*Indicates equal contribution as first authors. ^#Indicates joint correspondence as corresponding authors.

Statistics

Li, Z., Liu, Y., Lin X. (2022). Simultaneous detection of signal regions using quadratic scan statistics with applications in whole genome association studies. Journal of American Statistical Association, 117(538), 823-834. (link)

Liu, Y., Li, Z., Lin X. (2022). A minimax optimal ridge-type set test for global hypothesis with applications in whole genome sequencing association studies. Journal of American Statistical Association, 117(538), 897-908. (link)

Li, Z., Wang, S., Lin, X. (2012). Variable selection and estimation in generalized linear models with the seamless L0 penalty. The Canadian Journal of Statistics, 40(4), 745-769. (link)

Lin, X., Lee, S., Wu, M. C., 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. (link)

Statistical Genetics

Li, X., Quick, C., Zhou, H., Gaynor, S., Liu, Y., Chen, H., Selvaraj, M., Sun, R., Dey, R., Arnett D., Bielak, L., Bis, J., Blangero, J., Boerwinkle, E., Bowden, D., Brody, J., Cade, B., Correa, A., Cupples, L.A., Curran, J., De Vries, P., Duggirala, R., Freedman, B., Goring, H., Guo, X., Haessler, J., Kalyani, R., Kooperberg, C., Kral, B., Lange, L., Manichaikul, A., Martin, L., McGarvey, S., Mitchell, B., Montasser, M., Morrison, A., Naseri, T., O’Connell, J., Palmer, N., Peyser, P., Psaty, B., Raffield, L., Redline, S., Reiner, A., Reupena, M., Rice, K., Rich, S., Sitlani, C., Smith, J., Taylor, K., Vasan, R., Wilson, J., Willer, C., Yanek, L., Zhao, W., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter, J., Natarajan, P., Peloso, G., 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, 155-164. (link)

Li, Z.*^#, Li, X.*, Zhou, H., Gaynor, S.M., Selvaraj, M., Arapoglou, T., Quick, C., Liu, Y., Chen, H., Sun, R., Dey, R., Arnett D., Auer, P., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Boerwinkle, E., Bowden, D., Brody, J., Cade, B., Conomos, M., Correa, A., Cupples, L.A., Curran, J., De Vries, P., Duggirala, R., Franceschini, N., Freedman, B., Goring, H., Guo, X., Kalyani, R., Kooperberg, C., Kral, B., Lange, L., Lin, B., Manichaikul, A., Manning, A., Martin, L., Mathias, R., Mitchell, B., Montasser, M., Morrison, A., Naseri, T., O’Connell, J., Palmer, N., Peyser, P., Psaty, B., Raffield, L., Redline, S., Reiner, A., Reupena, M., Rice, K., Rich, S., Smith, J., Taylor, K., Taub, M., Vasan, R., Week, D., Wilson, J., Yanek, L., Zhao, W., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Rotter, J., Willer, C., Natarajan, P., Peloso, G., Lin, X.^# (2022). A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19, 1599–1611. (link) (Media Coverage: IU School of Medicine Newsroom)

Li, X.*, Li, Z.*, Zhou, H., Gaynor, S.M., Liu, Y., Chen, H., Sun, R., Dey, R., Arnett, D.K., Aslibekyan, S., Ballantyne, C.M., Bielak, L.F., Blangero, J., Boerwinkle, E., Bowden, D.W., Broome, J.G., Conomos, M.P., Correa, A., Cupples, L.A., Curran, J.E., Freedman, B.I., Guo, X., Hindy, G., Irvin, M.R., Kardia, S.L.R., Kathiresan, S., Khan, A.T., Kooperberg, C.L., Laurie, C.C., Liu, X.S., Mahaney, M.C., Manichaikul, A.W., Martin, L.W., Mathias, R.A., McGarvey, S.T., Mitchell, B.D., Montasser, M.E., Moore, J.E., Morrison, A.C., O’Connell, J.R., Palmer, N.D., Pampana, A., Peralta, J.M., Peyser, P.A., Psaty, B.M., Redline, S., Rice, K.M., Rich, S.S., Smith, J.A., Tiwari, H.K., Tsai, M.Y., Vasan, R.S., Wang, F.F., Weeks, D.E., Weng, Z., Wilson, J.G., Yanek, L.R., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Neale, B.M., Sunyaev, S.R., Abecasis, G.R., Rotter, J.I., Willer, C.J., Peloso, G.M., 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, 969-983. (link)

Li, Z., Li, X., Liu, Y., Shen, J., Chen, H., Zhou, H., Morrison, A.C., 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. (link)

Feofanova, E., Brown, M., Alkis, T., Manuel, A., Li, X., Tahir, U., Li, Z., et al. (2023). Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations. Nature Communications, 14, 3111. (link)

Huang, X., Yao, M., Tian, P., Wong, J., Li, Z., Liu, Z., Zhao, J. (2023). Genome-wide cross-trait analysis and Mendelian randomization reveal a shared genetic etiology and causality between COVID-19 and venous thromboembolism. Communication Biology, 6, 441. (link)

Zhou, H., Arapoglou, T., Li, X., Li, Z., Zheng, X., Moore, J., Asok, A., Kumar, S., Blue, E.E., Buyske, S., Cox, N., Felsenfeld, A., Gerstein, M., Kenny, E., Li, B., Matise, T., Philippakis, A., Rehm, H.L., Sofia, H.J., Snyder, G., NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng, Z., Neale, B., Sunyaev, S.R., 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. (link)

Selvaraj, M., Li, X., Li, Z., et al. (2022). Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nature Communications, 13, 5995. (link)

Li, X., Yung, G., Zhou, H., Sun, R., Li, Z., Hou, K., Zhang, M.J., 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. (link)

Gaynor, S., Westerman, K., Ackovic, L., Li, X., Li, Z., Manning, A., Philippakis, A., Lin, X. (2022). STAAR Workflow: A cloud-based workflow for scalable and reproducible rare variant analysis. Bioinformatics, 38(11), 3116-3117. (link)

Sun, R., Xu, M., Li, X., Gaynor, S., Zhou, H., Li, Z., Bosse, Y., Lam, S., Tsao, M., Tardon, A., Chen, C., Doherty, J., Goodman, G., Egil Bojesen, S., Teresa, M.T., Johansson, M., Field, J.K., Bickeboller, H., Wichmann, H., Risch, A., Rennert, G., Arnold, S., Wu, X., Melander, O., Brunnstrom, H., Marchand, L.L., Zong, X., Liu, G., Andrew, A., Duell, E., Kiemeney, L.A., Shen, H., Haugen, A., Johansson, M., Grankvist, K., Caporaso, N., Woll, P., Teare, M.D., Scelo, G., Hong, Y., Yuan, J., Lazarus, P., Schabath, M.B., Aldrich, M.C., Albanes, D., Brennan, P., Barbie, D., Mak, R., Hung, R.J., Amos, C.I., Christiani, D.C., Lin, X. (2021). Integration of multi-omic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genetic Epidemiology, 45(1), 99-114. (link)

Liu, Y., Chen, S., Li, Z., Morrison, A., Boerwinkle, E., Lin, X. (2019). ACAT: A fast and powerful p Value combination method for rare-variant analysis in sequencing studies. The American Journal of Human Genetics, 104(3), 410-421. (link)

Chen, H., Huffman, J., Brody, J., Wang C., Lee, S., Li, Z., Gogarten, S.M., Sofer, T., Bielak, L.F., Bis, J.C., Blangero, J., Bowler, R.P., Cade, B.E., Cho, M.H., Correa, A., Curran, J.E., de Vries, P.S., Glahn, D.C., Guo, X., Johnson, A.D., Kardia, S., Kooperberg, C., Lewis, J.P., Liu, X., Mathias, R.A., Mitchell, B.D., O’Connell, J.R., Peyser, P.A., Post, W.S., Reiner, A.P., Rich, S.S., Rotter, J.I., Silverman, E.K., Smith, J.A., Vasan, R.S., Wilson, J.G., Yanek, L.R., Redline, S., Smith, N.L., Boerwinkle, E., Borecki, I.B., Cupples, L.; Laurie, C.C., Morrison, A.C., Rice, K.M.; Lin, X. (2019). Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole-genome sequencing studies. The American Journal of Human Genetics, 104(2), 260-274. (link)

Xu, Miao., Yao, Y., Chen, H., Zhang, S., Cao, S., Zhang, Z., Luo, B., Liu, Z., Li, Z., Xiang, T., He, G., Feng, Q., Chen, L., Guo, X., Jia, W., Chen, M., Zhang, X.; Xie, S., Peng, R., Chang, E.T., Pedergnana, V., Feng, L., Bei, J., Xu, R., Zeng, M., Ye, W., Adami, H., Lin, X., Zhai, W., Zeng, Y., Liu, J. (2019). Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nature Genetics, 51, 1131-1136. (link)

Chen, H., Wang, C., Conomos, M., Adrienne, M., Li, Z., Sofer, T., Szpiro, A., Chen, W., Brehm, J., Celedon, J., Redline S, Papanicolaou, G., Thornton, T., Laurie, C., Rice, K., Lin, X. (2016). Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models. The American Journal of Human Genetics, 98(4), 653-666. (link)