Publications

[ORCID Profile]   [Google Scholar Profile]

co-1st author: #        corresponding author: *

Zepu Miao#, Haiting Wang#, Xinyu Tu#, Zhengshen Huang, Shujing Huang, Xinxin Zhang, Fan Wang, Zhishen Huang, Huihui Li, Yue Jiao, Song Gao, Zhipeng Zhou, Chun-Min Shan*, Jing Li*, Jia-Xing Yue* (2024) GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. Yeast. 2024; 41:19–34 [LINK]

Jing Li, Simon Stenberg, Jia-Xing Yue, Ekaterina Mikhalev, Dawn Thompson, Jonas Warringer, Gianni Liti* (2023) Genome instability footprint under rapamycin and hydroxyurea treatments. PLoS Genetics 19(11): e1011012. [LINK]

Samuel O’Donnell#, Jia-Xing Yue#, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stéphane Delmas, Fabien Dutreux, Téo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer*, Gianni Liti* & Gilles Fischer* (2023) Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nature Genetics. 55, 1390–1399 [LINK]

Xinyu Tu#, Fan Wang#, Gianni Liti, Michael Breitenbach, Jia-Xing Yue*, Jing Li* (2023) Spontaneous Mutation Rates and Spectra of Respiratory-Deficient Yeast. Biomolecules. 2023, 13, 501. [LINK]

Simon Stenberg, Jing Li, Arne B Gjuvsland, Karl Persson, Erik Demitz-Helin, Carles González Peña, Jia-Xing Yue, Ciaran Gilchrist, Timmy Ärengård, Payam Ghiaci, Lisa Larsson-Berghund, Martin Zackrisson, Silvana Smits, Johan Hallin, Johanna L Höög, Mikael Molin, Gianni Liti, Stig W Omholt*, Jonas Warringer* (2022) Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation. eLife. 2022 Jul 8;11:e76095 [LINK]

Jing Li, Bertrand Llorente, Gianni Liti*, Jia-Xing Yue* (2022) RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis. PLoS Genetics 18(5): e1010047. [LINK]

Jing Li#, Mark Rinnerthaler#, Johannes Hartl, Manuela Weber, Thomas Karl, Hannelore Breitenbach-Koller, Michael Mülleder, Jakob Vowinckel, Hans Marx, Michael Sauer, Diethard Mattanovich, Özge Ata, Sonakshi De, Gregor P. Greslehner, Florian Geltinger, Bill Burhans, Chris Grant, Victoria Doronina, Meryem Ralser, Maria Karolin Streubel, Christian Grabner, Stefanie Jarolim, Claudia Moßhammer, Campbell W. Gourlay, Jiri Hasek, Paul J. Cullen, Gianni Liti, Markus Ralser* and Michael Breitenbach* (2020) Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3. G3: Genes, Genomes, Genetics. vol. 10 no. 12 4637-4648 [LINK]

Eduardo I. Kessi-Pérez, Belén Ponce, Jing Li, Jennifer Molinet, Camila Baeza, David Figueroa, Camila Bastías, Marco Gaete, Gianni Liti, Alvaro Díaz-Barrera, Francisco Salinas and Claudio Martínez* (2020) Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations. Front. Microbiol. 11:1204. doi: 10.3389/fmicb.2020.01204 [LINK]

Liudmyla Lototska, Jia-Xing Yue, Jing Li, Marie-Josèphe Giraud-Panis, Zhou Songyang, Nicola J Royle, Gianni Liti, Jing Ye*, Eric Gilson*, Aaron Mendez-Bermudez*. (2020) Human RAP1 specifically protects telomeres of senescent cells from DNA damage. EMBO Reports, 21:e49076 [LINK]

Jing Li, Ignacio Vázquez-García, Karl Persson, Asier González, Jia-Xing Yue, Benjamin Barré, Michael N. Hall, Anthony D. Long, Jonas Warringer, Ville Mustonen, Gianni Liti*. (2019) Shared molecular targets confer resistance over short and long evolutionary timescales. Molecular Biology and Evolution, 36(4):691-708 [LINK]

Ju Huang#, Jing Li#, Jun Zhou, Long Wang, Sihai Yang, Laurence D. Hurst*, Wen-Hsiung Li*, Dacheng Tian*. (2018) Identifying a large number of high-yield genes in rice by pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 gene knockout. Proc Natl Acad Sci USA, 115(32):E7559-E7567 [LINK]

Haoxuan Liu#, Ju Huang#, Xiaoguang Sun#, Jing Li, Luyao Yu, Yingwen Hu, Gianni Liti, Dacheng Tian, Laurence D. Hurst*, Sihai Yang*. (2018) Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias. Nature Ecology & Evolution, 2, 164-173 [LINK]

Ignacio Vázquez-García*, Francisco Salinas, Jing Li, Andrej Fischer, Benjamin Barré, Johan Hallin, Anders Bergström, Elisa Alonso-Perez, Jonas Warringer, Ville Mustonen*, Gianni Liti*. (2017) Clonal heterogeneity influences the fate of new adaptive mutations. Cell Reports, 21(3): 732-744. [LINK]

Francesca Giordano*, Louise Aigrain, Michael A. Quail, Paul Coupland, James K. Bonfield, Robert M. Davies, German Tischler, David K. Jackson, Thomas M. Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning. (2017) De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Scientific Reports, 7(1):3935 [LINK]

Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti* (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 49, 913–924 (highlighted by CNRS Hebdo – Edition du 04.05.2017; Nice Matin samedi 13 mai, 2017) [LINK]

Changjiang Guo#, Xiaoguang Sun#, Xiao Chen, Sihai Yang, Jing Li, Long Wang*, Xiaohui Zhang* (2016) Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice. Plant Molecular Biology, 90: 95 [LINK]

Jing Li#, Jun Zhou#*, Ying Wu, Sihai Yang, Dacheng Tian* (2015) GC-content of synonymous codons profoundly influences amino acid usage. G3: Genes, Genomes, Genetics, 5:2027-2036 [LINK]

Sihai Yang#, Jing Li#, Xiaohui Zhang#, Qijun Zhang, Ju Huang, Jian-Qun Chen, Daniel L. Hartl*, Dacheng Tian* (2013) Rapidly evolving R-genes in diverse grass species confer resistance to rice blast disease. PNAS, 110(46): 18572-7 [LINK]

Sihai Yang#, Yang Yuan#, Long Wang#, Jing Li, Wen Wang, Haoxuan Liu, Jianqun Chen*, Laurence Hurst*, Dacheng Tian* (2012) Great majority of recombination events in Arabidopsis are gene conversion events. PNAS, 109(51): 20992-7 [LINK]

Jiao Wang#, Li Zhang#, Jing Li, Amy Lawton-Rauh*, Dacheng Tian* (2011) Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species. Gene, 482, 24–33 [LINK]

Jing Li#, Jing Ding#, Wen Zhang, Yuanli Zhang, Ping Tang, Jian-Qun Chen, Dacheng Tian*, Sihai Yang* (2010) Unique evolutionary pattern of numbers of gramineous NBS–LRR genes. Molecular Genetics & Genomics, 283(5): 427-38 [LINK]