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Genomicus: five genome browsers for comparative genomics in eukaryota

 Alexandra Louis , Matthieu Muffato , Hugues Roest Crollius
Nucleic Acids Research, 2012, 41 (D1), pp.D700-D705. ⟨10.1093/nar/gks1156⟩
Article dans une revue hal-03352666v1
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A functional operon delineates an extracellular pathway that controls body asymmetry only in animals with a ciliated left-right organizer

 Emmanuelle Szenker-Ravi , Tim Ott , Muznah Khatoo , Anne Moreau de Bellaing , Wei Xuan Goh , et al.
Nature Genetics, 2022, 54 (1), pp.62-72. ⟨10.1038/s41588-021-00970-4⟩
Article dans une revue hal-03876795v1

The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions

 Camille Berthelot , Matthieu Muffato , Judith Abecassis , Hugues Roest Crollius
Cell Reports, 2015, 10 (11), pp.1913-1924. ⟨10.1016/j.celrep.2015.02.046⟩
Article dans une revue hal-02415838v1
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Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

 Elise Parey , Alexandra Louis , Cédric Cabau , Yann Guiguen , Hugues Roest-Crollius , et al.
2020
Pré-publication, Document de travail hal-02791038v1
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Classification of non-coding variants with high pathogenic impact

 Lambert Moyon , Camille Berthelot , Alexandra Louis , Nga Thi Thuy Nguyen , Hugues Roest Crollius
PLoS Genetics, 2022, 18 (4), pp.e1010191. ⟨10.1371/journal.pgen.1010191⟩
Article dans une revue hal-03698847v1

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.

 Jérôme Saulière , Valentine Murigneux , Zhen Wang , Emélie Marquenet , Isabelle Barbosa , et al.
Nature Structural and Molecular Biology, 2012, 19 (11), pp.1124-31. ⟨10.1038/nsmb.2420⟩
Article dans une revue istex hal-00982626v1
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Signaling Switch of the Axon Guidance Receptor Robo3 during Vertebrate Evolution

 Pavol Zelina , Heike Blockus , Yvrick Zagar , Amélie Péres , François Friocourt , et al.
Neuron, 2014, 84 (6), pp.1258-1272. ⟨10.1016/j.neuron.2014.11.004⟩
Article dans une revue hal-01102724v1
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Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas

 Elodie Bal , Hyun-Sook Park , Zakia Belaid-Choucair , Hulya Kayserili , Magali Naville , et al.
Nature Medicine, 2017, 23 (10), pp.1226-1233. ⟨10.1038/nm.4368⟩
Article dans une revue hal-02415844v1

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⟩
Article dans une revue hal-01168460v1
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Conserved Small Nucleotidic Elements at the Origin of Concerted piRNA Biogenesis from Genes and lncRNAs

 Silke Jensen , Emilie Brasset , Elise Parey , Hugues Roest Crollius , Igor Sharakhov , et al.
Cells, 2020, 9 (6), pp.1491. ⟨10.3390/cells9061491⟩
Article dans une revue hal-02935810v1
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The bowfin genome illuminates the developmental evolution of ray-finned fishes

 Andrew W Thompson , M Brent Hawkins , Elise Parey , Dustin J Wcisel , Tatsuya Ota , et al.
Nature Genetics, 2021, 53, pp.1373 - 1384. ⟨10.1038/s41588-021-00914-y⟩
Article dans une revue hal-03457561v1
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Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

 Brian P. Cusack , Peter F. Arndt , L. Duret , Hugues Roest Crollius
PLoS Genetics, 2011, 7 (10), pp.e1002276. ⟨10.1371/journal.pgen.1002276⟩
Article dans une revue inserm-00711772v1
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Directed acyclic coloured multigraphs for expert eukaryotic gene annotation

 Sarah Djebali , Franck Delaplace , Hugues Roest Crollius
Journée Ouverte Biologie Informatique Mathématiques (JOBIM 2005), 2005, Paris, France
Communication dans un congrès hal-00339795v1

Master regulators in primary skin fibroblast fate reprogramming in a human ex vivo model of chronic wounds

 Maïté Noizet , Emilie Lagoutte , Marlène Gratigny , Marielle Bouschbacher , Isabelle Lazareth , et al.
Wound Repair and Regeneration, 2016, 24 (2), pp.247-262. ⟨10.1111/wrr.12392⟩
Article dans une revue hal-02415822v1
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GC content shapes mRNA storage and decay in human cells

 Maïté Courel , Yves Clément , Clémentine Bossevain , Dominika Foretek , Olivia Vidal Cruchez , et al.
eLife, 2019, 8, pp.e49708. ⟨10.7554/elife.49708⟩
Article dans une revue hal-03457618v1
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Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome.

 Magali Naville , Minaka Ishibashi , Marco Ferg , Hemant Bengani , Silke Rinkwitz , et al.
Nature Communications, 2015, 6, pp.6904. ⟨10.1038/ncomms7904⟩
Article dans une revue hal-01156469v1
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Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing

 Nga thi thuy Nguyen , Pierre Vincens , Hugues Roest Crollius , Alexandra Louis
Nucleic Acids Research, 2018, 46 (D1), pp.D816-D822. ⟨10.1093/nar/gkx1003⟩
Article dans une revue hal-02415691v1
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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⟩
Article dans une revue hal-02630062v1

The loss of adipokine genes in the chicken genome and implications for insulin metabolism

 Natasa Dakovic , Morgane Terezol , Frederique Pitel , Virginie Maillard , Sébastien Elis , et al.
Molecular Biology and Evolution, 2014, 31 (10), pp.2637-2646. ⟨10.1093/molbev/msu208⟩
Article dans une revue hal-01129850v1

GC content shapes mRNA storage and decay in human cells

 Maïté Courel , Yves Clément , Clémentine Bossevain , Dominika Foretek , Olivia Vidal Cruchez , et al.
eLife, 2019
Article dans une revue hal-03023372v1
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Chromosome evolution at the origin of the ancestral vertebrate genome

 Christine Sacerdot , Alexandra Louis , Céline Bon , Camille Berthelot , Hugues Roest Crollius
Genome Biology, 2018, 19 (1), pp.166. ⟨10.1186/s13059-018-1559-1⟩
Article dans une revue hal-04336857v1
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High precision detection of conserved segments from synteny blocks

 Joseph Mex Lucas , Hugues Roest Crollius
PLoS ONE, 2017, 12 (7), pp.e0180198. ⟨10.1371/journal.pone.0180198⟩
Article dans une revue hal-02415754v1

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

 Matthieu Muffato , Alexandra Louis , Nga Thi Thuy Nguyen , Joseph Lucas , Camille Berthelot , et al.
2022
Pré-publication, Document de travail hal-03765869v1

Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability

 Hemant Bengani , Detelina Grozeva , Lambert Moyon , Shipra Bhatia , Susana Louros , et al.
PLoS ONE, 2021, 16 (8), pp.e0256181. ⟨10.1371/journal.pone.0256181⟩
Article dans une revue hal-03455904v1
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On the importance of evolutionary constraint for regulatory sequence identification

 François Giudicelli , Hugues Roest Crollius
Briefings in Functional Genomics and Proteomics, 2021, 20 (6), pp.361-369. ⟨10.1093/bfgp/elab015⟩
Article dans une revue hal-03457553v1

The bowfin genome illuminates the developmental evolution of ray-finned fishes

 Andrew Thompson , M. Brent Hawkins , Elise Parey , Dustin Wcisel , Tatsuya Ota , et al.
Nature Genetics, 2021, ⟨10.1038/s41588-021-00914-y⟩
Article dans une revue hal-03329977v1
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Amphioxus functional genomics and the origins of vertebrate gene regulation

 Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic , et al.
Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩
Article dans une revue hal-02000511v1
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Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors

 Nga thi thuy Nguyen , Pierre Vincens , Jean François Dufayard , Hugues Roest crollius , Alexandra Louis
Nucleic Acids Research, 2022, 50 (D1), pp.D1025-D1031. ⟨10.1093/nar/gkab1091⟩
Article dans une revue hal-03438462v1
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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

 Matthieu Muffato , Alexandra Louis , Nga Thi Thuy Nguyen , Joseph Lucas , Camille Berthelot , et al.
Nature Ecology & Evolution, In press, ⟨10.1038/s41559-022-01956-z⟩
Article dans une revue hal-03943655v1
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Evolution is not Uniform Along Coding Sequences

 Raphaël Bricout , Dominique Weil , David Stroebel , Auguste Genovesio , Hugues Roest Crollius
Molecular Biology and Evolution, 2023, 40 (3), ⟨10.1093/molbev/msad042⟩
Article dans une revue hal-04051951v1
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