I study RNA systems biology in precision medicine.
Research Information
Research Interests
Human diseases are caused by the interplay between gene and environment. Deep sequencing reveals millions of mutations between the genomes of unrelated individuals; however, the consequences of these mutations remain mostly unclear. Besides genetic impact, the actual development of individuals' disease phenotypes is largely subjected to their lifestyle, behavior, and environmental exposures. Characterizing these highly diverse and dynamic factors goes beyond what can be achieved with regular medical records.
To enable precision medicine and health, my lab seeks to address these gaps by investigating the areas which have not been extensively studied before. On the genetic side, we will focus on investigating the impact of genetic variation on post-transcriptional regulation to study the mechanistic role of RNA binding proteins in human diseases. On the non-genetic side, we will exploit the emerging wearable technology for deep phenotypical and environmental profiling. With the big data strategy integrating multi-omics, phenotypical, and environmental datasets, we are delineating the gene-environment interaction at a personal resolution to achieve precise understandings of human diseases.
Research Projects
Visit the Li Lab Website
Publications
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Hong L, Herjan T, Chen X, Zagore LL, Bulek K, Wang H, Yang CJ, Licatalosi DD, Li X*, Li X*.
“Act1 drives chemoresistance via regulation of antioxidant RNA metabolism and redox homeostasis.” J Exp Med. 221(7). (2024) -
Beqari J, Powell J, Hurd J, Potter AL, McCarthy M, Srinivasan D, Wang D, Cranor J, Zhang L, Webster K, Kim J, Rosenstein A, Zheng Z, Lin TH, Li J, Fang Z, Zhang Y, Anderson A, Madsen J, Anderson J, Clark A, Yang ME, Nurko A, El-Jawahri AR, Sundt TM, Melnitchouk S, Jassar AS, D'Alessandro D, Panda N, Schumacher-Beal LY, Wright CD, Auchincloss HG, Sachdeva UM, Lanuti M, Colson YL, Langer N, Osho A, Yang CJ*, Li X*. “A pilot study using machine learning algorithms and wearable technology for the early detection of postoperative complications after cardiothoracic surgery.” Ann Surg. (2024)
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Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP*, Li X*, Pang B*. “Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs.” Nat Biomed Eng. (2024)
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Li X*+, Perelman D+, Leong AK, Fragiadakis G, Gardner CD*, Snyder MP*. “Distinct factors associated with short-term and long-term weight loss induced by low-fat or low-carbohydrate diet intervention” Cell Rep Med. 3(12):100870 (2022)
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Chen X, Zhao J, Herjan T, Hong L, Liao Y, Liu C, Vasu K, Wang H, Thompson A, Fox PL, Gastman BR, Li X*, Li X*. “IL-17-induced HIF1α drives resistance to anti-PD-L1 via fibroblast-mediated immune exclusion” J Exp Med. 219(6) (2022)
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Liu W, Zhou H, Wang H, Zhang Q, Zhang R, Willard B, Liu C, Kang Z, Li X*, Li X*. “IL-1R-IRAKM-Slc25a1 signaling axis reprograms lipogenesis in adipocytes to promote diet-induced obesity in mice” Nat Commun. 18;13(1):2748 (2022)
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Powell J, Li X. “Integrated, data-driven health management: A step closer to personalized and predictive healthcare” Cell Syst. 13(3):201-203 (2022)
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Bahmani A, Alavi A, Buergel T, Upadhyayula S, Wang Q, Ananthakrishnan SK, Alavi A, Celis D, Gillespie D, Young G, Xing Z, Nguyen MHH, Haque A, Mathur A, Payne J, Mazaheri G, Li JK, Kotipalli P, Liao L, Bhasin R, Cha K, Rolnik B, Celli A, Dagan-Rosenfeld O, Higgs E, Zhou W, Berry CL, Van Winkle KG, Contrepois K, Ray U, Bettinger K, Datta S, Li X*, Snyder MP*. “A scalable, secure, and interoperable platform for deep data-driven health management” Nat Commun. 12(1):5757 (2021)
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Zhao J, Liao Y, Miller-Little W, Xiao J, Liu C, Li X, Li X*, Kang Z*. "STEAP4 expression in CNS resident cells promotes Th17 cell-induced autoimmune encephalomyelitis." J Neuroinflammation. 18(1):98 (2021)
- Yang Y., Li X., Ma Z., Wang C., Yang Q., Hong R., Min Q., Zhou G., Cheng Y., Qin G., Youngyunpipatkul J., Byrne-Steele M., Wing J., Sakaguchi S., Wang Y., Toonstra C., Wang L., Vilches-Moure J., Wang D., Snyder M., Han J., Herzenberg L.
“CTLA-4 expression by B-1a B cells is essential for immune tolerance”
Nat Commun. 12(1):525 (2021) - Mishra T., Wang M., Metwally A., Bogu G., Brooks A., Bahmani A., Alavi A., Celli A., Higgs E., Dagan-Rosenfeld O., Fay B., Kirkpatrick S., Kellogg R., Gibson M., Wang T., Hunting E., Mamic P., Ganz A., Rolnik B., Li X*., Snyder MP*.
“Pre-symptomatic detection of COVID-19 from smartwatch data”
Nat Biomed Eng 4, 1208–1220 (2020) - Lihua J., Wang M., Lin S., Jian R., Li X., Chan J., Fang H., Dong G., GTEx Consortium, Snyder MP.
“A Quantitative Proteome Map of the Human Body”
Cell 183 (1), 269– 283e19 (2020) - Kobayashi Y., Tremblay-Gravel M., Boralkar K.A., Li X., Nishi T., Amsallem M., Moneghetti K.J., Bouajila S., Selej M., Ozen M.O., Demirci U., Ashley E., Wheeler M., Knowlton K.U., Kouznetsova T., Haddad F.
“Approaching Higher Dimension Imaging Data Using Cluster-Based Hierarchical Modeling in Patients with Heart Failure Preserved Ejection Fraction”
Sci Rep. 9(1):10431 (2019) - Li J., Li X., Zhang S., Snyder M.
“Gene environment interaction in the era of precision medicine”
Cell 177(1):38-44 (2019) - Zhou H.*, Bulek K.*, Li X.*, Herjan T.*, Yu M., Qian W., Wang H., Zhou G., Chen X., Yang H., Hong L., Zhao J., Qin L., Fukuda K., Flotho A., Gao J., Dongre A., Carman J.A., Kang Z., Su B., Kern T.S., Smith J.D., Hamilton T.A., Melchior F., Fox P.L., Li X.
“IRAK2 directs stimulus-dependent nuclear export of inflammatory mRNAs”
eLife 6: e29630 (2017) - Li X.*, Dunn J.*, Salins D.*, Zhou G., Zhou W., Rose M.S., Perelman D., Colbert E., Runge R., Rego S., Sonecha R., Datta S., McLaughlin T., Snyder M.P.
“Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information”
PLOS Biol. 15(1): e2001402 (2017) - Li X.*, Kazan H.*, Lipshitz H.D., Morris Q.D.
“Finding the target sites of RNA-binding proteins”
Wiley Interdiscip Rev RNA 5:111-130 (2014) - Laver J.D.*, Li X.*, Ancevicius K.*, Westwood J.T., Smibert C.A., Morris Q.D., Lipshitz H.D.
“Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity”
Nucleic Acids Res. 41:9438-9460. (2013) - Li X., Quon G., Lipshitz H.D., Morris Q.
“Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure”
RNA 16:1096-1107 (2010)