代表论文
通讯作者 *
共同一作 #
Xubing Liu#, Zhao Chen#, Qian Jiang#, Haoyu Shen#, Hongyu Liu, Zhenguo Wang, Zhe Li, Jihong Wu*, Hong Jiang*, Xin Li*. Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome. Genome Medicine 10.1186/s13073-026-01653-7
揭示结构变异的组织特异性致病机制
PathoSV分析框架量化结构变异对不同组织转录本的破坏效应，揭示组织特异性基因剂量扰动是结构变异的重要致病机制。在遗传性视网膜疾病和遗传性共济失调队列中，分别为10.1%和3.2%的既往未确诊病例提供了分子诊断。
Zhenguo Wang#, Zhe Li, Hongyu Liu, Chenghua Yang, Xin Li*. Mitochondrial clonal mosaicism encodes a biphasic molecular clock of aging. Nature Aging 10.1038/s43587-025-00890-6
建立线粒体双相分子时钟，揭示人体器官的异步衰老
揭示增殖组织与终末分化组织中线粒体突变积累的不同演化规律，建立刻画人体不同组织衰老差异的分子时钟。
Danyue Dong#, Haoyu Shen, Zhenguo Wang, Jiaqi Liu, Zhe Li, Xin Li*. An RNA-informed dosage sensitivity map reflects intrinsic functional nature of genes. American Journal of Human Genetics 110:1–13, 2023.
构建组织特异性基因剂量敏感性图谱
整合多组织 RNA 表达与遗传变异信息，量化基因对剂量扰动的组织特异性敏感程度，为理解基因功能约束及遗传病的组织选择性提供分析框架。
Xin Li#, Yungil Kim#, Emily K. Tsang#, Joe R. Davis#, Farhan N. Damani, Colby Chiang, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Andrea Ganna, Jason Merker, Daniel MacArthur, GTEx Consortium, Ira M. Hall, Alexis Battle* and Stephen B. Montgomery*. The impact of rare variation on gene expression across tissues. Nature 550:239-243, 2017.
揭示罕见遗传变异对跨组织基因表达的影响
利用大规模人类多组织转录组数据，系统揭示罕见遗传变异与基因表达异常之间的关系，为通过转录组解析遗传变异的功能效应提供了依据。
Xin Li*, Alexis Battle, Konrad J. Karczewski, Zach Zappala, David A. Knowles, Kevin S. Smith, Kim R. Kukurba, Eric Wu, Noah Simon, Stephen B. Montgomery*. Transcriptome sequencing of a large human family identifies the impact of rare non-coding variants. American Journal of Human Genetics 95(3):245-256, 2014.
通过家系转录组测序解析罕见非编码变异的功能效应
利用大型人类家系的转录组数据，将罕见非编码变异与基因表达变化联系起来，探索从RNA分子表型识别遗传变异功能效应的研究路径。
2018-2024
Zengming Wang#, Haolan Yu#, Wei Bao#, Min Qu#, Yan Wang, Liandong Zhang, Xubing Liu, Chen Liu, Miaoxia He, Jing Li, Zhenyang Dong, Yun Zhang, Bo Yang, Jianguo Hou, Chuanliang Xu, Linhui Wang*, Xin Li*, Xu Gao*, Chenghua Yang*. Proteomic and phosphoproteomic landscape of localized prostate cancer unveils distinct molecular subtypes and insights into precision therapeutics. PNAS. 2024 Sep 25;121(40):e2402741121.
前列腺癌的分子亚型
和精准治疗
Xubing Liu#, Fangyuan Hu#, Daowei Zhang, Zhe Li, Jianquan He, Shenghai Zhang, Zhenguo Wang, Yingke Zhao, Jiawen Wu, Chen Liu, Chenchen Li, Xin Li*, Jihong Wu*. Whole genome sequencing enables new genetic diagnosis for inherited retinal diseases by identifying pathogenic variants. NPJ Genom Med. 2024 Jan 20;9(1):6.
全基因组测序在遗传视网膜
疾病诊断中的应用
Xuebin Zhang#, Zengming Wang#, Shengsong Huang#, Dongyin He#, Weiwei Yan, Qian Zhuang, Zixian Wang, Chenyang Wang, Qilong Tan, Ziqun Liu, Tao Yang, Ying Liu, Ruobing Ren, Jing Li, William Butler, Huiru Tang, Gong-Hong Wei, Xin Li*, Denglong Wu*, Zhenfei Li*. Active DHEA uptake in the prostate gland correlates with aggressive prostate cancer. J Clin Invest. 2023 Dec 15;133(24):e171199.
Smail C*, Ferraro NM, Hui Q, Durrant MG, Aguirre M, Tanigawa Y, Keever-Keigher MR, Rao AS, Justesen JM, Li X, Gloudemans MJ, Assimes TL, Kooperberg C, Reiner AP, Huang J, O'Donnell CJ, Sun YV; Million Veteran Program; Rivas MA, Montgomery SB*. Integration of rare expression outlier-associated variants improves polygenic risk prediction. Am J Hum Genet. 2022 Jun 2;109(6):1055-1064.
Matsushita K#, Li X#, Nakamura Y, Dong D, Mukai K, Tsai M, Montgomery SB, Galli SJ*. The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice. JCI Insight. 2021 Jun 22;6(12):e146572.
Bonder MJ#*,, Smail C#*,, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE; HipSci Consortium; iPSCORE consortium; Undiagnosed Diseases Network; PhLiPS consortium; Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O*. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet. 2021 Mar;53(3):313-321.
Ferraro NM#, Strober BJ#, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR, Greenwald E, Hess GT, Hilliard AT, Kember RL, Kotis B, Park Y, Peloso G, Ramdas S, Scott AJ, Smail C, Tsang EK, Zekavat SM, Ziosi M, Aradhana; TOPMed Lipids Working Group; Ardlie KG, Assimes TL, Bassik MC, Brown CD, Correa A, Hall I, Im HK, Li X, Natarajan P; GTEx Consortium; Lappalainen T, Mohammadi P*, Montgomery SB*, Battle A*. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science. 2020 Sep 11;369(6509):eaaz5900.
Liu B#, Calton MA#, Abell NS, Benchorin G, Gloudemans MJ, Chen M, Hu J, Li X, Balliu B, Bok D, Montgomery SB*, Vollrath D*. Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. Commun Biol. 2019 May 20;2:186.
Balliu B#, Durrant M, Goede O, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E#, Montgomery SB#. Genetic regulation of gene expression and splicing during a 10-year period of human aging. Genome Biol. 2019 Nov 4;20(1):230.
2014-2017
Emily K. Tsang, Nathan S. Abell, Xin Li, Vanessa Anaya, Konrad J. Karczewski, David A. Knowles, Raymond G. Sierra, Kevin S. Smith, and Stephen B. Montgomery*. Small RNA sequencing in cells and exosomes identifies eQTLs and 14q32 as a region of active export. G3: Genes|Genomes|Genetics 7(1):31-39, 2017.
Mauro Pala#, Zachary Zappala#, Mara Marongiu, Xin Li, Joe Reese Davis, Roberto Cusano, Francesca Crobu, Kimberly Kukurba, Frederic Reinier, Riccardo Berutti, Maria Giovanna Piras, Antonella Mulas, Magdalena Zoledziewska, Michele Marongiu, Fabio Busonero, Andrea Maschio, Maristella Steri, Carlo Sidore, Serena Sanna, Edoardo Fiorillo, Alexis Battle, John Novembre, Chris Jones, Andrea Angius, Goncalo Rocha Abecasis, David Schlessinger, Francesco Cucca*, Stephen Montgomery*. Population and individual effects of non-coding variants inform genetic risk factors. Nature genetics 49 (5):700-707,2017.
Colby Chiang, Alexandra Scott, Joe Davis, Emily Tsang, Xin Li, Yungil Kim, Farhan Damani, Liron Ganel, GTEx Consortium, Stephen Montgomery, Alexis Battle, Donald Conrad* and Ira Hall*. The impact of structural variation on human gene expression. Nature genetics 49(5):692-699, 2017.
Kimberly R Kukurba, Princy Parsana, Brunilda Balliu, Kevin S Smith, Zachary Zappala, David A Knowles, Marie-Julie FavôL, Joe R Davis, Xin Li, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Anshul Kundaje, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, Alexis Battle, Stephen B Montgomery*. Impact of the x chromosome and sex on regulatory variation. Genome Research 26(6):768-777, 2016.
Tomas Babak, Brian DeVeale, Emily K Tsang, Yiqi Zhou, Xin Li, Kevin S Smith, Kim R Kukurba, Rui Zhang, Jin Billy Li, Derek van der Kooy, Stephen B Montgomery, Hunter B Fraser*. Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. Nature genetics 47(5):544549, 2015.
Kimberly R Kukurba, Rui Zhang, Xin Li, Kevin S Smith, David A Knowles, Meng How Tan, Robert Piskol, Monkol Lek, Michael Snyder, Daniel G MacArthur, Jin Billy Li*, Stephen B Montgomery*. Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues. PLoS genetics 10(5):e1004304, 2014.
Rui Zhang, Xin Li, Gokul Ramaswami, Kevin S Smith, Gustavo Turecki, Stephen B Montgomery*, Jin Billy Li*. Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. Nature methods 11(1), 51-54, 2014.
2014以前
Xin Li and Jing Li*. Haplotype reconstruction in large pedigrees with untyped individuals through IBD Inference. Journal of Computational Biology 18(11):1411-21, 2011.
Xin Li, Xiaolin Yin and Jing Li*. Efficient identification of identical-by-descent status in pedigrees with many untyped individuals. Bioinformatics 26(12):i191-i198, 2010.
Xin Li and Jing Li*. An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. Journal of Bioinformatics and Computational Biology 7(3):521-545, 2009.