Superfund Research Program

Xihong Lin

Harvard School of Public Health
Biostatistics, Bldg 2-451
655 Huntington Dr.
Boston, Massachusetts 02115
Phone: 617-432-2914
Fax: 617-432-5619
Email: xlin@hsph.harvard.edu

Projects

• Harvard School of Public Health: Data Management and Analysis Core (2020-2025)
• Harvard School of Public Health: Environmental Statistics Core (2010-2015)

Publications

2024

• Van Buren E, Azzara D, Rangel-Moreno J, Garcia-Hernandez M, Murphy S, Cohen ED, Lewis E, Lin X, Park H. 2024. Single-cell RNA sequencing reveals placental response under environmental stress. Nat Commun 15(1):doi:10.1038/s41467-024-50914-9 PMID:39095385 PMCID:11297347

2023

• McCaw Z, Gaynor S, Sun R, Lin X. 2023. Leveraging a surrogate outcome to improve inference on a partially missing target outcome. Biometrics 79(2):1472-1484. doi:10.1111/biom.13629 PMID:35218565 PMCID:11023615
• Sun R, Shi A, Lin X. 2023. Differences in set-based tests for sparse alternatives when testing sets of outcomes compared to sets of explanatory factors in genetic association studies. Biostatistics 25(1):171-187. doi:10.1093/biostatistics/kxac036 PMID:36000269 PMCID:10724113
• Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore JE, Asok A, Kumar S, Blue EE, Buyske S, Cox NJ, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, Weng Z, Neale BM, Sunyaev SR, Lin X. 2023. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res 51:1300-1311. doi:10.1093/nar/gkac966 PMID:36350676 PMCID:9825437

2022

• 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. Am J Hum Genet 103(3):446-456. doi:10.1016/j.ajhg.2022.01.017 PMID:35216679 PMCID:8948160
• Li Z, Liu Y, Lin X. 2022. Simultaneous detection of signal regions using quadratic scan statistics with applications to whole genome association studies. J Am Stat Assoc 117(538):823-834. doi:10.1080/01621459.2020.1822849 PMID:35845434 PMCID:PMC9285665
• Liu Z, Shen J, Barfield R, Schwartz J, Baccarelli A, Lin X. 2022. Large-scale hypothesis testing for causal mediation effects with Applications in genome-wide epigenetic studies. J Am Stat Assoc 117(537):67-81. doi:10.1080/01621459.2021.1914634 PMID:35989709 PMCID:9385159

2020

• Chen S, Lin X. 2020. Analysis in case-control sequencing association studies with different sequencing depths. Biostatistics 21:577-593. doi:10.1093/biostatistics/kxy073 PMID:30590456 PMCID:PMC7308042
• Li X, Li Z, Zhou H, Gaynor S, Liu Y, Chen H, Sun R, Dey R, Arnett D, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples A, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SL, 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, 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 F, Weeks DE, Weng Z, Wilson JG, Yanek LR, 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. Nat Genet 52:969-983. doi:10.1038/s41588-020-0676-4 PMID:32839606 PMCID:PMC7483769
• Sun R, Xu M, Li X, Gaynor S, Zhou H, Li Z, Bosse Y, Lam S, Tsao M, Tardon A, Chen C, Doherty JA, Goodman G, Bojesen SE, Landi MT, Johansson M, Field JK, Bickeboller H, Wichmann H, Risch A, Rennert G, Arnold S, Wu X, Melander O, Brunnstrom H, Le Marchand L, Liu G, Andrew AS, Duell EJ, Kiemeney LA, Shen H, Haugen A, Johansson M, Grankvist K, Caporaso N, Woll P, Dawn Teare M, Scelo G, Hong Y, Yuan J, Lazarus P, Schabath MB, Aldrich MC, Albanes D, Mak R, Barbie D, Brennan P, Hung RJ, Amos CI, Christiani DC, Lin X. 2020. Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genet Epidemiol doi:10.1002/gepi.22358 PMID:32924180

2018

• Sun R, Wang Z, Henn BC, Su L, Lu Q, Lin X, Wright RO, Bellinger DC, Kile ML, Mazumdar M, Tellez-Rojo MM, Schnaas L, Christiani DC. 2018. Identification of novel loci associated with infant cognitive ability. Mol Psychiatry PMID:30120420

2017

• Sun R, Carroll RJ, Christiani DC, Lin X. 2017. Testing for gene-environment interaction under exposure misspecification. Biometrics doi:10.1111/biom.12813 PMID:29120492
• Wang Z, Henn BC, Wang C, Wei Y, Li S, Sun R, Chen H, Wagner PJ, Lu Q, Lin X, Wright RO, Bellinger DC, Kile ML, Mazumdar M, Tellez-Rojo M, Schnaas L, Christiani DC. 2017. Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment. Environ Health 16:81. doi:10.1186/s12940-017-0288-3 PMID:28754176 PMCID:PMC5534076

2016

• Lin X, Lee S, Wu MC, Wang C, Chen H, Li Z, Lin X. 2016. Test for rare variants by environment interactions in sequencing association studies. Biometrics 72(1):156-164. doi:10.1111/biom.12368 PMID:26229047 PMCID:PMC4733434

2015

• Seow W, Pan W, Kile ML, Tong L, Baccarelli A, Quamruzzaman Q, Rahman M, Mostofa G, Rakibuz-Zaman M, Ahsan H, Lin X, Christiani DC, Kibriya MG. 2015. A distinct and replicable variant of the squamous cell carcinoma gene inositol polyphosphate-5-phosphatase modifies the susceptibility of arsenic-associated skin lesions in Bangladesh. Cancer 121(13):2222-2229. doi:10.1002/cncr.29291 PMID:25759212 PMCID:PMC4565788
• Wang C, Zhan X, Liang L, Abecasis GR, Lin X. 2015. Improved ancestry estimation for both genotyping and sequencing data using projection procrustes analysis and genotype imputation. Am J Hum Genet 96(6):926-937. doi:10.1016/j.ajhg.2015.04.018 PMID:26027497 PMCID:PMC4457959

2014

• Fan T, Fang SC, Cavallari JM, Barnett IJ, Wang Z, Su L, Byun H, Lin X, Baccarelli A, Christiani DC. 2014. Heart rate variability and DNA methylation levels are altered after short-term metal fume exposure among occupational welders: a repeated-measures panel study. BMC Public Health 14:1279. doi:10.1186/1471-2458-14-1279 PMID:25512264 PMCID:PMC4302115
• Lee S, Abecasis GR, Boehnke M, Lin X. 2014. Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet 95(1):5-23. doi:10.1016/j.ajhg.2014.06.009 PMID:24995866 PMCID:PMC4085641
• Seow W, Kile ML, Baccarelli A, Pan W, Byun H, Mostofa G, Quamruzzaman Q, Rahman M, Lin X, Christiani DC. 2014. Epigenome-wide DNA methylation changes with development of arsenic-induced skin lesions in Bangladesh: a case-control follow-up study. Environ Mol Mutagen 55(6):449-456. doi:10.1002/em.21860 PMID:24677489 PMCID:PMC4082746

2013

• Lin X, Lee S, Christiani DC, Lin X. 2013. Test for interactions between a genetic marker set and environment in generalized linear models. Biostatistics 14(4):667-681. doi:10.1093/biostatistics/kxt006 PMID:23462021 PMCID:PMC3769996

2012

• Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, Christiani DC, Wurfel MM, Lin X. 2012. Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet 91(2):224-237. doi:10.1016/j.ajhg.2012.06.007 PMID:22863193 PMCID:PMC3415556
• Lee S, Epstein MP, Duncan R, Lin X. 2012. Sparse principal component analysis for identifying ancestry-informative markers in genome-wide association studies. Genet Epidemiol 36(4):293-302. doi:10.1002/gepi.21621 PMID:22508067 PMCID:PMC3596262
• Liu C, Maity A, Wright RO, Christiani DC, Lin X. 2012. Design and analysis issues in gene and environment studies. Environ Health 11:93. doi:10.1186/1476-069X-11-93 PMID:23253229 PMCID:PMC3551668
• Seow W, Pan W, Kile ML, Baccarelli A, Quamruzzaman Q, Rahman M, Mahiuddin G, Mostofa G, Lin X, Christiani DC. 2012. Arsenic reduction in drinking water and improvement in skin lesions: A follow-up study in Bangladesh. Environ Health Perspect 121:1733-1738. doi:10.1289/ehp.1205381 PMID:23060367 PMCID:PMC3548283
• Sofer T, Maity A, Coull BA, Baccarelli A, Schwartz J, Lin X. 2012. Multivariate gene selection and testing in studying the exposure effects on a gene set. Stat Biosci 4(2):319-338. doi:10.1007/s12561-012-9072-7 PMID:23264831 PMCID:PMC3524591

2011

• Lin X, Cai T, Wu MC, Zhou Q, Liu G, Christiani DC, Lin X. 2011. Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies. Genet Epidemiol 35:620-631. doi:10.1002/gepi.20610 PMID:21818772 PMCID:PMC3373190

2010

• Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X. 2010. Powerful SNP set analvsis for case-control genome-wide association studies. Am J Hum Genet 86(6):929-942. doi:10.1016/j.ajhg.2010.05.002 PMID:20560208 PMCID:PMC3032061