Gianni Liti

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Publications

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Predicting natural variation in the yeast phenotypic landscape with machine learning

Sakshi Khaiwal , Matteo de Chiara , Benjamin P Barré , Inigo Barrio-Hernandez , Simon Stenberg et al.

Molecular Systems Biology, 2025, 21 (11), pp.1466-1489. ⟨10.1038/s44320-025-00136-y⟩

Article dans une revue hal-05485183v1
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Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution

Nina Vittorelli , Cintia Gómez-Muñoz , Irina Andriushchenko , Louis Ollivier , Nicolas Agier et al.

Proceedings of the National Academy of Sciences of the United States of America, 2025, 123 (2), pp.e2525679123. ⟨10.1073/pnas.2525679123⟩

Article dans une revue hal-05404528v2
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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-04797383v1
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Ancient and recent origins of shared polymorphisms in yeast

Nicolò Tellini , Matteo de Chiara , Simone Mozzachiodi , Lorenzo Tattini , Chiara Vischioni et al.

Nature Ecology & Evolution, 2024, 8 (4), pp.761-776. ⟨10.1038/s41559-024-02352-5⟩

Article dans une revue hal-05226449v1

Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones

Melania D’angiolo , Jia-Xing Yue , Matteo de Chiara , Benjamin Barré , Marie-Josèphe Giraud-Panis et al.

Genetics, 2023, 223 (3), ⟨10.1093/genetics/iyac186⟩

Article dans une revue hal-05138555v1
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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-04305689v1
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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-03869238v1
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Unlocking the functional potential of polyploid yeasts

Simone Mozzachiodi , Kristoffer Krogerus , Brian Gibson , Alain Nicolas , Gianni Liti

Nature Communications, 2022, 13 (1), pp.2580. ⟨10.1038/s41467-022-30221-x⟩

Article dans une revue hal-05485156v1
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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-03474924v1
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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-03455850v1
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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-03455912v1
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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-03086108v1
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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-03455905v1
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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-02991696v1
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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-03430146v1
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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-03013736v1
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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-05022750v1
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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-02971513v1
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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-03455791v1
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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-02877129v1
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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-03430153v1

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-02381487v1

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-02381500v1
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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-02265082v1
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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-02381480v1

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-02381458v1

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-02381492v1
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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-01872910v1
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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-02381498v1
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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-01546021v1
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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-01306737v1
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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-01488132v1

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-01528407v1
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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-01138788v1
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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-00799236v1

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-05020469v1