Institut de Biologie de l'École Normale Supérieure ENS . CNRS UMR8197 . Inserm U1024 Directeur : Pierre Paoletti

2024

• Elise Parey, Camille Berthelo, tHugues Roest Crollius, Yann Guiguen. Solving an enigma in the tree of life, at the origins of teleost fishes Comptes Rendus. Biologies, Volume 347 (2024), pp. 1-8. (March 2023)

2023

• Raphaël Bricout, Dominique Weil, David Stroebel, Auguste Genovesio, Hugues Roest Crollius. Evolution is not uniform along coding sequences Molecular Biology and Evolution (March 2023)
• Elise Parey, Hugues Roest Crollius & Camille Berthelot. SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event. Part of the Methods in Molecular Biology book series. Polyploidy
  Methods and Protocols. (Feb 2023)
• Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Céline Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cécile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cédric Cabau, Christophe Klopp, Andrew Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius and Yann Guiguen. Genome structures resolve the early diversification of teleost fishes. Science (Jan 2023)
• Matthieu Muffato, Alexandra Louis, Nga Thi Thuy Nguyen, Joseph M. Lucas, Camille Berthelot, Hugues Roest Crollius. Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom. Nat Ecol Evol (Jan 2023).

2022

• Franklin Delehelle, Hugues Roest Crollius. FUSTA : leveraging FUSE for manipulation of multiFASTA files at scale.
  Bioinformatics advances, Volume 2, Issue 1, 2022.
• Elise Parey, Alexandra Louis, Jerome Montfort, Yann Guiguen, Hugues Roest Crollius, and Camille Berthelot. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication Genome Research. Published in Advance August 12, 2022.
• Moyon L, Berthelot C, Louis A, Nguyen NTT, Roest Crollius H. Classification of non-coding variants with high pathogenic impact. PLoS Genetics., 2022 ;

2021

• Nga Thi Thuy Nguyen, Pierre Vincens, Jean François Dufayard, Hugues Roest Crollius, Alexandra Louis, Genomicus in 2022 : comparative tools for thousands of genomes and reconstructed ancestors, Nucleic Acids Research, 2021 ;
• Jean-François Dufayard, Stéphanie Bocs, Valentin Guignon, Delphine Larivière, Alexandra Louis, Nicolas Oubda, Mathieu Rouard, Manuel Ruiz, Frédéric de Lamotte, RapGreen, an interactive software and web package to explore and analyze phylogenetic trees, NAR Genomics and Bioinformatics, Volume 3, Issue 3, September 2021
• Andrew W. Thompson, M. Brent Hawkins, Elise Parey, Dustin J. Wcisel, Tatsuya Ota, Kazuhiko Kawasaki, Emily Funk, Mauricio Losilla, Olivia E. Fitch, Qiaowei Pan, Romain Feron, Alexandra Louis, Jérôme Montfort, Marine Milhes, Brett L. Racicot, Kevin L. Childs, Quenton Fontenot, Allyse Ferrara, Solomon R. David, Amy R. McCune, Alex Dornburg, Jeffrey A. Yoder, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Matthew P. Harris & Ingo Braasch. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nature Genetics 2021 august 30.

2020

• Elise Parey, Alexandra Louis, Cédric Cabau, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications, Molecular Biology and Evolution, 2020 June 18
  

• Yves Clément, Patrick Torbey, Pascale Gilardi-Hebenstreit, Hugues Roest Crollius, Enhancer–gene maps in the human and zebrafish genomes using evolutionary linkage conservation, Nucleic Acids Research, 2020 Jan 16

2019

• Justine Dardaillon, Delphine Dauga, Paul Simion, Emmanuel Faure, Takeshi A Onuma, Melissa B DeBiasse, Alexandra Louis, Kazuhiro R Nitta, Magali Naville, Lydia Besnardeau, Wendy Reeves, Kai Wang, Marie Fagotto, Marion Guéroult-Bellone, Shigeki Fujiwara, Rémi Dumollard, Michael Veeman, Jean-Nicolas Volff, Hugues Roest Crollius, Emmanuel Douzery, Joseph F Ryan, Bradley Davidson, Hiroki Nishida, Christelle Dantec, Patrick Lemaire, ANISEED 2019 : 4D exploration of genetic data for an extended range of tunicates, Nucleic Acids Research, 2019 Nov 04

2018

• Camille Berthelot, Jane Clarke, Thomas Desvignes, H William Detrich, Paul Flicek, Lloyd S Peck, Michael Peters, John H Postlethwait, Melody S Clark ; Adaptation of proteins to the cold in Antarctic fish : A role for Methionine ? Genome Biology and Evolution , 2018 Nov 29

• Ferdinand Marlétaz, Panos N Firbas, Ignacio Maeso, Juan J Tena, Ozren Bogdanovic, Malcolm Perry, Christopher D R Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael D Acemel, Simon J van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna Kozmikova, Jon Permanyer, Alexandra Louis, Beatriz Albuixech-Crespo, Yann Le Petillon, Anthony Leon, Lucie Subirana, Piotr J Balwierz, Paul Edward Duckett, Ensieh Farahani, Jean-Marc Aury, Sophie Mangenot, Patrick Wincker, Ricard Albalat, Èlia Benito-Gutiérrez, Cristian Cañestro, Filipe Castro, Salvatore D’Aniello, David E K Ferrier, Shengfeng Huang, Vincent Laudet, Gabriel A B Marais, Pierre Pontarotti, Michael Schubert, Hervé Seitz, Ildiko Somorjai, Tokiharu Takahashi, Olivier Mirabeau, Anlong Xu, Jr-Kai Yu, Piero Carninci, Juan Ramon Martinez-Morales, Hugues Roest Crollius, Zbynek Kozmik, Matthew T Weirauch, Jordi Garcia-Fernàndez, Ryan Lister, Boris Lenhard, Peter W H Holland, Hector Escriva, Jose Luis Gómez-Skarmeta, and Manuel Irimia (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature, 2018 Nov 21

• Sacerdot,C., Louis, A., Bon, C., Berthelot, C., Roest Crollius, H. (2018) Chromosome evolution at the origin of the ancestral vertebrate genome Genome Biology, 2018 Oct 17

2017

• Berthelot,C., Villar,D., Horvath,J., Odom,D., Flicek,P. (2017) Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression Nature Ecology and Evolution, 2017 Nov 27

• Brozovic,M., Dantec,C., Dardaillon,J., Dauga, D., Faure E., Gineste, M., Louis,A. et al (2017) ANISEED 2017 : extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res, 2017 Nov 15.

• Chica,C., Louis,A., Roest Crollius,H., Colot,V. and Roudier,F. (2017) Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. Genome Biology, 18, 207.

• Nguyen,N.T.T., Vincens,P., Roest Crollius,H. and Louis,A. (2017) Genomicus 2018 : karyotype evolutionary trees and on-the-fly synteny computing. Nucleic Acids Res, 2017 Oct 26.

• Pasquier J, Braasch I, Batzel P, Cabau C, Montfort J, Nguyen T, Jouanno E, Berthelot C, Klopp C, Journot L, Postlethwait JH, Guiguen Y, Bobe J. Evolution of gene expression after whole-genome duplication : New insights from the spotted gar genome. J Exp Zool (Mol Dev Evol). 2017 ;00:1–13. doi : 10.1002/jez.b.22770

• Bal E, Park HS, Belaid-Choucair Z, Kayserili H, Naville M, Madrange M, Chiticariu E, Hadj-Rabia S, Cagnard N, Kuonen F, Bachmann D, Huber M, Le Gall C, Côté F, Hanein S, Rosti RÖ, Aslanger AD, Waisfisz Q, Bodemer C, Hermine O, Morice-Picard F, Labeille B, Caux F, Mazereeuw-Hautier J, Philip N, Levy N, Taieb A, Avril MF, Headon DJ, Gyapay G, Magnaldo T, Fraitag S, Roest Crollius H, Vabres P, Hohl D, Munnich A, Smahi A. Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas. Nature Medicine. 23, 1226–1233 (2017) doi : 10.1038/nm.4368.

• Lucas JM, Roest Crollius H. High precision detection of conserved segments from synteny blocks. PLoS One. 2017 Jul 3 ;12(7):e0180198. doi : 10.1371/journal.pone.0180198

• Khalaf-Nazzal R, Stouffer MA, Olaso R, Muresan L, Roumegous A, Lavilla V, Carpentier W, Moutkine I, Dumont S, Albaud B, Cagnard N, Roest Crollius H, Francis F.(2017). Early born neurons are abnormally positioned in the doublecortin knockout hippocampus. Hum Mol Genet. 26(1):90-108.

2016

• Noizet M, Lagoutte E, Gratigny M, Bouschbacher M, Lazareth I, Roest Crollius H, Darzacq X, Dugast-Darzacq C.(2016).Master regulators in primary skin fibroblast fate reprogramming in a human ex vivo model of chronic wounds.Wound Repair Regen. 24(2):247-62.

2015

• Murat F, Louis A, Maumus F, Armero A,Cooke R,Quesneville H, Roest Crollius H and Salse J (2015). Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biology 16, 262.

• Naville M, Ishibashi M, Ferg M, Bengani H, Rinkwitz S, Krecsmarik M, Hawkins T, Wilson S, Manning E, Chilamakuri C, Wilson D, Louis A, Raymond F ,Rastegar S, Strähle U, Lenhard Boris ,Bally-Cuif L, Van Heyningen V, Fitzpatrick D, Becker T, and Roest Crollius H (2015) Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nature Communications 6:6904

• Berthelot C, Muffato M, Abecassis J, Roest Crollius H. (2015) The 3D organisation of the chromatin explains evolutionary fragile genomic regions. Cell Reports . 10:1913–1924.

• Louis A, Nguyen NT, Muffato M, Roest Crollius H. (2015) Genomicus update 2015 : KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. Nucleic Acids Res. 43:D682-9.

• Louis A, Murat F, Salse J, Roest Crollius H. (2015) GenomicusPlants : A Web Resource to Study Genome Evolution in Flowering Plants. Plant and Cell Physiology. 56(1):e4.

2014

• Zelina P, Blockus H, Zagar Y, Péres A, Friocourt F, Wu Z, Rama N, Fouquet C, Hohenester E, Tessier-Lavigne M, Schweitzer J, Roest Crollius H, Chédotal A. (2014) Signaling Switch of the Axon Guidance Receptor Robo3 during Vertebrate Evolution. Neuron. 17 ;84(6):1258-72
• Berthelot C, Brunet F, Chalopin C, Juanchich A, Bernard M, Noël B, Bento P, Dasilva C, Labadie K, Alberti A, Aury J-M, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet E, Guyomard R, Galiana D, Bobe J, Volff J-N, Genêt C, Wincker P, Jaillon O, Roest Crollius H, Guiguen Y (2014) The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications 5:3657 ;

• Zaucker A, Bodur T, Roest Crollius H, Hadzhiev Y, Gehrig J, Loosli F, Watson C, Müller F. (2014) Description of Embryonic Development of Spotted Green Pufferfish (Tetraodon nigroviridis). Zebrafish 11(6):509-17
• Lucas J, Muffato M, Roest Crollius H (2014) PhylDiag : identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees. BMC Bioinformatics.15(1):268.
• Daković N, Térézol M, Pitel F, Maillard V, Elis S, Leroux S, Lagarrigue S, Gondret F, Klopp C, Baeza E, Duclos MJ, Roest Crollius H, Monget P. (2014) The loss of adipokine genes in the chicken genome and implications for insulin metabolism. Mol Biol Evol. 2014 ;31(10):2637-46.

2013

• Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Eliott D, Threadgold G, Harden G, Ware D, Mortimer B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL. (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature. 496(7446):498-503.

• Murigneux V., Saulière J., Roest Crollius H., Le Hir H. (2013) Transcriptome-wide identification of RNA binding sites by CLIP-seq. Methods 63(1):32-40

• Louis, A., Muffato, M. Roest Crollius, H. (2013) Genomicus : five genome browsers for comparative genomics in eukaryota. Nucleic Acids Research 41(D1):D700-5

2012

• Saulière, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Le Tonquèze, O., Audic, Y., Paillard, L., Roest Crollius, H. and Le Hir, H. (2012) CLIP-seq of the DEAD-box RNA Helicase eIF4AIII Reveals Transcriptome-wide Mapping of the Exon Junction Complex in Human. Nature Structural and Molecular Biology 19(11):1124-31

• Louis, A., Roest Crollius, H., Robinson-Rechavi, M. (2012) How much does the amphioxus genome represent the ancestor of chordates ? Briefings in Functional Genomics 11(2):89-95.

2011

• Cusack, B.P., Arndt, P.F., Duret, L., Roest Crollius, H. (2011) Preventing Dangerous Nonsense : Selection for Robustness to Transcriptional Error in Human Genes. PLoS Genetics 7(10) : e1002276.

2010

• Denoeud F., Henriet S., Mungpakdee S., Aury J.M., Da Silva C., Brinkmann H., Mikhaleva J., Olsen L.C., Jubin C., Cañestro C., Bouquet J.M., Danks G., Poulain J., Campsteijn C., Adamski M., Cross I., Yadetie F., Muffato M., Louis A., Butcher S., Tsagkogeorga G., Konrad A., Singh S., Jensen M.F., Cong E.H., Eikeseth-Otteraa H., Noel B., Anthouard V., Porcel B.M., Kachouri-Lafond R., Nishino A., Ugolini M., Chourrout P., Nishida H., Aasland R., Huzurbazar S., Westhof E., Delsuc F., Lehrach H., Reinhardt R., Weissenbach J., Roy S.W., Artiguenave F., Postlethwait J.H., Manak J.R., Thompson E.M., Jaillon O., Du Pasquier L., Boudinot P., Liberles D.A., Volff J.N., Philippe H., Lenhard B., Roest Crollius H., Wincker P., Chourrout D. (2010) Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate. Science. 330(6009):1381-5

• Hebert C, Roest Crollius H. (2010) Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes. Genome Biology. 2010 ;11(5):R51

• Muffato, M., Louis, A., Poisnel, C-E., Roest Crollius, H. (2010) Genomicus : a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26:1119-21

• Enard, D., Depaulis, F., Roest Crollius, H. (2010) Human and non-human primate genomes share hotspots of positive selection. Plos Genetics 6(2) : e1000840. doi:10.1371/journal.pgen.1000840

2009

• Benko, S., Fantes, J., Amiel, J., Heaney, S., Thomas, S., Ramsay, J., Jamshidi, R., Kleinjan, D., Gordon, C., McBride, D., Golzio, C., Hastie, N., Perry, P., Abadie, V., Ayuso, C., Holder, M., Kilpatrick, N., Lees, M., Picard, A., Temple, I.K., Thomas, P., Vazquez, M-P., Vekemans, M., Roest Crollius, H., Munnich, A., Etchevers, H., Farlie, P., Pelet, A., Essafi, A., Fisher, M., FitzPatrick, M., Lyonnet, S. (2009) Disruption of very distant highly conserved non-coding elements on either side of the SOX9 gene is associated with Pierre Robin sequence. Nature Genetics 41:359-64.

2008

• Muffato, M., Roest Crollius, H. (2008) Paleogenomics, or the recovery of lost genomes from the mist of times. BioEssays 30:122-134.

2006

• Brunet F.G., Roest Crollius H., Paris M., Aury J.M., Gibert P., Jaillon O., Laudet V., Robinson-Rechavi M. (2006) Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol. 23:1808-16.

• Djebali, S., Delaplace, F., Roest Crollius, H. (2006) Exogean : a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biology, 7(Suppl 1) :S7.1-10.

2004

• Jaillon O., Aury JM., Brunet F., Petit JL., Stange-Thomann N., Mauceli E., Bouneau L., Fischer C.,Ozouf-Costaz C., Bernot A., Nicaud S., Jaffe D., Fisher S., Lutfalla G., Dossat C., Segurens B.,Dasilva C., Salanoubat M., Levy M., Boudet N., Castellano S., Anthouard V., Jubin C., Castelli V., Katinka M., Vacherie B., Biémont C., Skalli Z., Cattolico L., Poulain J., de Berardinis V., Cruaud C.,Duprat S., Brottier P., Coutanceau JP., Gouzy J., Parra G., Lardier G., Chapple C., McKernan KJ.,McEwan P., Bosak S., Kellis M., Volff JN., Guigó R., Zody MC., Mesirov J., Lindblad-Toh K.,Birren B., Nusbaum C., Kahn D., Robinson-Rechavi M., Laudet V., Schachter V., Quétier F., SaurinW., Scarpelli C., Wincker P., Lander ES., Weissenbach J., Roest Crollius H. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the bony vertebrate proto-karyotype. Nature ; 431:946-957
• Roest Crollius, H. and Weissenbach, J. (2005) Fish genomics and biology. Genome Research 15:1675-82.

Previous Publications

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