Publications – Evomics Lab

[ORCID] [Google Scholar] [Web of Science] [ResearchGate]
Total papers: 44; Total citations: 3836; h-index: 23; i10-index: 30.
(based on the Google Scholar statistics; last accessed on 2024/11/15)

*: corresponding author; ^: co-first author; bold: team members

Submitted Manuscripts

Selected Publications

Full Publications

Submitted Manuscripts

Zepu Miao, Jia-Xing Yue*. (2024) VRPG: an interactive visualization framework for reference-projected pangenome graph. BioRxiv, (in revision; doi: 10.1101/2023.01.20.524991; demonstration available at https://www.evomicslab.org/app/vrpg/; software available at https://github.com/codeatcg/VRPG) [LINK]

Selected Publications

Zepu Miao^, Yifan Ren^, Andrea Tarabini^, Ludong Yang, Huihui Li, Chang Ye, Gianni Liti, Gilles Fischer, Jing Li*, Jia-Xing Yue*. (2024) ScRAPdb, an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel. Nucleic Acids Research, gkae955. (doi: 10.1093/nar/gkae955; database available at https://www.evomicslab.org/db/ScRAPdb/ ) [LINK]

Ludong Yang^, Xinxin Zhang^, Fan Wang^, Li Zhang*, Jing Li*, Jia-Xing Yue*. (2024) NanoTrans: an integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing. Journal of Genetics and Genomics, 51(11):1300-1309. (doi: 10.1016/j.jgg.2024.07.007; software available at https://github.com/yjx1217/NanoTrans ) [LINK]

Zegeng Chen^, He Huang^, Huangming Hong^, Huageng Huang, Huawei Weng, Le Yu, Jian Xiao, Zhao Wang, Xiaojie Fang, Yuyi Yao, Jia-Xing Yue*, Tongyu Lin*. (2024) Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression. Genome Medicine, 16(1):48. (doi: 10.1186/s13073-024-01324-5) [LINK]

Samuel O’Donnell^, Jia-Xing Yue^, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo 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(8):1390-1399. (doi: 10.1038/s41588-023-01459-y) [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. (doi: 10.1371/journal.pgen.1010047; software available at https://github.com/yjx1217/RecombineX ) [LINK]

Jia-Xing Yue*, Gianni Liti*. (2019) simuG: a general-purpose genome simulator. Bioinformatics, 35(21):4442-4444. (doi:10.1093/bioinformatics/btz424; software available at https://github.com/yjx1217/simuG) [LINK]

Jia-Xing Yue*, Gianni Liti*. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols, 13(6):1213-1231. (doi:10.1038/nprot.2018.025; software available at https://github.com/yjx1217/LRSDAY) [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 genome dynamics between domesticated and wild yeasts. Nature Genetics, 49(6):913-924. (doi:10.1038/ng.3847) [LINK]

Jia-Xing Yue, Iryna Kozmikova, Hiroki Ono, Carlos W. Nossa, Zbynek Kozmik, Nicholas H. Putnam, Jr-Kai Yu, Linda Z. Holland*. (2016) Conserved noncoding elements in the most distant genera of cephalochordates: the Goldilocks principle. Genome Biology and Evolution, 8(8):2387-2405. (doi:10.1093/gbe/evw158) [LINK]

Jia-Xing Yue, Jr-Kai Yu, Nicholas H. Putnam, Linda Z. Holland*. (2014) The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution. Genome Biology and Evolution, 6(10):2681-2696. (doi:10.1093/gbe/evu212) [LINK]

Jia-Xing Yue, Blake C. Meyers, Jian-Qun Chen, Dacheng Tian*, Sihai Yang*. (2012) Tracing the origin and evolutionary history of plant NBS-LRR genes. New Phytologist, 193(4):1049-1063. (doi:10.1111/j.1469-8137.2011.04006.x) [LINK]

Jia-Xing Yue, Jinpeng Li, Dan Wang, Hitoshi Araki, Dacheng Tian, Sihai Yang*. (2010) Genome-wide investigation reveals high evolutionary rates in annual model plants. BMC Plant Biology, 10:242. (doi:10.1186/1471-2229-10-242) [LINK]

Full Publications

Bruno Lopes-Bastos, Joana Nabais, Tânia Ferreira, Mounir El Maï, Malia Bird, Seniye Targen, Da Kang, Jia-Xing Yue, Tânia Carvalho, Miguel Godinho Ferreira*. (2023) Absence of telomerase leads to immune response and tumor regression in zebrafish melanoma. Cell Reports (in press; BioRxiv preprint with doi: 10.1101/2023.03.24.534079) [LINK]

CNCB-NGDC Members and Partners. (2024) Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Research, gkae978, (doi: 10.1093/nar/gkae978) [LINK]

Han-Ying Huang^, Yan-Zhou Chen^, Xin-Nan Zheng, Jia-Xing Yue, Huai-Qiang Ju, Yan-Xia Shi, Lin Tian*. (2024) Availability of an inflammatory macrophage niche drives phenotypic and functional alterations in Kupffer cells. Nature Communications, 15(1):9337. (doi: 10.1038/s41467-024-53659-7) [LINK]

Da Kang^, Shanshan Huang^, Yijun Liao^, Siyuan Mi^, Jingying Zhou, Yu Feng, Riming Huang, Zhen-hai Lu, Z. Z. Pan, Wenjuan Ma, Gong Chen*, Jia-Xing Yue*, Jingxiu Huang*, R. X. Zhang*. (2024) Vasorin (VASN) overexpression promotes pulmonary metastasis and resistance to adjuvant chemotherapy in patients with locally advanced rectal cancer. Journal of Translational Medicine, 22:742. (doi: 10.1186/s12967-024-05473-4) [LINK]

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, 41(1-2):19-34. (doi: 10.1002/yea.3916; webserver available at https://www.evomicslab.org/app/getprimers/; software available at https://github.com/codeatcg/GetPrimers) [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. (doi: 10.1371/journal.pgen.1011012) [LINK]

Mounir El Maï, Malia Bird, Asma Allouche, Seniye Targen, Naz Şerifoğlu, Bruno Lopes-Bastos, Jean-Marie Guigonis, Da Kang, Thierry Pourchet, Jia-Xing Yue, Miguel Godinho Ferreira*. (2023) Gut-specific telomerase expression counteracts systemic aging in telomerase deficient zebrafish. Nature Aging, 3(5):567-584. (doi: 10.1038/s43587-023-00401-5) [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, 13(3):501 (doi: 10.3390/biom13030501) [LINK]

Melania D’Angiolo, Jia-Xing Yue, Matteo De Chiara, Benjamin P. Barré, Marie-Josèphe Giraud-Panis, Eric Gilson*, Gianni Liti*. (2022) Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones. Genetics, 223(3):iyac186. (doi: 10.1093/genetics/iyac186) [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, 11:e76095. (doi: 10.7554/eLife.76095) [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. (doi: 10.1371/journal.pgen.1010047; software available at https://github.com/yjx1217/RecombineX ) [LINK]

Simone Mozzachiodi^, Lorenzo Tattini^, Agnes Llored, Agurtzane Irizar, Neža Škofljanc, Melania D’Angiolo, Matteo De Chiara, Benjamin P. Barré, Jia-Xing Yue, Angela Lutazi, Sophie Loeillet, Raphaelle Laureau, Souhir Marsit, Simon Stenberg, Benoit Albaud, Karl Persson, Jean-Luc Legras, Sylvie Dequin, Jonas Warringer, Alain Nicolas, Gianni Liti*. (2021) Aborting meiosis allows recombination in sterile diploid yeast hybrids. Nature Communications, 12:6564. (doi: 10.1038/s41467-021-26883-8) [LINK]

Mingjun Gao^, Yang He^, Xin Yin^, Xiangbin Zhong*^, Bingxiao Yan, Yue Wu, Jin Chen, Xiaoyuan Li, Keran Zhai, Yifeng Huang, Xiangyu Gong, Huizhong Chang, Shenghan Xie, Jiyun Liu, Jia-Xing Yue, Jianlong Xu, Guiquan Zhang, Yiwen Deng, Ertao Wang, Didier Tharreau, Guo-Liang Wang, Weibing Yang*, Zuhua He*. (2021) Ca2+ sensor-mediated ROS scavenging suppresses rice immunity and is exploited by a fungal effector. Cell, 184(21): 5391-5404. (doi: 10.1016/j.cell.2021.09.009)[LINK]

Kristoffer Krogerus, Frederico Magalhães, Sandra Castillo, Gopal Peddinti, Virve Vidgren, Matteo De Chiara, Jia-Xing Yue, Gianni Liti, Brian Gibson*. (2021) Lager yeast design through meiotic segregation of a Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid. Frontiers in Fungal Biology, 2:733655. (doi: 10.3389/ffunb.2021.733655) [LINK]

Chun-Min Shan, Jin-Kwang Kim, Jiyong Wang, Kehan Bao, Yadong Sun, Huijie Chen, Jia-Xing Yue, Alessandro Stirpe, Zhiguo Zhang, Chao Lu, Thomas Schalch, Gianni Liti, Peter L. Nagy, Liang Tong, Feng Qiao, Songtao Jia*. (2021) The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin. Cell Reports, 35(7):109137. (doi: 10.1016/j.celrep.2021.109137) [LINK]

Leopold Parts*, Amandine Batté, Maykel Lopes, Michael W Yuen, Meredith Laver, Bryan‐Joseph San Luis, Jia‐Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen*. (2021) Natural variants suppress mutations in hundreds of essential genes. Molecular Systems Biology, 17(5):e10138. (doi: 10.15252/msb.202010138) [LINK]

Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yi-Hua Chen, Fu-Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L Hwang, Yi-Hsien Su*, Jr-Kai Yu*. (2020) Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLoS Genetics, 16(12):e1009294. (doi: 10.1371/journal.pgen.1009294) [LINK]

Raphaelle Laureau, Annie Dyatel, Gizem Dursuk, Samantha Brown, Hannah Adeoye, Jia-Xing Yue, Matteo De Chiara, Anthony Harris, Elçin Ünal, Gianni Liti, Ian R Adams, Luke E Berchowitz*. (2020) Meiotic cells counteract programmed retrotransposon activation via RNA-binding translational repressor assemblies. Developmental Cell, 56:1-14. (doi: 10.1016/j.devcel.2020.11.008) [LINK]

Melania D’Angiolo^, Matteo De Chiara, Jia-Xing Yue, Agurtzane Irizar, Simon Stenberg, Karl Persson, Agnès Llored, Benjamin Barré, Joseph Schacherer, Roberto Marangoni, Eric Gilson, Jonas Warringer, Gianni Liti*. (2020) A yeast living ancestor reveals the origin of genomic introgressions. Nature, 587:420-425. (doi: 10.1038/s41586-020-2889-1) [LINK]

Oleg Simakov^*, Ferdinand Marlétaz^, Jia-Xing Yue, Brendan O’Connell, Jerry Jenkins, Alexander Brandt, Robert Calef, Che-Huang Tung, Tzu-Kai Huang, Jeremy Schmutz, Nori Satoh, Jr-Kai Yu, Nicholas H. Putnam, Richard E. Green, Daniel S. Rokhsar. (2020) Deeply conserved synteny resolves early events in vertebrate evolution. Nature Ecology and Evolution, 4:820-830. (doi: 10.1038/s41559-020-1156-z) [LINK]

Benjamin P Barré, Johan Hallin, Jia-Xing Yue, Karl Persson, Ekaterina Mikhalev, Agurtzane Irizar, Dawn Thompson, Mikael Molin, Jonas Warringer, Gianni Liti*. (2020) Intragenic repeat expansions in the cell wall protein gene HPF1 control yeast chronological aging. Genome Research, 30: 697-710. (doi: 10.1101/gr.253351.119) [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. (doi: 10.15252/embr.201949076) [LINK]

Jia-Xing Yue*, Gianni Liti*. (2019) simuG: a general-purpose genome simulator. Bioinformatics, 35(21):4442-4444. (doi: 10.1093/bioinformatics/btz424; software available at https://github.com/yjx1217/simuG) [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. (doi: 10.1093/molbev/msz006) [LINK]

Jia-Xing Yue*, Gianni Liti*. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols, 13(6):1213-1231. (doi: 10.1038/nprot.2018.025; software available at https://github.com/yjx1217/LRSDAY) [LINK]

Jackson Peter^, Matteo De Chiara^, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barré, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Gianni Liti*, Joseph Schacherer*. (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature, 556(7701):339-344. (doi: 10.1038/s41586-018-0030-5) [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 Nin. (2017) De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Scientific Reports, 7:3935. (doi: 10.1038/s41598-017-03996-z) [LINK]

Chun-Min Shan^, Jiyong Wang^, Ke Xu^, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates III, Peter L. Nagy, Liang Tong*, Songtao Jia*. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. eLife, 5:e17903. (doi: 10.7554/eLife.17903) [LINK]

Jia-Xing Yue*, Nicholas D. Holland, Linda Z. Holland, Dimitri D. Deheyn*. (2016) The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus). Scientific Reports, 6:28350. (co-corresponding author) (doi: 10.1038/srep28350) [LINK]

Kristoffer Krogerus*, Mikko Arvas, Matteo De Chiara, Frederico Magalhães, Laura Mattinen, Merja Oja, Virve Vidgren, Jia-Xing Yue, Gianni Liti, Brian Gibson. (2016) Ploidy influences the functional attributes of de novo lager yeast hybrids. Applied Microbiology and Biotechnology, 100(16):7203. (doi: 10.1007/s00253-016-7588-3) [LINK]

Oleg Simakov*^, Takeshi Kawashima^, Ferdinand Marlétaz, Jerry Jenkins, Ryo Koyanagi, Therese Mitros, Kanako Hisata, Jessen Bredeson, Eiichi Shoguchi, Fuki Gyoja, Jia-Xing Yue, Yi-Chih Chen, Robert M. Freeman, Jr, Akane Sasaki, Tomoe Hikosaka-Katayama, Atsuko Sato, Manabu Fujie, Kenneth W. Baughman, Judith Levine, Paul Gonzalez, Christopher Cameron, Jens H. Fritzenwanker, Ariel M. Pani, Hiroki Goto, Miyuki Kanda, Nana Arakaki, Shinichi Yamasaki, Jiaxin Qu, Andrew Cree, Yan Ding, Huyen H. Dinh, Shannon Dugan, Michael Holder, Shalini N. Jhangiani, Christie L. Kovar, Sandra L. Lee, Lora R. Lewis, Donna Morton, Lynne V. Nazareth, Geoffrey Okwuonu, Jireh Santibanez, Rui Chen, Stephen Richards, Donna M. Muzny, Andrew Gillis, Leonid Peshkin, Michael Wu, Tom Humphreys, Yi-Hsien Su, Nicholas H. Putnam, Jeremy Schmutz, Asao Fujiyama, Jr-Kai Yu, Kunifumi Tagawa, Kim C. Worley, Richard A. Gibbs, Marc W. Kirschner, Christopher J. Lowe, Noriyuki Satoh*, Daniel S. Rokhsar*, John Gerhart*. (2015) Hemichordate genomes and deuterostome origins. Nature, 527(7579):459-465. (doi: 10.1038/nature16150) [LINK]

Roser Buscà, Richard Christen, Matthew Lovern, Alexander M. Clifford, Jia-Xing Yue, Greg G. Goss, Jacques Pouysségur, Philippe Lenormand*. (2015) ERK1 and ERK2 present functional redundancy in tetrapods despite higher evolution rate of ERK1. BMC Evolutionary Biology, 15(1):179. (doi: 10.1186/s12862-015-0450-x) [LINK]

Jia-Xing Yue, Kun-Lung Li, Jr-Kai Yu*. (2015) Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data. Marine Genomics, 24(Part 2):147-157. (doi: 10.1016/j.margen.2015.03.010) [LINK]

Carlos W. Nossa, Paul Havlak, Jia-Xing Yue, Jie Lv, Kimberly Y. Vincent, H. Jane Brockmann, Nicholas H. Putnam*. (2014) Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. GigaScience, 3:9. (doi: 10.1186/2047-217X-3-9) [LINK]

Sihai Yang^, Xiaohui Zhang^, Jia-Xing Yue, Dacheng Tian*, Jian-Qun Chen*. (2008) Recent duplication dominates the expansion of the NBS-encoding genes in two woody species. Molecular Genetics and Genomics, 280(3):187-198. (doi: 10.1007/s00438-008-0355-0) [LINK]