plants, 71, Elsevier Ltd, pp.25, 2014, Advances in Botanical Research, 978-0-12-408062-1. ⟨10.1016/B978-0-12-408062-1.00015-9⟩
Book sections hal-02801766v1