co-first author #
corresponding author *
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.
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.
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.
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.
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.
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.
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.
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.
Hyunghoon Cho, Joe Davis, Xin Li, Kevin S. Smith, Alexis Battle*, Stephen B. Montgomery*. High-resolution transcriptome analysis with long-read RNA sequencing. PLoS ONE 9(9): e108095, 2014.
Sunah Song, Robert Shields, Xin Li, Jing Li*. Joint analysis of sequence data and SNP data using pedigree information for imputation and recombination inference. BMC Proceedings 8 (Suppl 1), S20.
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.