Gianni Liti

31
Documents

Publications

Publications

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ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel

Zepu Miao , Yifan Ren , Andrea Tarabini , Ludong Yang , Huihui Li et al.
Nucleic Acids Research, 2024, pp.gkae955. ⟨10.1093/nar/gkae955⟩
Article dans une revue hal-04797383 v1
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Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

Samuel O’donnell , Jia-Xing Yue , Omar Abou Saada , Nicolas Agier , Claudia Caradec et al.
Nature Genetics, 2023, 55 (8), pp.1390 - 1399. ⟨10.1038/s41588-023-01459-y⟩
Article dans une revue hal-04305689 v1
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RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis

Jing Li , Bertrand Llorente , Gianni Liti , Jia-Xing Yue
PLoS Genetics, 2022, 18 (5), pp.e1010047. ⟨10.1371/journal.pgen.1010047⟩
Article dans une revue hal-03869238 v1
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The budding yeast life cycle: More complex than anticipated?

Gilles Fischer , Gianni Liti , Bertrand Llorente
Yeast, 2021, 38 (1), pp.5-11. ⟨10.1002/yea.3533⟩
Article dans une revue hal-03086108 v1
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Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies

Raphaelle Laureau , Annie Dyatel , Gizem Dursuk , Samantha Brown , Hannah Adeoye et al.
Developmental Cell, 2021, 56, pp.22 - 35.e7. ⟨10.1016/j.devcel.2020.11.008⟩
Article dans une revue hal-03455850 v1
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Aborting meiosis allows recombination in sterile diploid yeast hybrids

Simone Mozzachiodi , Lorenzo Tattini , Agnes Llored , Agurtzane Irizar , Neža Škofljanc et al.
Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-26883-8⟩
Article dans une revue hal-03474924 v1
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Natural variants suppress mutations in hundreds of essential genes

Leopold Parts , Amandine Batté , Maykel Lopes , Michael W Yuen , Meredith Laver et al.
Molecular Systems Biology, 2021, 17 (1), pp.e10138. ⟨10.15252/msb.202010138⟩
Article dans une revue hal-03455912 v1
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The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin

Chun-Min Shan , Jin-Kwang Kim , Jiyong Wang , Kehan Bao , Yadong Sun et al.
Cell Reports, 2021, 35 (7), pp.109137. ⟨10.1016/j.celrep.2021.109137⟩
Article dans une revue hal-03455905 v1
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Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

Vassiliki Koufopanou , Susan Lomas , Olga Pronina , Pedro Almeida , Jose Paulo Sampaio et al.
Genome Biology and Evolution, 2020, 12 (9), pp.1636-1645. ⟨10.1093/gbe/evaa141⟩
Article dans une revue hal-03430146 v1
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Human RAP 1 specifically protects telomeres of senescent cells from DNA damage

Liudmyla Lototska , Jia‐xing Yue , M.J. Giraud-Panis , Zhou Songyang , Nicola Royle et al.
EMBO Reports, 2020, 21 (4), ⟨10.15252/embr.201949076⟩
Article dans une revue hal-03013736 v1
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CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations

Hayley R Stoneman , Russell L Wrobel , Michael Place , Michael Graham , David J Krause et al.
G3, 2020, 10 (11), pp.4287--4294. ⟨10.1534/g3.120.401498⟩
Article dans une revue hal-05022750 v1
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Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Matteo de Chiara , Anne Friedrich , Benjamin Barré , Michael Breitenbach , Joseph Schacherer et al.
BMC Biology, 2020, 18 (1), pp.49. ⟨10.1186/s12915-020-00786-4⟩
Article dans une revue inserm-02971513 v1
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Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3

Jing Li , Mark Rinnerthaler , Johannes Hartl , Manuela Weber , Thomas Karl et al.
G3, 2020, 10 (12), pp.4637 - 4648. ⟨10.1534/g3.120.401537⟩
Article dans une revue hal-03455791 v1

Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging

Benjamin Barré , Johan Hallin , Jia-Xing Yue , Karl Persson , Ekaterina Mikhalev et al.
Genome Research, 2020, 30 (5), pp.697-710. ⟨10.1101/gr.253351.119⟩
Article dans une revue hal-02991696 v1
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A yeast living ancestor reveals the origin of genomic introgressions

Melania d'Angiolo , Matteo de Chiara , Jia-Xing Yue , Agurtzane Irizar , Simon Stenberg et al.
Nature, 2020, 587 (7834), pp.420-425. ⟨10.1038/s41586-020-2889-1⟩
Article dans une revue hal-03430153 v1
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An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages

Roberto F Nespolo , Carlos A Villarroel , Christian I Oporto , Sebastián M Tapia , Franco Vega-Macaya et al.
PLoS Genetics, 2020, 16 (5), pp.e1008777. ⟨10.1371/journal.pgen.1008777⟩
Article dans une revue inserm-02877129 v1
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Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation

Jennifer Molinet , Francisco A Cubillos , Francisco Salinas , Gianni Liti , Claudio Martínez
PLoS ONE, 2019, 14 (7), pp.e0220515. ⟨10.1371/journal.pone.0220515⟩
Article dans une revue inserm-02265082 v1

André Goffeau's imprinting on second generation yeast “genomologists”

Cécile Fairhead , Gilles Fischer , Gianni Liti , Cécile Neuvéglise , Joseph Schacherer
Yeast, 2019, 36 (4), pp.167-175. ⟨10.1002/yea.3377⟩
Article dans une revue hal-02381500 v1

simuG: a general-purpose genome simulator

Jia-Xing Yue , Gianni Liti
Bioinformatics, 2019, 35 (21), pp.4442-4444. ⟨10.1093/bioinformatics/btz424⟩
Article dans une revue hal-02381480 v1

Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales

Jing Li , Ignacio Vázquez-García , Karl Persson , Asier González , Jia-Xing Yue et al.
Molecular Biology and Evolution, 2019, 36 (4), pp.691-708. ⟨10.1093/molbev/msz006⟩
Article dans une revue hal-02381487 v1

Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes

Lorenzo Tattini , Nicolò Tellini , Simone Mozzachiodi , Melania d'Angiolo , Sophie Loeillet et al.
Molecular Biology and Evolution, 2019, 36 (12), pp.2861-2877. ⟨10.1093/molbev/msz177⟩
Article dans une revue hal-02381458 v1
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Long-read sequencing data analysis for yeasts

Jia-Xing Yue , Gianni Liti
Nature Protocols, 2018, 13 (6), pp.1213-1231. ⟨10.1038/nprot.2018.025⟩
Article dans une revue hal-02381498 v1

Yeast chromosome numbers minimized using genome editing

Gianni Liti
Nature, 2018, 560 (7718), pp.317-318. ⟨10.1038/d41586-018-05309-4⟩
Article dans une revue hal-02381492 v1
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Genome evolution across 1,011 $Saccharomyces\ cerevisiae$ isolates

Jackson Peter , Matteo de Chiara , Anne Friedrich , Jia-Xing Yue , David Pflieger et al.
Nature, 2018, 556 (7701), pp.339 - 344. ⟨10.1038/s41586-018-0030-5⟩
Article dans une revue cea-01872910 v1
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Contrasting evolutionary genome dynamics between domesticated and wild yeasts

Jia-Xing Yue , Jing Li , Louise Aigrain , Johan Hallin , Karl Persson et al.
Nature Genetics, 2017, 49 (6), pp.913-924. ⟨10.1038/ng.3847⟩
Article dans une revue hal-01546021 v1
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Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion

Raphaëlle Laureau , Sophie Loeillet , Francisco Salinas , Anders Bergström , Patricia Legoix-Né et al.
PLoS Genetics, 2016, 12 (2), pp.e1005781. ⟨10.1371/journal.pgen.1005781⟩
Article dans une revue hal-01306737 v1
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Filling annotation gaps in yeast genomes using genome-wide contact maps.

Hervé Marie-Nelly , Martial Marbouty , Axel Cournac , Gianni Liti , Gilles Fischer et al.
Bioinformatics, 2014, 30 (15), pp.2105-13. ⟨10.1093/bioinformatics/btu162⟩
Article dans une revue pasteur-01488132 v1

A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes

Helene Louvel , Alexandre Gillet-Markowska , Gianni Liti , Gilles Fischer
Yeast, 2014, 31 (3), pp.91-101. ⟨10.1002/yea.2991⟩
Article dans une revue hal-01528407 v1
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High-quality genome (re)assembly using chromosomal contact data

Hervé Marie-Nelly , Martial Marbouty , Axel Cournac , Jean-François Flot , Gianni Liti et al.
Nature Communications, 2014, 5, pp.5695. ⟨10.1038/ncomms6695⟩
Article dans une revue hal-01138788 v1
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High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.

Gianni Liti , Alex N. Nguyen Ba , Martin Blythe , Carolin Müller , Anders Bergström et al.
BMC Genomics, 2013, 14 (1), pp.69. ⟨10.1186/1471-2164-14-69⟩
Article dans une revue inserm-00799236 v1

The rise of yeast population genomics

Gianni Liti , Joseph Schacherer
Comptes Rendus - Biologies, 2011, 334 (8-9), pp.612--619. ⟨10.1016/j.crvi.2011.05.009⟩
Article dans une revue hal-05020469 v1