Publications

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. 2022 Jun 6;219(6). doi: 10.1084/jem.20210693. Epub 2022 Apr 7. PubMed PMID: 35389431; PubMed Central PMCID: PMC8996325.

Mayne NR, Elser H, Lin BK, Raman V, Liou D, Li X, D'Amico TA, Jeffrey Yang CF. The Impact of Extended Delayed Surgery for Indolent Lung Cancer or Part-Solid Ground Glass Nodules. Ann Thorac Surg. 2022 Jun;113(6):1827-1834. doi: 10.1016/j.athoracsur.2021.05.099. Epub 2021 Jul 27. PubMed PMID: 34329603; PubMed Central PMCID: PMC8604629.

Mayne NR, Potter AL, Bharol K, Darling AJ, Raman V, Cao C, Li X, D'Amico TA, Jeffrey Yang CF. Perioperative Outcomes and Survival After Preoperative Immunotherapy for Non-Small Cell Lung Cancer. Ann Thorac Surg. 2022 Jun;113(6):1811-1820. doi: 10.1016/j.athoracsur.2021.06.058. Epub 2021 Jul 24. PubMed PMID: 34314692.

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. 2022 May 18;13(1):2748. doi: 10.1038/s41467-022-30470-w. PubMed PMID: 35585086; PubMed Central PMCID: PMC9117277.

Mayne NR, Bajaj SS, Powell J, Elser HC, Civiello BS, Fintelmann FJ, Li X, Yang CJ. Extended Delay to Treatment for Stage III-IV Non-Small-Cell Lung Cancer and Survival: Balancing Risks During the COVID-19 Pandemic. Clin Lung Cancer. 2022 May 5;. doi: 10.1016/j.cllc.2022.05.001. [Epub ahead of print] PubMed PMID: 35660355.


Powell J, Li X. Integrated, data-driven health management: A step closer to personalized and predictive healthcare. Cell Syst. 2022 Mar 16;13(3):201-203. doi: 10.1016/j.cels.2022.02.001. PubMed PMID: 35298911.

Cauwenberghs N, Prunicki M, Sabovčik F, Perelman D, Contrepois K, Li X, Snyder MP, Nadeau KC, Kuznetsova T, Haddad F, Gardner CD. Temporal changes in soluble angiotensin-converting enzyme 2 associated with metabolic health, body composition, and proteome dynamics during a weight loss diet intervention: a randomized trial with implications for the COVID-19 pandemic. Am J Clin Nutr. 2021 Nov 8;114(5):1655-1665. doi: 10.1093/ajcn/nqab243. PubMed PMID: 34375388; PubMed Central PMCID: PMC8574695.

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. 2021 Oct 1;12(1):5757. doi: 10.1038/s41467-021-26040-1. PubMed PMID: 34599181; PubMed Central PMCID: PMC8486823.

Butte KD, Bahmani A, Butte AJ, Li X, Snyder MP. Five-year pediatric use of a digital wearable fitness device: lessons from a pilot case study. JAMIA Open. 2021 Jul;4(3):ooab054. doi: 10.1093/jamiaopen/ooab054. eCollection 2021 Jul. PubMed PMID: 34350390; PubMed Central PMCID: PMC8327370.

Mayne NR, Elser H, Lin BK, Raman V, Liou D, Li X, D'Amico TA, Yang CJ. The Impact of Extended Delayed Surgery for Indolent Lung Cancer or Part-solid Ground Glass Nodules. Ann Thorac Surg. 2021 Jul 27;. doi: 10.1016/j.athoracsur.2021.05.099. [Epub ahead of print] PubMed PMID: 34329603; PubMed Central PMCID: PMC8604629.

Mayne NR, Potter AL, Bharol K, Darling AJ, Raman V, Cao C, Li X, D'Amico TA, Jeffrey Yang CF. Perioperative Outcomes and Survival After Preoperative Immunotherapy for Non-Small Cell Lung Cancer. Ann Thorac Surg. 2021 Jul 24;. doi: 10.1016/j.athoracsur.2021.06.058. [Epub ahead of print] PubMed PMID: 34314692.

Dunn J, Kidzinski L, Runge R, Witt D, Hicks JL, Schüssler-Fiorenza Rose SM, Li X, Bahmani A, Delp SL, Hastie T, Snyder MP. Wearable sensors enable personalized predictions of clinical laboratory measurements. Nat Med. 2021 Jun;27(6):1105-1112. doi: 10.1038/s41591-021-01339-0. Epub 2021 May 24. PubMed PMID: 34031607; PubMed Central PMCID: PMC8293303.

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. 2021 Apr 20;18(1):98. doi: 10.1186/s12974-021-02146-7. PubMed PMID: 33879167; PubMed Central PMCID: PMC8059164.

Yang Y, Li X, Ma Z, Wang C, Yang Q, Byrne-Steele M, Hong R, Min Q, Zhou G, Cheng Y, Qin G, Youngyunpipatkul JV, Wing JB, Sakaguchi S, Toonstra C, Wang LX, Vilches-Moure JG, Wang D, Snyder MP, Wang JY, Han J, Herzenberg LA. CTLA-4 expression by B-1a B cells is essential for immune tolerance. Nat Commun. 2021 Jan 22;12(1):525. doi: 10.1038/s41467-020-20874-x. PubMed PMID: 33483505; PubMed Central PMCID: PMC7822855.

Mishra T, Wang M, Metwally AA, Bogu GK, Brooks AW, Bahmani A, Alavi A, Celli A, Higgs E, Dagan-Rosenfeld O, Fay B, Kirkpatrick S, Kellogg R, Gibson M, Wang T, Hunting EM, Mamic P, Ganz AB, Rolnik B, Li X, Snyder MP. Pre-symptomatic detection of COVID-19 from smartwatch data. Nat Biomed Eng. 2020 Dec;4(12):1208-1220. doi: 10.1038/s41551-020-00640-6. Epub 2020 Nov 18. PubMed PMID: 33208926.

Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, Snyder MP. A Quantitative Proteome Map of the Human Body. Cell. 2020 Oct 1;183(1):269-283.e19. doi: 10.1016/j.cell.2020.08.036. Epub 2020 Sep 10. PubMed PMID: 32916130; PubMed Central PMCID: PMC7575058.

Kobayashi Y, Tremblay-Gravel M, Boralkar KA, Li X, Nishi T, Amsallem M, Moneghetti KJ, Bouajila S, Selej M, Ozen MO, Demirci U, Ashley E, Wheeler M, Knowlton KU, Kouznetsova T, Haddad F. Approaching Higher Dimension Imaging Data Using Cluster-Based Hierarchical Modeling in Patients with Heart Failure Preserved Ejection Fraction. Sci Rep. 2019 Jul 18;9(1):10431. doi: 10.1038/s41598-019-46873-7. PubMed PMID: 31320698; PubMed Central PMCID: PMC6639369.

Li J, Li X, Zhang S, Snyder M. Gene-Environment Interaction in the Era of Precision Medicine. Cell. 2019 Mar 21;177(1):38-44. doi: 10.1016/j.cell.2019.03.004. PubMed PMID: 30901546; PubMed Central PMCID: PMC8108774.

Sun K, Li X, Chen X, Bai Y, Zhou G, Kokiko-Cochran ON, Lamb B, Hamilton TA, Lin CY, Lee YS, Herjan T. Neuron-Specific HuR-Deficient Mice Spontaneously Develop Motor Neuron Disease. J Immunol. 2018 Jul 1;201(1):157-166. doi: 10.4049/jimmunol.1701501. Epub 2018 May 14. PubMed PMID: 29760195; PubMed Central PMCID: PMC6008238.

Herjan T, Hong L, Bubenik J, Bulek K, Qian W, Liu C, Li X, Chen X, Yang H, Ouyang S, Zhou H, Zhao J, Vasu K, Cockman E, Aronica M, Asosingh K, Licatalosi DD, Qin J, Fox PL, Hamilton TA, Driscoll D, Li X. IL-17-receptor-associated adaptor Act1 directly stabilizes mRNAs to mediate IL-17 inflammatory signaling. Nat Immunol. 2018 Apr;19(4):354-365. doi: 10.1038/s41590-018-0071-9. Epub 2018 Mar 21. PubMed PMID: 29563620; PubMed Central PMCID: PMC6082628.

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nat Genet. 2017 Dec;49(12):1664-1670. doi: 10.1038/ng.3969. Epub 2017 Oct 11. PubMed PMID: 29019975; PubMed Central PMCID: PMC6636856.

Yang F, Wang J, Pierce BL, Chen LS. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 Nov;27(11):1859-1871. doi: 10.1101/gr.216754.116. Epub 2017 Oct 11. PubMed PMID: 29021290; PubMed Central PMCID: PMC5668943.

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017 Nov;27(11):1843-1858. doi: 10.1101/gr.216721.116. Epub 2017 Oct 11. PubMed PMID: 29021288; PubMed Central PMCID: PMC5668942.

Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017 Oct 11;550(7675):249-254. doi: 10.1038/nature24041. PubMed PMID: 29022589; PubMed Central PMCID: PMC5723435.

Battle A, Brown CD, Engelhardt BE, Montgomery SB. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. doi: 10.1038/nature24277. PubMed PMID: 29022597; PubMed Central PMCID: PMC5776756.

Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues. Nature. 2017 Oct 11;550(7675):244-248. doi: 10.1038/nature24265. PubMed PMID: 29022598; PubMed Central PMCID: PMC5685192.

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 JA, Kang Z, Su B, Kern TS, Smith JD, Hamilton TA, Melchior F, Fox PL, Li X. IRAK2 directs stimulus-dependent nuclear export of inflammatory mRNAs. Elife. 2017 Oct 9;6. doi: 10.7554/eLife.29630. PubMed PMID: 28990926; PubMed Central PMCID: PMC5675595.

Yan KS, Janda CY, Chang J, Zheng GXY, Larkin KA, Luca VC, Chia LA, Mah AT, Han A, Terry JM, Ootani A, Roelf K, Lee M, Yuan J, Li X, Bolen CR, Wilhelmy J, Davies PS, Ueno H, von Furstenberg RJ, Belgrader P, Ziraldo SB, Ordonez H, Henning SJ, Wong MH, Snyder MP, Weissman IL, Hsueh AJ, Mikkelsen TS, Garcia KC, Kuo CJ. Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal. Nature. 2017 May 11;545(7653):238-242. doi: 10.1038/nature22313. Epub 2017 May 3. PubMed PMID: 28467820; PubMed Central PMCID: PMC5641471.

Li X, Dunn J, Salins D, Zhou G, Zhou W, Schüssler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP. Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. PLoS Biol. 2017 Jan;15(1):e2001402. doi: 10.1371/journal.pbio.2001402. eCollection 2017 Jan. PubMed PMID: 28081144; PubMed Central PMCID: PMC5230763.

Luo H, Li X, Claycomb JM, Lipshitz HD. The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition. G3 (Bethesda). 2016 Nov 8;6(11):3541-3551. doi: 10.1534/g3.116.034199. PubMed PMID: 27591754; PubMed Central PMCID: PMC5100853.

Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA. Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol. 2015 May 12;16:94. doi: 10.1186/s13059-015-0659-4. PubMed PMID: 25962635; PubMed Central PMCID: PMC4460960.

Chen L, Dumelie JG, Li X, Cheng MH, Yang Z, Laver JD, Siddiqui NU, Westwood JT, Morris Q, Lipshitz HD, Smibert CA. Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biol. 2014 Jan 7;15(1):R4. doi: 10.1186/gb-2014-15-1-r4. PubMed PMID: 24393533; PubMed Central PMCID: PMC4053848.

Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):111-30. doi: 10.1002/wrna.1201. Epub 2013 Nov 11. Review. PubMed PMID: 24217996; PubMed Central PMCID: PMC4253089.

Heraud-Farlow JE, Sharangdhar T, Li X, Pfeifer P, Tauber S, Orozco D, Hörmann A, Thomas S, Bakosova A, Farlow AR, Edbauer D, Lipshitz HD, Morris QD, Bilban M, Doyle M, Kiebler MA. Staufen2 regulates neuronal target RNAs. Cell Rep. 2013 Dec 26;5(6):1511-8. doi: 10.1016/j.celrep.2013.11.039. Epub 2013 Dec 19. PubMed PMID: 24360961.

Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Nucleic Acids Res. 2013 Nov;41(20):9438-60. doi: 10.1093/nar/gkt702. Epub 2013 Aug 13. PubMed PMID: 23945942; PubMed Central PMCID: PMC3814352.

Herjan T, Yao P, Qian W, Li X, Liu C, Bulek K, Sun D, Yang WP, Zhu J, He A, Carman JA, Erzurum SC, Lipshitz HD, Fox PL, Hamilton TA, Li X. HuR is required for IL-17-induced Act1-mediated CXCL1 and CXCL5 mRNA stabilization. J Immunol. 2013 Jul 15;191(2):640-9. doi: 10.4049/jimmunol.1203315. Epub 2013 Jun 14. PubMed PMID: 23772036; PubMed Central PMCID: PMC3722902.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311. PubMed PMID: 23846655; PubMed Central PMCID: PMC3929597.

Siddiqui NU, Li X, Luo H, Karaiskakis A, Hou H, Kislinger T, Westwood JT, Morris Q, Lipshitz HD. Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells. Genome Biol. 2012 Feb 20;13(2):R11. doi: 10.1186/gb-2012-13-2-r11. PubMed PMID: 22348290; PubMed Central PMCID: PMC3334568.

Li X, Quon G, Lipshitz HD, Morris Q. Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA. 2010 Jun;16(6):1096-107. doi: 10.1261/rna.2017210. Epub 2010 Apr 23. PubMed PMID: 20418358; PubMed Central PMCID: PMC2874161.