Florent Murat

Documents

Publications

	FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes Jérôme Montfort , Francisca Hervas-Sotomayor , Aurélie Le Cam , Florent Murat Nucleic Acids Research, inPress, ⟨10.1093/nar/gkae264⟩ Journal articles hal-04537581v1
	Mapping pediatric brain tumors to their origins in the developing cerebellum Konstantin Okonechnikov , Piyush Joshi , Mari Sepp , Kevin Leiss , Ioannis Sarropoulos Neuro-Oncology, inPress, ⟨10.1093/neuonc/noad124⟩ Journal articles hal-04181467v1
	Cellular development and evolution of the mammalian cerebellum Mari Sepp , Kevin Leiss , Florent Murat , Konstantin Okonechnikov , Piyush Joshi Nature, 2023, ⟨10.1038/s41586-023-06884-x⟩ Journal articles hal-04315980v1
	A lamprey neural cell type atlas illuminates the origins of the vertebrate brain Francesco Lamanna , Francisca Hervas-Sotomayor , A. Phillip Oel , David Jandzik , Daniel Sobrido-Cameán Nature Ecology & Evolution, 2023, ⟨10.1038/s41559-023-02170-1⟩ Journal articles hal-04208085v1
	The molecular evolution of spermatogenesis across mammals Florent Murat , Noe Mbengue , Sofia Boeg Winge , Timo Trefzer , Evgeny Leushkin Nature, 2023, 613, pp.308-316. ⟨10.1038/s41586-022-05547-7⟩ Journal articles hal-03910315v1
	Exploring the rapid evolution of the mammalian testis Noe Mbengue , Florent Murat Nature, 2022, ⟨10.1038/d41586-022-04221-2⟩ Journal articles hal-03910316v1
	auts2 Features and Expression Are Highly Conserved during Evolution despite Different Evolutionary Fates Following Whole Genome Duplication Constance Merdrignac , Antoine Clement , Jérôme Montfort , Florent Murat , Julien Bobe Cells, 2022, 11 (17), pp.2694. ⟨10.3390/cells11172694⟩ Journal articles hal-03777731v1
	The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution Daniel Lang , Kristian Ullrich , Florent Murat , Jörg Fuchs , Jerry Jenkins Plant Journal, 2018, 93 (3), pp.515 - 533. ⟨10.1111/tpj.13801⟩ Journal articles hal-01760352v1
	Oak genome reveals facets of long lifespan Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩ Journal articles hal-01820559v1
	The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩ Journal articles hal-01603287v1
	Reconstructing the genome of the most recent common ancestor of flowering plants Florent Murat , Alix Armero Villanueva , Caroline Pont , Christophe C. Klopp , Jerome Salse Nature Genetics, 2017, 49, pp.490-496. ⟨10.1038/ng.3813⟩ Journal articles hal-01605642v1
	Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015) Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero , Richard Cooke Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩ Journal articles hal-02630062v1
	Reconciling the evolutionary origin of bread wheat (Triticum aestivum) Moaine El Baidouri , Florent Murat , Maeva Veyssière , Mélanie Molinier , Raphaël-Gauthier Flores New Phytologist, 2016, 213 (3), ⟨10.1111/nph.14113⟩ Journal articles hal-01361976v1
	Understanding Brassicaceae evolution through ancestral genome reconstruction Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero Villanueva , Richard Cooke Genome Biology, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩ Journal articles hal-01281832v1
	Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩ Journal articles hal-01579667v1
	FRIZZY PANICLE drives supernumerary spikelets in bread wheat (T. aestivum L.) Oxana Dobrovolskaya , Caroline Pont , Richard Sibout , Petr Martinek , Ekaterina Badaeva Plant Physiology, 2015, 167 (1), pp.189-199. ⟨10.1104/pp.114.250043⟩ Journal articles hal-01204099v1
	The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release Isabelle Lesur , Grégoire G. Le Provost , Pascal Bento , Corinne da Silva , Jean-Charles Leplé BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩ Journal articles hal-02285504v1
	Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops Florent Murat , Rongzhi R. Zhang , Sébastien Guizard , Haris Gavranovic , Raphael Flores Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩ Journal articles hal-01133906v1
	GenomicusPlants: a web resource to study genome evolution in flowering plants Alexandra Louis , Florent Murat , Jerome Salse , Hugues Roest Crollius Plant and Cell Physiology, 2015, 56 (1), pp.e4. ⟨10.1093/pcp/pcu177⟩ Journal articles hal-01168460v1
	Evidence of intense chromosomal shuffling during conifer evolution Marina de Miguel , Jérôme Bartholome , François Ehrenmann , Florent Murat , Yoshinari Moriguchi Genome Biology and Evolution, 2015, 7 (10), pp.evv185. ⟨10.1093/gbe/evv185⟩ Journal articles hal-02285512v1
	Paleogenomics in Triticeae for translational research Florent Murat , Caroline Pont , Jérôme Salse Current Plant Biology, 2014, 1, pp.34-39. ⟨10.1016/j.cpb.2014.08.003⟩ Journal articles hal-02285486v1
	Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication G Albert Wu , Simon Prochnik , Jerry Jenkins , Jérôme Salse , Uffe Hellsten Nature Biotechnology, 2014, 32 (7), pp.656-662. ⟨10.1038/nbt.2906⟩ Journal articles hal-02285484v1
	Paleo-evolutionary plasticity of plant disease resistance genes Rongzhi R. Zhang , Florent Murat , Caroline Pont , Thierry Langin , Jerome Salse BMC Genomics, 2014, 15 (1), pp.187. ⟨10.1186/1471-2164-15-187⟩ Journal articles hal-02285469v1
	The genome of Eucalyptus grandis Alexander Myburg , Dario Grattapaglia , Gerald Tuskan , Uffe Hellsten , Richard Hayes Nature, 2014, 510 (7505), pp.356-362. ⟨10.1038/nature13308⟩ Journal articles hal-02285478v1
	Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes Caroline C. Pont , Florent Murat , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Séverine S. Foucrier Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩ Journal articles hal-00964421v1
	The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions Shaogui Guo , Jianguo Zhang , Honghe Sun , Jerome Salse , William J. Lucas Nature Genetics, 2013, 45 (1), pp.51 - U82. ⟨10.1038/ng.2470⟩ Journal articles hal-01190670v1
	Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes Florent Murat , Rongzhi R. Zhang , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Alix A. Armero Villanueva Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩ Journal articles hal-00964190v1
	Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Florent Murat , Rongzhi Zhang , Sébastien Guizard , Raphael Flores , Alix Armero Genome Biology and Evolution, 2013, 6 (1), pp.12-33 Journal articles hal-01218128v1
	Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes Florent Murat , Yves Y. van de Peer , Jerome J. Salse Genome Biology and Evolution, 2012, 4 (9), pp.917 - 928. ⟨10.1093/gbe/evs066⟩ Journal articles hal-00964328v1
	Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication Michaël M. Abrouk , Rongzhi R. Zhang , Florent Murat , Aili A. Li , Caroline C. Pont The Plant cell, 2012, 24 (5), pp.1776 - 1792. ⟨10.1105/tpc.112.095752⟩ Journal articles hal-00964371v1
	Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses Bianca Dibari , Florent Murat , Audrey Chosson , Véronique Gautier , Charles C. Poncet BMC Genomics, 2012, 13 (1), pp.221. ⟨10.1186/1471-2164-13-221⟩ Journal articles hal-02285438v1
	Comparative mapping in the Fagaceae and beyond with EST-SSRs Catherine Bodenes-Brezard Bodénès , Emilie E. Chancerel , Oliver O. Gailing , Giovanni G. G. G. Vendramin , Francesca F. Bagnoli BMC Plant Biology, 2012, 12 (153), 40 p. ⟨10.1186/1471-2229-12-153⟩ Journal articles hal-00964224v1
	Unlocking the barley genome by chromosomal and comparative genomics Klaus F. X. K. F. X. Mayer , Mihaela M. Martis , Pete E. P. E. Hedley , Hana H. Simkova , Hui H. Liu The Plant cell, 2011, 23 (4), pp.1249-1263. ⟨10.1105/tpc.110.082537⟩ Journal articles hal-00964348v1
	The genome of Theobroma cacao. Xavier Argout , Jerome Salse , Jean-Marc Aury , Mark J Guiltinan , Gaetan Droc Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩ Journal articles hal-00855922v1
	Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.) Umar Masood Quraishi Masood-Quraishi , Florent Murat , Michaël M. Abrouk , Caroline C. Pont , Carole C. Confolent Functional and Integrative Genomics, 2011, 11 (1), pp.71 - 83. ⟨10.1007/s10142-010-0183-2⟩ Journal articles hal-00964164v1
	Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L. Amandine A. Bordat , Vincent V. Savois , Marie M. Nicolas , Jerome J. Salse , Aurelie A. Chauveau G3, 2011, 1 (juillet), pp.93-103. ⟨10.1534/g3.111.000349⟩ Journal articles hal-00964213v1
	RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) Caroline Pont , Florent Murat , Carole Confolent , Sandrine Balzergue , Jerome Salse Genome Biology, 2011, 12 (12), ⟨10.1186/gb-2011-12-12-r119⟩ Journal articles hal-01190508v1
	Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution Umar Masood Quraishi Masood-Quraishi , Michaël M. Abrouk , Florent Murat , Caroline C. Pont , Séverine S. Foucrier Plant Journal, 2011, 65 (5), pp.745 - 756. ⟨10.1111/j.1365-313X.2010.04461.x⟩ Journal articles hal-00964149v1
	Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Michael Abrouk , Florent Murat , Caroline Pont , Joachim Messing , Scott Jackson Trends in Plant Science, 2010, 15 (9), pp.479-87. ⟨10.1016/j.tplants.2010.06.001⟩ Journal articles hal-00681093v1
	Genome sequencing and analysis of the model grass Brachypodium distachyon Jerome J. Salse , Florent Murat , Michaël M. Abrouk , Elisabeth E.J. Chapman , Richard R. Sibout Nature, 2010, 463, pp.763-768. ⟨10.1038/nature08747⟩ Journal articles hal-00964370v1
	Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. Saneyoshi Ueno , Grégoire Le Provost , Valérie Léger , Christophe C. Klopp , Céline Noirot BMC Genomics, 2010, 11, pp.650. ⟨10.1186/1471-2164-11-650⟩ Journal articles hal-00645933v1
	Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Florent Murat , Jian-Hong Xu , Eric Tannier , Michael Abrouk , Nicolas Guilhot Genome Research, 2010, 20 (11), pp.1545-57. ⟨10.1101/gr.109744.110⟩ Journal articles hal-00680636v1
	Improved criteria and comparative genomics tool provide new insights into grass paleogenomics Jerome J. Salse , Michaël M. Abrouk , Florent Murat , Umar Masood Quraishi Masood-Quraishi , Catherine C. Feuillet Briefings in Bioinformatics, 2009, 10 (6), pp.619-630. ⟨10.1093/bib/bbp037⟩ Journal articles hal-00964321v1

	FEVER: An interactive web-based resource for evolutionary transcriptomics across fishes Jérôme Montfort , Francisca Hervas-Sotomayor , Aurélie Le Cam , Florent Murat 2024 Preprints, Working Papers, ... hal-04536177v1
	Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas Francesco Lamanna , Francisca Hervas-Sotomayor , A. Phillip Oel , David Jandzik , Daniel Sobrido-Cameán 2022 Preprints, Working Papers, ... hal-03593464v1
	Cellular development and evolution of the mammalian cerebellum Mari Sepp , Kevin Leiss , Ioannis Sarropoulos , Florent Murat , Konstantin Okonechnikov 2022 Preprints, Working Papers, ... hal-03516528v1
	Mapping pediatric brain tumors to their origins in the developing cerebellum Konstantin Okonechnikov , Piyush Joshi , Mari Sepp , Kevin Leiss , Ioannis Sarropoulos 2022 Preprints, Working Papers, ... hal-03516521v1
	The molecular evolution of spermatogenesis across mammals Florent Murat , Noe Mbengue , Sofia Boeg Winge , Timo Trefzer , Evgeny Leushkin 2022 Preprints, Working Papers, ... hal-03516462v1

	The molecular evolution of spermatogenesis across mammals Florent Murat ReproSciences, May 2023, Paris, France Conference papers hal-04093483v1
	Integrating TGF-beta signalling pathways and epigenetic modulations for controlling sex determination in medaka Alexandra Depince , Florent Murat , Mateus Contar Adolfi , Violette Thermes , Yann Guiguen 2. European Symposium on Sex Determination in Vertebrates, Oct 2022, Giens, France Conference papers hal-03833209v1
	The molecular evolution of spermatogenesis across mammals Florent Murat 2. European Symposium on Sex Determination in Vertebrates, Oct 2022, Hyères, France Conference papers hal-03910317v1
	An integrated information system dedicated to oak genomics and genetics Joëlle Amselem , Nicolas Francillonne , Célia Michotey , Thomas Letellier , Jean-Marc Aury PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides Conference papers hal-01839185v1
	Oak genome sequencing and evolution Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p Conference papers hal-02741698v1
	Evidence of intense chromosomal shuffling during conifer evolution Marina de Miguel , Jérôme Bartholome , François Ehrenmann , Florent Murat , Yoshinari Moriguchi ProCoGen final open conference, Promoting Conifer Genomic Resources, Nov 2015, Orléans, France. 75 p Conference papers hal-02741312v1
	Bioinformatic analysis of Sanger and 454 ESTs in oak Saneyoshi S. Ueno , Grégoire G. Le Provost , Valérie V. Léger , Christophe C. Klopp , Celine C. Noirot Conference on Forest Ecosystem Genomics and Adaptation, Jun 2010, Madrid, Spain. pp.73 Conference papers hal-00964385v1

	Investigating the role of gene duplication in fish phenotypic evolution Jérôme Montfort , Yann Guiguen , Florent Murat The evolution of animal genomes / EMBO workshop, Sep 2023, Sevilla, Spain Conference poster hal-04320410v1
	auts2 expression is highly conserved during evoluion despite different evolutionary fates following whole genome duplication Constance Merdrignac , Antoine Clement , Jérôme Montfort , Florent Murat , Julien Bobe International Congres on the Biology of Fish, Jun 2022, Montpellier, France Conference poster hal-03777897v1
	From whole-genome scans for divergence to the discovery of speciation genes in oaks Thibault Leroy , Jean Marc Aury , Catherine Bodenes-Brezard Bodénès , Laure Villate , Grégoire G. Le Provost 15. Congress of the European Society for Evolutionary Biology (ESEB), Aug 2015, Lausanne, Switzerland. , 1 p., 2015 Conference poster hal-02797182v1

	Improvement of the grain filling of wheat through the modulation of NADH-glutamate synthase activity Jerome Salse , Umar Masood Quraishi , Caroline C. Pont , Florent Murat , Jacques Le Gouis France, Patent n° : WO/2011/095958. 2010 Patents hal-02809507v1

	Etude de la plasticité évolutive et structurale des génomes de plantes Florent Murat Sciences du Vivant [q-bio]. Université Blaise Pascal (Clermont Ferrand 2), 2016. Français. ⟨NNT : ⟩ Theses tel-02796944v1

Florent Murat

Publications

FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes

Mapping pediatric brain tumors to their origins in the developing cerebellum

Cellular development and evolution of the mammalian cerebellum

A lamprey neural cell type atlas illuminates the origins of the vertebrate brain

The molecular evolution of spermatogenesis across mammals

Exploring the rapid evolution of the mammalian testis

auts2 Features and Expression Are Highly Conserved during Evolution despite Different Evolutionary Fates Following Whole Genome Duplication

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

Oak genome reveals facets of long lifespan

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Reconstructing the genome of the most recent common ancestor of flowering plants

Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015)

Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Understanding Brassicaceae evolution through ancestral genome reconstruction

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

FRIZZY PANICLE drives supernumerary spikelets in bread wheat (T. aestivum L.)

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

GenomicusPlants: a web resource to study genome evolution in flowering plants

Evidence of intense chromosomal shuffling during conifer evolution

Paleogenomics in Triticeae for translational research

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Paleo-evolutionary plasticity of plant disease resistance genes

The genome of Eucalyptus grandis

Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes

Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.

Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

Comparative mapping in the Fagaceae and beyond with EST-SSRs

Unlocking the barley genome by chromosomal and comparative genomics

The genome of Theobroma cacao.

Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.)

Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L.

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution

Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.

Improved criteria and comparative genomics tool provide new insights into grass paleogenomics

FEVER: An interactive web-based resource for evolutionary transcriptomics across fishes

Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas

Cellular development and evolution of the mammalian cerebellum

Mapping pediatric brain tumors to their origins in the developing cerebellum

The molecular evolution of spermatogenesis across mammals

The molecular evolution of spermatogenesis across mammals

Integrating TGF-beta signalling pathways and epigenetic modulations for controlling sex determination in medaka

The molecular evolution of spermatogenesis across mammals

An integrated information system dedicated to oak genomics and genetics

Oak genome sequencing and evolution

Evidence of intense chromosomal shuffling during conifer evolution

Bioinformatic analysis of Sanger and 454 ESTs in oak

Investigating the role of gene duplication in fish phenotypic evolution

auts2 expression is highly conserved during evoluion despite different evolutionary fates following whole genome duplication

From whole-genome scans for divergence to the discovery of speciation genes in oaks

Improvement of the grain filling of wheat through the modulation of NADH-glutamate synthase activity

Etude de la plasticité évolutive et structurale des génomes de plantes