Gianni Liti

Publications

Article dans une revue (36)

Predicting natural variation in the yeast phenotypic landscape with machine learning Sakshi Khaiwal,Matteo de Chiara,Benjamin P Barré,Inigo Barrio-Hernandez,Simon Stenberget al. Molecular Systems Biology, 2025, 21 (11), pp.1466-1489. ⟨10.1038/s44320-025-00136-y⟩ Article dans une revue hal-05485183v1
Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution Nina Vittorelli,Cintia Gómez-Muñoz,Irina Andriushchenko,Louis Ollivier,Nicolas Agieret 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
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel Zepu Miao,Yifan Ren,Andrea Tarabini,Ludong Yang,Huihui Liet al. Nucleic Acids Research, 2024, pp.gkae955. ⟨10.1093/nar/gkae955⟩ Article dans une revue hal-04797383v1
Ancient and recent origins of shared polymorphisms in yeast Nicolò Tellini,Matteo de Chiara,Simone Mozzachiodi,Lorenzo Tattini,Chiara Vischioniet 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-Paniset al. Genetics, 2023, 223 (3), ⟨10.1093/genetics/iyac186⟩ Article dans une revue hal-05138555v1
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 Caradecet al. Nature Genetics, 2023, 55 (8), pp.1390 - 1399. ⟨10.1038/s41588-023-01459-y⟩ Article dans une revue hal-04305689v1
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
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
Natural variants suppress mutations in hundreds of essential genes Leopold Parts,Amandine Batté,Maykel Lopes,Michael W Yuen,Meredith Laveret al. Molecular Systems Biology, 2021, 17 (1), pp.e10138. ⟨10.15252/msb.202010138⟩ Article dans une revue hal-03455912v1
Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies Raphaelle Laureau,Annie Dyatel,Gizem Dursuk,Samantha Brown,Hannah Adeoyeet al. Developmental Cell, 2021, 56, pp.22 - 35.e7. ⟨10.1016/j.devcel.2020.11.008⟩ Article dans une revue hal-03455850v1
Aborting meiosis allows recombination in sterile diploid yeast hybrids Simone Mozzachiodi,Lorenzo Tattini,Agnes Llored,Agurtzane Irizar,Neža Škofljancet al. Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-26883-8⟩ Article dans une revue hal-03474924v1
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
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 Sunet al. Cell Reports, 2021, 35 (7), pp.109137. ⟨10.1016/j.celrep.2021.109137⟩ Article dans une revue hal-03455905v1
Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging Benjamin Barré,Johan Hallin,Jia-Xing Yue,Karl Persson,Ekaterina Mikhalevet al. Genome Research, 2020, 30 (5), pp.697-710. ⟨10.1101/gr.253351.119⟩ Article dans une revue hal-02991696v1
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 Sampaioet al. Genome Biology and Evolution, 2020, 12 (9), pp.1636-1645. ⟨10.1093/gbe/evaa141⟩ Article dans une revue hal-03430146v1
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 Krauseet al. G3, 2020, 10 (11), pp.4287--4294. ⟨10.1534/g3.120.401498⟩ Article dans une revue hal-05022750v1
Human RAP 1 specifically protects telomeres of senescent cells from DNA damage Liudmyla Lototska,Jia‐xing Yue,M.J. Giraud-Panis,Zhou Songyang,Nicola Royleet al. EMBO Reports, 2020, 21 (4), ⟨10.15252/embr.201949076⟩ Article dans une revue hal-03013736v1
Discordant evolution of mitochondrial and nuclear yeast genomes at population level Matteo de Chiara,Anne Friedrich,Benjamin Barré,Michael Breitenbach,Joseph Schachereret al. BMC Biology, 2020, 18 (1), pp.49. ⟨10.1186/s12915-020-00786-4⟩ Article dans une revue inserm-02971513v1
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 Karlet al. G3, 2020, 10 (12), pp.4637 - 4648. ⟨10.1534/g3.120.401537⟩ Article dans une revue hal-03455791v1
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-Macayaet al. PLoS Genetics, 2020, 16 (5), pp.e1008777. ⟨10.1371/journal.pgen.1008777⟩ Article dans une revue inserm-02877129v1
A yeast living ancestor reveals the origin of genomic introgressions Melania d'Angiolo,Matteo de Chiara,Jia-Xing Yue,Agurtzane Irizar,Simon Stenberget al. Nature, 2020, 587 (7834), pp.420-425. ⟨10.1038/s41586-020-2889-1⟩ Article dans une revue hal-03430153v1
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
Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales Jing Li,Ignacio Vázquez-García,Karl Persson,Asier González,Jia-Xing Yueet al. Molecular Biology and Evolution, 2019, 36 (4), pp.691-708. ⟨10.1093/molbev/msz006⟩ Article dans une revue hal-02381487v1
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
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 Loeilletet 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
Genome evolution across 1,011 $Saccharomyces\ cerevisiae$ isolates Jackson Peter,Matteo de Chiara,Anne Friedrich,Jia-Xing Yue,David Pfliegeret al. Nature, 2018, 556 (7701), pp.339 - 344. ⟨10.1038/s41586-018-0030-5⟩ Article dans une revue cea-01872910v1
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
Contrasting evolutionary genome dynamics between domesticated and wild yeasts Jia-Xing Yue,Jing Li,Louise Aigrain,Johan Hallin,Karl Perssonet al. Nature Genetics, 2017, 49 (6), pp.913-924. ⟨10.1038/ng.3847⟩ Article dans une revue hal-01546021v1
Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion Raphaëlle Laureau,Sophie Loeillet,Francisco Salinas,Anders Bergström,Patricia Legoix-Néet al. PLoS Genetics, 2016, 12 (2), pp.e1005781. ⟨10.1371/journal.pgen.1005781⟩ Article dans une revue hal-01306737v1
Filling annotation gaps in yeast genomes using genome-wide contact maps. Hervé Marie-Nelly,Martial Marbouty,Axel Cournac,Gianni Liti,Gilles Fischeret 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
High-quality genome (re)assembly using chromosomal contact data Hervé Marie-Nelly,Martial Marbouty,Axel Cournac,Jean-François Flot,Gianni Litiet al. Nature Communications, 2014, 5, pp.5695. ⟨10.1038/ncomms6695⟩ Article dans une revue hal-01138788v1
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. Gianni Liti,Alex N. Nguyen Ba,Martin Blythe,Carolin Müller,Anders Bergströmet 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

Pré-publication, Document de travail (1)

Regulation of cell proliferation by a novel feedback system on Cdk function Joseph C Ryan,Baptiste Leray,Akanksha Jain,Nelson Coehlo,Maria Rosa Domingo-Sananeset al. 2025 Pré-publication, Document de travail hal-05390741v1

Poster de conférence (1)

Frequent heterothallism in natural populations of Saccharomyces cerevisiae Nina Vittorelli,Cintia Gómez-Muñoz,Irina Andriushchenko,Nicolas Agier,Stéphane Delmaset al. EMBO Workshop on Molecular mechanisms in evolution and ecology, Oct 2024, Heidelberg, Germany Poster de conférence hal-05563805v1