Research Areas:
Human genetic variation, functional consequences of rare variation. 1) Personal burden of rare genetic variants and its health implication. 2) Non-coding variation and function. 3) RNA-seq and application in undiagnosed diseases. 4) Machine learning methods for understanding genome function and their application in precision medicine.

Brief Biography:
2018/12-Now: Professor, Principal Investigator CAS-MPG Partner Institute for Computational Biology
2016/06-2018/11: Research Associate, Stanford University
2012/01-2016/05: Postdoctoral Fellow, Stanford University
2010/01-2011/12: Postdoctoral Fellow, Case Western Reserve University
2005/08-2010/01: Ph.D. in Computer Science, Case Western Reserve University
2001/07-2005/07: B.S. in Computer Science, Tsinghua University

Selected Publications: (*Corresponding Author)

1. Dong, D.^#, H. Shen, Z. Wang, J. Liu, Z. Li, X. Li* (2023). An RNA-informed dosage sensitivity map reflects intrinsic functional nature of genes. Am J Hum Genet Sep 7;110(9):1509-1521.
2. Matsushita, K.^#, X. Li^#, Y. Nakamura, D. Dong, K. Mukai, M. Tsai, S. B. Montgomery, S. J. Galli* (2021). The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice. JCI Insight Jun 22;6(12):e146572.
3. Bonder, M. J.*, C. Smail*, M. J. Gloudemans, L. Fresard, D. Jakubosky, M. D'Antonio, X. Li, N. M. Ferraro, I. Carcamo-Orive, B. Mirauta, D. D. Seaton, N. Cai, D. Vakili, D. Horta, C. Zhao, D. B. Zastrow, D. E. Bonner, C. HipSci, P. c. i, N. Undiagnosed Diseases, P. S. c. PhLi, M. T. Wheeler, H. Kilpinen, J. W. Knowles, E. N. Smith, K. A. Frazer, S. B. Montgomery*, O. Stegle* (2021). Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet Mar;53(3):313-321.
4. Ferraro, N. M., B. J. Strober, J. Einson, N. S. Abell, F. Aguet, A. N. Barbeira, M. Brandt, M. Bucan, S. E. Castel, J. R. Davis, E. Greenwald, G. T. Hess, A. T. Hilliard, R. L. Kember, B. Kotis, Y. Park, G. Peloso, S. Ramdas, A. J. Scott, C. Smail, E. K. Tsang, S. M. Zekavat, M. Ziosi, Aradhana, T. O. L. W. Group, K. G. Ardlie, T. L. Assimes, M. C. Bassik, C. D. Brown, A. Correa, I. Hall, H. K. Im, X. Li, P. Natarajan, G. T. Consortium, T. Lappalainen, P. Mohammadi*, S. B. Montgomery*, A. Battle* (2020). Transcriptomic signatures across human tissues identify functional rare genetic variation. Science Sep 11;369(6509):eaaz5900.
5. Fresard, L.*, C. Smail, N. M. Ferraro, N. A. Teran, X. Li, K. S. Smith, D. Bonner, K. D. Kernohan, S. Marwaha, Z. Zappala, B. Balliu, J. R. Davis, B. Liu, C. J. Prybol, J. N. Kohler, D. B. Zastrow, C. M. Reuter, D. G. Fisk, M. E. Grove, J. M. Davidson, T. Hartley, R. Joshi, B. J. Strober, S. Utiramerur, N. Undiagnosed Diseases, C. Care4Rare Canada, L. Lind, E. Ingelsson, A. Battle, G. Bejerano, J. A. Bernstein, E. A. Ashley, K. M. Boycott, J. D. Merker, M. T. Wheeler, S. B. Montgomery* (2019). Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nat Med Jun;25(6):911-919.
6. Pala, M., Z. Zappala, M. Marongiu, X. Li, J. R. Davis, R. Cusano, F. Crobu, K. R. Kukurba, M. J. Gloudemans, F. Reinier, R. Berutti, M. G. Piras, A. Mulas, M. Zoledziewska, M. Marongiu, E. P. Sorokin, G. T. Hess, K. S. Smith, F. Busonero, A. Maschio, M. Steri, C. Sidore, S. Sanna, E. Fiorillo, M. C. Bassik, S. J. Sawcer, A. Battle, J. Novembre, C. Jones, A. Angius, G. R. Abecasis, D. Schlessinger, F. Cucca*, S. B. Montgomery* (2017). Population- and individual-specific regulatory variation in Sardinia. Nat Genet May;49(5):700-707.
7. Li, X.^#, Y. Kim^#, E. K. Tsang^#, J. R. Davis^#, F. N. Damani, C. Chiang, G. T. Hess, Z. Zappala, B. J. Strober, A. J. Scott, A. Li, A. Ganna, M. C. Bassik, J. D. Merker, G. T. Consortium, D. A. Laboratory, G. Coordinating Center -Analysis Working, G. Statistical Methods groups-Analysis Working, G. g. Enhancing, N. I. H. C. Fund, Nih/Nci, Nih/Nhgri, Nih/Nimh, Nih/Nida, N. Biospecimen Collection Source Site, R. Biospecimen Collection Source Site, V. Biospecimen Core Resource, B. Brain Bank Repository-University of Miami Brain Endowment, M. Leidos Biomedical-Project, E. Study, I. Genome Browser Data, E. B. I. Visualization, I. Genome Browser Data, U. o. C. S. C. Visualization-Ucsc Genomics Institute, I. M. Hall, A. Battle*, S. B. Montgomery* (2017). The impact of rare variation on gene expression across tissues. Nature Oct 11;550(7675):239-243.
8. Chiang, C., A. J. Scott, J. R. Davis, E. K. Tsang, X. Li, Y. Kim, T. Hadzic, F. N. Damani, L. Ganel, G. T. Consortium, S. B. Montgomery, A. Battle, D. F. Conrad*, I. M. Hall* (2017). The impact of structural variation on human gene expression. Nat Genet May;49(5):692-699.
9. Babak, T., B. DeVeale, E. K. Tsang, Y. Zhou, X. Li, K. S. Smith, K. R. Kukurba, R. Zhang, J. B. Li, D. van der Kooy, S. B. Montgomery, H. B. Fraser* (2015). Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. Nat Genet May;47(5):544-549.
10. Zhang, R., X. Li, G. Ramaswami, K. S. Smith, G. Turecki, S. B. Montgomery*, J. B. Li* (2014). Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. Nat Methods Jan;11(1):51-54.
11. Li, X.*, A. Battle, K. J. Karczewski, Z. Zappala, D. A. Knowles, K. S. Smith, K. R. Kukurba, E. Wu, N. Simon, S. B. Montgomery* (2014). Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. Am J Hum Genet Sep 4;95(3):245-256.
12. Li, X., J. Li* (2011). Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference. J Comput Biol Nov;18(11):1411-1421.
13. Li, X., X. Yin, J. Li* (2010). Efficient identification of identical-by-descent status in pedigrees with many untyped individuals. Bioinformatics Jun 15;26(12):i191-198.