Journal Articles

Jiang MZ, Gaynor SM, Li X, Van Buren E, et al., Reiner AP, Bowler RP, Lin X, Auer PL, Raffield LM, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & TOPMed Inflammation Working Group. (2024). Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium. Human Molecular Genetics, ddae050.

Sun Q, Yang Y, Rosen JD, Chen J, Li X, Guan W, Jiang MZ, Wen J, Pace RG, Blackman SM, Bamshad MJ, Gibson RL, Cutting GR, O’Neal WK, Knowles MR, Kooperberg C, Reiner AP, Raffield LM, Carson AP, Rich SS, Rotter JI, Loos RJF, Kenny E, Jaeger BC, Min YI, Fuchsberger C, & Li Y. (2024). MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric. The American Journal of Human Genetics, 111(5), 990-995.

Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MS, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Manning AK, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O’Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter JI, Natarajan P, Peloso GM, Li Z, & Lin X. (2023). Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nature Genetics, 55(1), 154-164.

Wang Y, Selvaraj MS, Li X, et al., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Rotter JI, Lin X, Natarajan P, & Peloso GM. (2023). Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study. The American Journal of Human Genetics, 110(10), 1704-1717.

Feofanova EV, Brown MR, Alkis T, Manuel AM, Li X, Tahir UA, Li Z, Mendez KM, Kelly RS, Qi Q, Chen H, Larson MG, Lemaitre RN, Morrison AC, Grieser C, Wong KE, Gersztern RE, Zhao Z, Lasky-Su J, NHLBI Trans-Omics for Precision Medicine (TOPMed), & Bing Yu. (2023). Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations. Nature Communications, 14, 3111.

Hasbani NR, Westerman KE, Kwak SH, Chen H, Li X, et al., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Atherosclerosis Working Group, TOPMed Diabetes Working Group, Wu JC, Malhotra R, Peyser PA, Morrison AC, Vasan RS, Lin X, Rotter JI, Meigs JB, Manning AK, & de Vries PS. (2023). Type 2 Diabetes Modifies the Association of CAD Genomic Risk Variants With Subclinical Atherosclerosis. Circulation: Genomic and Precision Medicine, 16(6), e004176.

Li Z*, Li X*, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O’Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter JI, Willer CJ, Natarajan P, Peloso GM, & Lin X. (2022). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19(12), 1599-1611.

Li X*, Yung G*, Zhou H, Sun R, Li Z, Hou K, Zhang MJ, Liu Y, Arapoglou T, Wang C, Ionita-Laza I, & Lin X. (2022). A multi-dimensional integrative scoring framework for predicting functional variants in the human genome. The American Journal of Human Genetics, 109(3), 446-456.

• This paper was chosen by the IGES Communications Committee as the selection for February 2022.

Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody, JA, Cade BE, Chuang LM, Chung RH, Curran JE, de las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, Kral BG, Lange L, Li X, Martin L, Lubitz SA, Manichaikul AW, Preuss M, Montasser ME, Morrison AC, Naseri T, O’Connell, JR, Palmer ND, Peyser PA, Reupena MS, Smith JA, Sun X, Taylor KD, Tracy RP, Tsai MY, Wang Z, Wang Y, Wei B, Wilkins JT, Yanek LR, Zhao W, Arnett DK, Blangero J, Boerwinkle E, Bowden DW, Chen YDI, Correa A, Cupples LA, Dutcher SK, Ellinor PT, Fornage M, Gabriel S, Germer S, Gibbs R, He J, Kaplan RC, Kardia SLR, Kim R, Kooperberg C, Loos RJF, Martinez K, Mathias RA, McGarvey ST, Mitchell BD, Nickerson D, North KE, Psaty BM, Redline S, Reiner AP, Vasan RS, Rich SS, Willer C, Rotter JI, Rader DJ, Lin X, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Peloso GM, & Natarajan P. (2022). Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nature Communications, 13, 5995.

Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Relm HL, Sofia HJ, Snyder G, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Z, Neale B, Sunyaev SR, & Lin X. (2023). FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Research, 51(D1), D1300-D1311.

Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, & Amos CI. (2022). Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nature Genetics, 54(8), 1167-1177.

Gaynor SM, Westerman KE, Ackovic LL, Li X, Li Z, Manning AK, Philippakis A, & Lin X. (2022). STAAR Workflow: A cloud-based workflow for scalable and reproducible rare variant analysis. Bioinformatics, btac272.

West ER, Lapan SW, Lee CH, Kajderowicz KM, Li X, & Cepko CL. (2022). Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity. Cell Reports, 38(1), 110191.

Kim DH, Li X, Bian S, Wei LJ, & Sun R. (2021). Utility of restricted mean survival time for analyzing time to nursing home placement among patients with dementia. JAMA Network Open, 4(1), e2034745.

Sun R, Xu M, Li X, Gaynor S, Zhou H, Li Z, Bossé Y, Lam S, Tsao MS, Tardon A, Chen C, Doherty J, Goodman G, Bojesen SE, Landi MT, Johansson M, Field JK, Bicheböller H, Wichmann HE, Risch A, Rennert G, Arnold S, Wu X, Melander O, Brunnström H, Marchand LL, Liu G, Andrew A, Duell E, Kiemeney LA, Shen H, Haugen A, Johansson M, Grankvist K, Caporaso N, Woll P, Teare MD, Scelo G, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Albanes D, Mak R, Barbie D, Brennan P, Hung RJ, Amos CI, Christiani DC, & Lin X. (2021). Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genetic Epidemiology, 45(1), 99-114.

Wang X, Ricciuti B, Nguyen T, Li X, Rabin MS, Awad MM, Lin X, Johnson BE, & Christiani DC. (2021). Association between smoking history and tumor mutation burden in advanced non-small cell lung cancer. Cancer Research, 81(9), 2566-2573.

Li X*, Li Z*, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O’Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, & Lin X. (2020). Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics, 52(9), 969-983.

• This paper was chosen by the IGES Communications Committee as the selection for October 2020.

Li X, & Song Y. (2020). Target population statistical inference with data integration across multiple sources - an approach to mitigate information shortage in rare disease clinical trials. Statistics in Biopharmaceutical Research, 12(3), 322-333.

Li Z, Li X, Liu Y, Shen J, Chen H, Zhou H, Morrison AC, Boerwinkle E, & Lin X. (2019). Dynamic scan procedure for detecting rare-variant association regions in whole-genome sequencing studies. The American Journal of Human Genetics, 104(5), 802-814.

Zhu Z, Wang X, Li X, Lin Y, Shen S, Liu CL, Hobbs BD, Hasegawa K, Liang L, International COPD Genetics Consortium, Boezen HM, Camargo CA, Cho MH, & Christiani DC. (2019). Genetic overlap of chronic obstructive pulmonary disease and cardiovascular diseases: A large-scale genome-wide cross-trait analysis. Respiratory Research, 20(1), 64.

Lin CK, Chen T, Li X, de Marcellis-Warin N, Zigler C, & Christiani DC. (2019). Are per capita carbon emissions predictable across countries? Journal of Environmental Management, 237, 569-575.

Zhu Z, Lin Y, Li X, Driver JA, & Liang L. (2019). Shared genetic architecture between metabolic traits and Alzheimer’s disease: a large-scale genome-wide cross-trait analysis. Human Genetics, 138(3), 271-285.

Lee PH, Lee C, Li X, Wee B, Dwivedi T, & Daly M. (2018). Principles and methods of in-silico prioritization of non-coding regulatory variants. Human Genetics, 137(1), 15-30.

* Indicates equal contribution as first authors.