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ParTIES: a toolbox for Paramecium interspersed DNA elimination studies

Cyril Denby Wilkes , Olivier Arnaiz , Linda Sperling
Bioinformatics, 2016, 32 (4), pp.599 - 601. ⟨10.1093/bioinformatics/btv691⟩
Journal articles hal-01412717v1

ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology

Olivier Arnaiz , Eric Meyer , Linda Sperling
Nucleic Acids Research, 2019, ⟨10.1093/nar/gkz948⟩
Journal articles hal-02379386v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret , Jean Cohen , Claire Jubin , Philippe Dessen , Jean-François Goût et al.
Genome Research, 2008, 18 (4), pp.585-96. ⟨10.1101/gr.074534.107⟩
Journal articles hal-00282468v1

Genome-defence small RNAs exapted for epigenetic mating-type inheritance.

Deepankar Pratap Singh , Baptiste Saudemont , Gérard Guglielmi , Olivier Arnaiz , Jean-François Goût et al.
Stem Cells and Development, 2014, 509 (7501), pp.447-52. ⟨10.1038/nature13318⟩
Journal articles hal-01015302v1
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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek , Alexey Potekhin , Deepankar Pratap Singh , Inessa Grevtseva , Olivier Arnaiz et al.
Genome Biology and Evolution, 2020, evaa258, ⟨10.1093/gbe/evaa258⟩
Journal articles hal-03102341v1

A meiosis-specific Spt5 homolog involved in non-coding transcription

Julita Gruchota , Cyril Denby Wilkes , Olivier Arnaiz , Linda Sperling , Jacek K. Nowak et al.
Nucleic Acids Research, 2017, ⟨10.1093/nar/gkw1318⟩
Journal articles hal-02195050v1

ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.

Olivier Arnaiz , Scott Cain , Jean Cohen , Linda Sperling
Nucleic Acids Research, 2007, 35 (Database issue), pp.D439-44. ⟨10.1093/nar/gkl777⟩
Journal articles hal-00130942v1
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Functional diversification of Paramecium Ku80 paralogs safeguards genome integrity during precise programmed DNA elimination

Arthur Abello , Vinciane Régnier , Olivier Arnaiz , Romain Le Bars , Mireille Bétermier et al.
PLoS Genetics, 2020, 16 (4), pp.e1008723. ⟨10.1371/journal.pgen.1008723⟩
Journal articles hal-02547876v1
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The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements

Augustin de Vanssay , Amandine Touzeau , Olivier Arnaiz , Andrea Frapporti , Jamie Phipps et al.
PLoS Genetics, 2020, 16 (7), pp.e1008949. ⟨10.1371/journal.pgen.1008949⟩
Journal articles hal-02990752v1
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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis , Frédéric Guérin , Olivier Arnaiz , Walker Pett , Emmanuelle Lerat et al.
Plos Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩
Journal articles hal-03366429v1
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Annotation des génomes de paramécies

Olivier Arnaiz
Bio-Informatique, Biologie Systémique [q-bio.QM]. Université Paris-Saclay, 2020. Français. ⟨NNT : 2020UPASL046⟩
Theses tel-03175069v1

Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury , Olivier Jaillon , * Laurent Duret , Benjamin Noel , Claire Jubin et al.
Nature, 2006, 444 (7116), pp.171-178. ⟨10.1038/nature05230⟩
Journal articles hal-00090904v1

The Ciliary Protein IFT57 in the Macronucleus of Paramecium

Lei Shi , France Koll , Olivier Arnaiz , Jean Cohen
The Journal of Eukaryotic Microbiology, 2018, 65 (1), pp.12--27. ⟨10.1111/jeu.12423⟩
Journal articles hal-02183683v1
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MKS-NPHP module proteins control ciliary shedding at the transition zone

Delphine Gogendeau , Michel Lemullois , Pierrick Le Borgne , Manon Castelli , Anne Aubusson-Fleury et al.
PLoS Biology, 2020, 18 (3), pp.e3000640. ⟨10.1371/journal.pbio.3000640⟩
Journal articles hal-02509016v1
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Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication

Jean-Francois Gout , Parul Johri , Olivier Arnaiz , Thomas Doak , Simran Bhullar et al.
2021
Preprints, Working Papers, ... hal-02990778v1

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz , Nathalie Mathy , Céline Baudry , Sophie Malinsky , Jean-Marc Aury et al.
PLoS Genetics, 2012, 8 (10), pp.e1002984. ⟨10.1371/journal.pgen.1002984⟩
Journal articles hal-00759182v1
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The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley , Syed Haider , Steffen Durinck , Luca Pandini , Paolo Provero et al.
Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩
Journal articles hal-01146849v1
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GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium

Stefano Gnan , Mélody Matelot , Marion Weiman , Olivier Arnaiz , Frédéric Guérin et al.
Genome Research, 2022, pp.699-709. ⟨10.1101/2021.08.05.455221⟩
Journal articles hal-03400776v1

Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium

Julien Bischerour , Simran Bhullar , Cyril Denby Wilkes , Vinciane Régnier , Nathalie Mathy et al.
eLife, 2018, 7, pp.e37927. ⟨10.7554/eLife.37927⟩
Journal articles hal-02176490v1

Loss of a Fragile Chromosome Region leads to the Screwy Phenotype in Paramecium tetraurelia

Irina Nekrasova , Vera Nikitashina , Simran Bhullar , Olivier Arnaiz , Deepankar P. Singh et al.
Genes, 2019, 10 (7), ⟨10.3390/genes10070513⟩
Journal articles hal-02183793v1

A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium

Simran Bhullar , Cyril Denby Wilkes , Olivier Arnaiz , Mariusz Nowacki , Linda Sperling et al.
Nucleic Acids Research, 2018, 46 (18), pp.9550--9562. ⟨10.1093/nar/gky772⟩
Journal articles hal-02176489v1

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.

Kamila Maliszewska-Olejniczak , Julita Gruchota , Robert Gromadka , Cyril Denby Wilkes , Olivier Arnaiz et al.
PLoS Genetics, 2015, 11 (7), pp.e1005383. ⟨10.1371/journal.pgen.1005383⟩
Journal articles hal-01234177v1

Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements

Frédéric Guérin , Olivier Arnaiz , Nicole Boggetto , Cyril Denby Wilkes , Eric Meyer et al.
BMC Genomics, 2017, 18 (1), ⟨10.1186/s12864-017-3713-7⟩
Journal articles hal-02146952v1

The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium

Andrea Frapporti , Caridad Miró Pina , Olivier Arnaiz , Daniel Holoch , Takayuki Kawaguchi et al.
Nature Communications, 2019, 10 (1), pp.2710. ⟨10.1038/s41467-019-10648-5⟩
Journal articles hal-02164121v1
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Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements

Caridad Miró Pina , Olivia Charmant , Takayuki Kawaguchi , Daniel Holoch , Audrey Michaud et al.
Developmental Cell, 2022, 57 (8), pp.1037-1052.e8. ⟨10.1016/j.devcel.2022.03.014⟩
Journal articles hal-03358389v1
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Developmental timing of programmed DNA elimination in $Paramecium\ tetraurelia$ recapitulates germline transposon evolutionary dynamics

Coralie Zangarelli , Olivier Arnaiz , Mickaël Bourge , Kevin Gorrichon , Yan Jaszczyszyn et al.
Genome Research, 2022, 2022, ⟨10.1101/gr.277027.122⟩
Journal articles hal-03840719v2

The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium

Andrea Frapporti , Caridad Miró Pina , Olivier Arnaiz , Daniel Holoch , Takayuki Kawaguchi et al.
Nature Communications, 2019, 10 (1), pp.2710. ⟨10.1038/s41467-019-10648-5⟩
Journal articles hal-03985655v1

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury , Olivier Jaillon , L. Duret , Benjamin Noel , Claire Jubin et al.
Nature, 2006, 444 (7116), pp.171-8. ⟨10.1038/nature05230⟩
Journal articles hal-00132091v1
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Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Olivier Arnaiz , Erwin van Dijk , Mireille Bétermier , Maoussi Lhuillier-Akakpo , Augustin de Vanssay et al.
BMC Genomics, 2017, 18, pp.1-12. ⟨10.1186/s12864-017-3887-z⟩
Journal articles hal-01602694v1