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Alexandra Louis

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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
Nature Ecology & Evolution, In press, ⟨10.1038/s41559-022-01956-z⟩
Journal articles hal-03943655v1
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Genome structures resolve the early diversification of teleost fishes

Elise Parey , Alexandra Louis , Jérôme Montfort , Olivier Bouchez , Céline Roques
Science, 2023, 379 (6632), pp.572-575. ⟨10.1101/2022.04.07.487469⟩
Journal articles hal-03765882v1
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An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication

Elise Parey , Alexandra Louis , Jérôme Montfort , Yann Guiguen , Hugues Roest Crollius
Genome Research, 2022, 32 (9), pp.1685 - 1697. ⟨10.1101/gr.276953.122⟩
Journal articles hal-03876769v1
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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⟩
Journal articles hal-03438462v1
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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⟩
Journal articles hal-03698847v1
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RapGreen, an interactive software and web package to explore and analyze phylogenetic trees

Jean-François Dufayard , Stéphanie Bocs , Valentin Guignon , Delphine Larivière , Alexandra Louis
NAR Genomics and Bioinformatics, 2021, 3 (3), 6 p. ⟨10.1093/nargab/lqab088⟩
Journal articles hal-03541670v1

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

Andrew Thompson , M. Brent Hawkins , Elise Parey , Dustin Wcisel , Tatsuya Ota
Nature Genetics, 2021, ⟨10.1038/s41588-021-00914-y⟩
Journal articles hal-03329977v1
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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
Molecular Biology and Evolution, 2020, 37, pp.3324 - 3337. ⟨10.1093/molbev/msaa149⟩
Journal articles hal-03457579v1
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ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Justine Dardaillon , Delphine Dauga , Paul Simion , Emmanuel Faure , Takeshi Onuma
Nucleic Acids Research, 2020, 48 (D1), pp.D668-D675. ⟨10.1093/nar/gkz955⟩
Journal articles hal-02415680v1

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
Molecular Biology and Evolution, 2020, 37 (11), pp.3324-3337. ⟨10.1093/molbev/msaa149⟩
Journal articles hal-03038540v1
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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⟩
Journal articles hal-02415691v1
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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
Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩
Journal articles hal-02000511v1
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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), ⟨10.1186/s13059-018-1559-1⟩
Journal articles hal-02415626v1
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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Matija Brozovic , Christelle Dantec , Justine Dardaillon , Delphine Dauga , Emmanuel Faure
Nucleic Acids Research, 2018, 46 (D1), pp.D718-D725. ⟨10.1093/nar/gkx1108⟩
Journal articles hal-01636650v1
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Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation

Claudia Chica , Alexandra Louis , Hugues Roest Crollius , Vincent Colot , François Roudier
Genome Biology, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1333-9⟩
Journal articles hal-02415743v1
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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
Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩
Journal articles hal-02630062v1

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
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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
Nature Communications, 2015, 6, pp.6904. ⟨10.1038/ncomms7904⟩
Journal articles hal-01156469v1
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Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics

Alexandra Louis , Nga thi thuy Nguyen , Matthieu Muffato , Hugues Roest crollius
Nucleic Acids Research, 2015, 43 (D1), pp.D682-D689. ⟨10.1093/nar/gku1112⟩
Journal articles hal-03352660v1
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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
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The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Camille Berthelot , Frédéric Brunet , Domitille Chalopin , Amélie Juanchich , Maria Bernard
Nature Communications, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩
Journal articles hal-01193812v1

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⟩
Journal articles hal-03352666v1

How much does the amphioxus genome represent the ancestor of chordates?

A. Louis , H. Roest Crollius , M. Robinson-Rechavi
Briefings in Functional Genomics and Proteomics, 2012, 11 (2), pp.89-95. ⟨10.1093/bfgp/els003⟩
Journal articles hal-03352669v1

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

M. Muffato , A. Louis , C. Poisnel , H. Crollius
Bioinformatics, 2010, 26 (8), pp.1119-1121. ⟨10.1093/bioinformatics/btq079⟩
Journal articles hal-03352670v1
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Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud , Simon Henriet , Sutada Mungpakdee , Jean-Marc Aury , Corinne da Silva
Science, 2010, 330 (6009), pp.1381-1385. ⟨10.1126/science.1194167⟩
Journal articles halsde-00544648v1

Identification of genomic features using microsyntenies of domains: Domain teams

S. Pasek , Anne Bergeron , Jean Loup Risler , Alexandra Louis , Emmanuelle Ollivier
Genome Research, 2005, 15 (6), pp.867-874. ⟨10.1101/gr.3638405⟩
Journal articles hal-03352673v1

PHYTOPROT: a database of clusters of plant proteins

S. Mohseni-Zadeh , Alexandra Louis
Nucleic Acids Research, 2004, 32 (90001), pp.351D-353. ⟨10.1093/nar/gkh040⟩
Journal articles hal-03352674v1

An incremental algorithm for Z-value computations

J.-C. Aude , A. Louis
Computers and Chemistry, 2002, 26 (5), pp.402-410. ⟨10.1016/S0097-8485(02)00003-7⟩
Journal articles hal-03352687v1

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations

A. Louis , H. Chiapello , C. Fabry , E. Ollivier , A. Hénaut
Computers and Chemistry, 2002, 26 (5), pp.511-519. ⟨10.1016/S0097-8485(02)00011-6⟩
Journal articles hal-03352685v1

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations

A. Louis , Hélène Chiapello , C. Fabry , E. Ollivier , A. Henaut
Computers and Chemistry, 2002, 26 (5), pp.511-519. ⟨10.1016/S0097-8485(02)00011-6⟩
Journal articles hal-02676436v1

Massive Sequence Comparisons as a Help in Annotating Genomic Sequences

Alexandra Louis , Emmanuelle Ollivier , Jean-Christophe Aude , Jean Loup Risler
Genome Research, 2001
Journal articles hal-03352694v1

Banques et bases de données en biologie

Hélène Chiapello , Alexandra Louis
Bio-Informatique - principes d'utilisation des outils, Editions Quae, 2010
Book sections hal-02823616v1

Encyclopedia of Life Sciences

Jean-Loup Risler , Alexandra Louis
Genetic Databases: Mining, John Wiley & Sons, Ltd, 2001, ⟨10.1038/npg.els.0005313⟩
Book sections hal-03352697v1