Link to my most highly-cited methodological papers based on Google scholar.

I have published both statistical methodological research in top statistics/biostatistics journals (JASA, AOS, AOAS, JRSS-B, Biometrika, Biometrics, Biostatistics etc ) and in top genetics journals (AJHG, Plos Genetics, Nature Genetics, Genome Research etc) and collaborative research in top scientific journals (NEJM, Science, Nature, Nature Methods, Nature Medicine, Science Tranlational Medicine, PNAS, Cancer Cell, Cell Host & Microbe, Developmental Cell etc).

By Year

[ Invited Book Chapters ] [ Invited Journal Discussions ]

[ 2029 | 2028 | 2027 | 2026 | 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | ]

[ 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | ]

[ 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | ]

[ 1999 | 1998 | 1997 | ]

* indicates names are Dr. Li's students/postdocs

2024 or in press

*Cai C, Cai TT and Li H (2023): Transfer Learning for Contextual Multi-armed Bandits. Annals of Statistics, in press.

*Li S, Zhang L, Cai TT and Li H (2023): Estimation and Inference for High-Dimensional Generalized Linear Models with Knowledge Transfer. Journal of American Statistical Association, accepted.

*Wang J, *Li S and Li H (2023): A Regression-based Approach to Robust Estimation and Inference for Genetic Covariance. Journal of American Statistical Association, accepted.

*Wang S, Yuan B, Cai TT and Li H (2023): Phylogenetic Association Analysis with Conditional Rank Correlation. Biometrika, accepted.

*Ma R, Guo Z, Cai T.T. and Li H (2024): Statistical inference for genetic relatedness based on high-dimensional logistic regression. Statistica Sinica, accepted.

*Xue F, *Ma R and Li H (2023): Statistical Inference for High-Dimensional Linear Regression with Blockwise Missing Data. Statistica Sinica, accepted.

*Li S, Cai TT and and Li H (2024): Statistical Inference for High Dimensional Regression with Proxy Data. Statistica Sinica, accepted.

*Zhang J, Shou H and L Li H (2023): Empirical Likelihood Inference of Variance Components in Linear Mixed-Effects Models. Statistica Sinica, accepted.

*Fei Xue and and Li H (2023): An empirical Bayes Regression for multi-tissue gene expression prediction. Statistica Sinica, accepted.

*Zhang J, Mathias Basner, Christopher W. Jones, David F. Dinges, Haochang Shou and Li H (2023): Mediation Analysis with Random Distribution as Mediator with an Application to iCOMPARE Trial. Statistics in Biosciences, accepted.

Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H , Susztak K (2024): Unraveling the Epigenetic Code: Human Kidney DNA Methylation and Chromatin Dynamics in Renal Disease Development. Nature Communications, 15, Article number: 873.

Bustamante MA, Sheila K. Pierson, Yue Ren, Adam Bagg, Joshua D. Brandstadter, Gordan Srkalovic, Natalie Mango, Daisy Alapat, Mary Jo Lechowicz, Li H , Frits van Rhee, Megan S. Lim, David C. Fajgenbaum (2024): Longitudinal, natural history study reveals the disease burden of idiopathic multicentric Castleman disease. Haematologica, accepted.


*Ma S and Li H (2023): A Tensor Decomposition Model for Longitudinal Microbiome Studies. Annals of Applied Statistics, 17: 1105-1126.

*Li S, Cai TT and Li H (2023): Transfer Learning in Large-scale Gaussian Graphical Models with False Discovery Rate Control. Journal of American Statistical Association, 118:2171-2183.

*Wang W, Chen Z, Li H (2023): Truncated Rank-Based Tests for Two-Part Models with Excessive Zeros and Applications to Microbiome Data. Annals of Applied Statistics, 17: 1663-1680.

*Deek R and Li H (2023): Inference of Microbial Co-variation Networks Using Copula Models with Mixture Margins. Bioinformatics, 39 (7), btad413.

Dubin RF, Deo R, Ren Y, Li H, Shou H, Feldman H, Kimmel P, Waikar S, Segal M, Ganz O on behalf of CKD Biomarkers Consortium (2023): Analytical and Biological Variability of the SomaScan V4 Assay in Plasma Samples of Patients with Chronic Kidney Disease. Journal of Applied Laboratory Medicine, 8(3):491-503.

Deo R, Ruth Dubin, Yue Ren, Ashwin C. Murthy, Jianqiao Wang, Haotian Zheng, Zihe Zheng, Harold Feldman, Haochang Shou, Josef Coresh, Morgan Grams, Aditya Surapaneni, Zeenat Bhat, Jordana Cohen, Mahboob Rahman, Jiang He, Santosh Saraf, Alan Go, Paul Kimmel, Ramachandran Vasan, Mark Segal, Li H, and Ganz P (2023): Proteomic Risk Assessment for Incident Cardiovascular Disease among Individuals with Chronic Kidney Disease. European Heart Journal, 44(23):2095-2110.

Kelly DE, Shweta Ramdas, Rong Ma, Renata A. Rawlings-Goss, Gregory R. Grant, Alessia Ranciaro, Jibril B. Hirbo, William Beggs, Meredith Yeager, Stephen Chanock, Thomas B. Nyambo, Sabah A Omar, Dawit Wolde Meske, Gurja Belay, Li H, CD Brown, SA Tishkoff (2023): The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans. Genome Biology, 24, Article number: 35.

Dubin R, Rajat Deo, Yue Ren, Jianqiao Wang, Zihe Zheng, Haochang Shou, Alan Go, Afshin Parsa, James Lash, Mahboob Rahman, Chi-yuan Hsu, Matthew Weir, Jing Chen, Amanda Anderson, Morgan Grams, Aditya Surapaneni, Josef Coresh, Lee H, Paul Kimmel, Ramachandran Vasan, Harold Feldman, Mark Segal, and Peter Ganz (2023): Proteomics of CKD Progression in the Chronic Renal Insufficiency Cohort. Nature Communications, 14(1):6340.

Carr R, Yun Li, Lillian Chau, Elliot S. Friedman, Jung-Jin Lee, Luciano Adorini, Mary Erickson, Luna Zaru, Reshma Shringarpure, Leigh MacConell, Kyle Bittinger, Li H, Wu GD (2023): An Integrated Analysis of Fecal Microbiome and Metabolomic Features Distinguish Non-cirrhotic NASH from Healthy Control Populations. Hepatology, 78(6):1843-1857.

Bass, R Ceylan Tanes, Kyle Bittinger, Yun Li, Li H, Elliot S. Friedman, Imhoi Koo, Andrew D. Patterson, Qing Liu, Gary D. Wu, Virginia A.Stallings (2023): Changes in fecal lipidome after treatment with Ivacaftor without changes in microbiome or bile acids. Journal of Cystic Fibrosis, , 7:S1569-1993(23)00915-3.

Pierson SK, Megan S. Lim, Gordan Srkalovic, Joshua D. Brandstadter, Mateo S. Bustamante, Saishravan Shyamsundar, Natalie Mango, Criswell Lavery, Bridget Austin, Daisy Alapat, Mary Jo Lechowicz, Adam Bagg, Lee H, Corey Casper, Frits van Rhee, David C. Fajgenbaum (2023): Treatment Consistent with Idiopathic Multicentric Castleman Disease Guidelines is Associated with Improved Outcomes. Blood Advances, 7 (21): 6652–6664.


*Wang J and Li H (2022): Estimation of genetic correlation with summary association statistics. Biometrika, 109: 421-438.

*Wang J, *Wang W, and Li H (2022):Sparse Block Signal Detection and Identification for Shared Cross-Trait Association Analysis. Annals of Applied Statistics, 16:866-886.

*Zhang J, Merikangas KR, Li H, Shou H (2022): Two-sample tests for multivariate repeated measurements of histogram objects with applications to wearable device data. Annals of Applied Statistics , 16(4): 2396-2416.

*Li S, Cai TT and Li H (2022): Inference for high-dimensional linear mixed-effects models: A quasi-likelihood approach. Journal of American Statistical Association, 117:540, 1835-1846

*Li S, Cai TT and Li H (2022): Transfer Learning for High-dimensional Linear Regression: Prediction, Estimation, and Minimax Optimality. Journal of the Royal Statistical Society B , 84: 149-173.

*Lu J and Li H (2022): Hypothesis Testing in High-Dimensional Instrumental Variables Regression with an Application to Genomics Data. Statistica Sinica, 32: 613-633.

*Ma R, Cai T,.T. and Li H (2022): Optimal estimation of simultaneous signal using absolute inner product with applications to integrative genomics. Statistica Sinica, 32: 1027-1048.

*Sohn M B, *Lu J and Li H (2022): Compositional mediation model for binary outcome: application to microbiome study. Bioinformatics, 38(1): 16-21.

*Liu M, Li Y and Li H (2022): Deep learning to predict the biosynthetic gene clusters in bacterial genomes. Journal of Molecular Biology, 434 (15), 16759.

*Huang Lu and Li H (2022): Bayesian balance mediation analysis in microbiome studies. In Henry Horng-Shing Lu, Bernard Scholkopf, Hongyu Zhao (eds). Handbook of Statistical Bioinformatics, Springer, pp 237-254.

*Ma R and Li H (2022): Interaction Networks in Microbiome Studies. In Piegorsch, W.W., Levine, R.A., Zhang, H.H., and Lee, T.C.M. (eds.). Computational Statistics in Data Science, pp 253-268. Chichester: John Wiley & Sons. ISBN: 978-1-119-56107-1.

*Ma S and Li H(2023): Statistical and computational methods for microbial strain analysis. In Brooke Fridley and Xuefeng Weng (eds). Statistical Genomics, Methods in Molecular Biology, vol 2629, 231–245. Humana, New York, NY. Springer.

Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni G, Abedini A, Miao Z, Palmer M, Voight B, Li H , Brown C, Ritchie M, Shu Y, and Susztak K (2022): Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Nature Genetics, 54:950-962.

Moroishi Y, Gui J, Hoen AG, Morrison HG, Baker ER, Nadeau KC, Li H , Li Z, Madan JC, Karagas MR (2022): The relationship between the gut microbiome and the risk of respiratory infections among newborns. Communications Medicine, 2, Article number, 87.

Mennella JA, Yun Li, Kyle Bittinger, Elliot S. Friedman, Chunyu Zhao, Li H, Wu GD and Trabulsi JC (2022): The macronutrient composition of infant formula produces differences in gut microbiota maturation that associates with weight gain velocity and weight status. Nutrients, 14(6), 1241.

McGinniss JE, Samantha A. Whiteside, Rebecca Deek, Aurea Simon-Soro, Jevon Graham-Wooten, Michelle Oyster, Melanie D. Brown, Edward Cantu, Joshua M. Diamond, Li H, Jason D. Christie, Frederic D. Bushman, Ronald G. Collman (2022): Primary graft dysfunction is associated with Prevotella-enriched allograft microbiome, elevated pepsin, and a hyper-inflammatory immune response at the time of lung transplantation. American Journal of Respiratory and Critical Care Medicine, 15; 206(12):1508-1521.


*Ma R, Cai TT and Li H (2021): Global and Simultaneous Hypothesis Testing for High-Dimensional Logistic Regression Models. Journal of American Statistical Association, 116: 984-998.

*Ma R, Cai TT and Li H (2021): Optimal Permutation Recovery in Permuted Monotone Matrix Model. Journal of American Statistical Association, 116: 1358-1372.

*Wang S, Cai TT and Li H (2021): Optimal estimation of Wasserstein distance on a tree with an application to microbiome studies. Journal of American Statistical Association, 116: 1237-1253.

*Wang S, Cai TT and Li H (2021): Hypothesis Testing for Phylogenetic Composition: A Minimum-cost Flow Perspective. Biometrika, 108 (1), 17-36.

*Ma R, Cai TT and Li H (2021): Optimal Estimation of Bacterial Growth Rates Based on Permuted Monotone Matrix. Biometrika, 108: 693-708.

Cai TT, Li H, and Ma R (2021): Optimal Structured Principal Subspace Estimation: Metric Entropy and Minimax Rates. Journal of Machine Learning Research, 22(46), 1-45.

Li Z, Tian L, O'Malley AJ, Karagas MR, Hoen AG, Christensen BC, Madan JC, Wu Q, Gharaibeh RA, Jobin C and Li H (2022): IFAA: Robust association identification and inference for absolute abundance in microbiome analyses. Journal of American Statistical Association, 116:1595-1608.

Viles WD, Madan JC, Li H, Karagas MR, Hoen AG (2021): Information content of higher-order association of the human microbiota network. Annals of Applied Statistics, 15(4): 1788-1807.

Wilson N, Zhao N, Zhan X, Koh H, Fu W, Chen J, Li H, Wu MC and Plantinga AM (2021): MiRKAT: Kernel Machine Regression-Based Global Association Tests for the Microbiome. Bioinformatics, 37: 1595-1597.

*Deek R and Li H (2021): A Zero-Inflated Latent Dirichlet Allocation Model for Microbiome Studies. Fronters in Genetics, 11:1844.

*Liu M and Li H (2021): Estimation of Heterogeneous Restricted Mean Survival Time Using Random Forest. Fronters in Genetics, 11:1727.

Li H, Zheng H (2021): Statistical and Computational Methods for Analysis of Shotgun Metagenomics Sequencing Data. Statistical Analysis of Microbiome Data,27-43, edited by Somnath Datta and Subharup Guba, Springer.

Huang L and Li H (2021): Bayesian Balance Regression in Microbiome Studies Using Stochastic Search. Festschrift in honor of Professor Vera Pawlowsky-Glahn, Edited by Peter Filzmoser, Karel Hron, Josep Antoni Martin-Fernandez and Javier Palarea-Albaladejo.

Rhee RL, Lu J, Bittinger K, Sreih AG, Lee JJ, Mattei LM, Miner JJ, Cohen NA, Kelly BJ, Grayson PC, Li H, Collman RG, Merkel PA (2021): Dynamic Changes in the Nasal Microbiome in Patients with Granulomatosis with Polyangiitis. Arthritis & Rheumatology, 73: 1703-1712.

Tanes C, Kyle Bittinger, Yuan Gao, Elliot S. Friedman, Lisa Nessel, Unmesha Roy Paladhi, Lillian Chau, Erika Panfen, Michael A. Fischbach, Jonathan Braun, Ramnik J. Xavier, Clary B. Clish, Li H, Frederic D. Bushman, James D. Lewis, Gary D. Wu (2021): Role of Diet in the Recovery of the Human Gut Microbiome and its Metabolome. Cell Host & Microbe, 29: 394-407.

Sheng Z, Qiu C, Liu H, Gluck C, Hsu J, He J, Hsu CY, Sha D, Weir MR, Isakova T, Raj DS, Ricon-Choles H, Feldman HI, Townsend R, Li H , Susztak K (2021): Integrated genetic-epigenetic analysis supports a causal role for inflammation in diabetic kidney disease pathogenesis. Proceedings of the National Academy of Sciences, 117 (46), 29013-29024.

Smith SA, Chau L, Ogawa SA, Whelan KA, Hamilton K, Chen J, Tan L, Chen EZ, Keibaugh S, Fogt F, Bewtra M, Braun J, Xavier RJ, Clish CB, Slaff B, Wiljie A, Bushman FDm Lewis JD, Li H , Bennett MJ, Nakagawa H and Wu GD (2021): Mitochondrial dysfunction alters intestinal epithelial metabolism of hepatic acylcarniteines. Journal of Clinical Investigation, 131(1): e133371.

Raj DS, Sohn MB, Dember LM, Charytan DM, Himmelfarb J, T. Alp Ikizler, Rajnish Mehrotra, Ramezani A, Regunathan-Shenk R, Hsu JY, Landis JR, Li H , Kimmel PL, Kliger AS, and Dember LM for the Hemodialysis Novel Therapies Consortium (2021): The Microbiome and p-Inulin in Hemodialysis: A Feasibility Study. Kidney360, 2(3): 445-455.

Gershuni V, Li Y, Elovitz M, Li H , Wu GD, Compher CW (2021): Maternal gut microbiota reflecting poor diet quality is associated with spontaneous perterm in a prospective cohort study. American Journal of Clinical Nutrition, 113(3): 602-611.

Ma J, Bowen Xing, Yan Cao, Xin He, Kate E. Bennett, Chao Tong, Chiying An, Taylor Hojnacki, Zijie Feng, Sunbin Ling, Sunbin Ling, Gengchen Xie, Yuan Wu, Yue Ren, Bryson W. Katona, Ming Yu, Li H , Ali Naji, Hua X (2021): The menin/JunD/Pbk axis regulates compensatory beta cell proliferation. EMBO Molecular Medicine, e13524.

Grams ME, Aditya Surapaneni, Jingsha Chen, Linda Zhou, Zhi Yu, Diptavo Dutta, Paul Welling, Nilanjan Chatterjee, Jingning Zhang, Dan E. Arking, Teresa K. Chen, Casey M. Rebholz, Bing Yu, Pascal Schlosser, Eugene P. Rhee, Christie M. Ballantyne, Eric Boerwinkle, Pamela L. Lutsey, Thomas Mosley, Harold Feldman, Ruth Dubin, Peter Ganz, Li H , Zihe Zheng, Josef Coresh (2021): Proteins associated with risk of kidney function decline in the general population. Journal of the American Society of Nephrology, 32: 2291-2302.

Lewis J, Sandler R. Brotherton C, Brensinger C, Li H, Kappelmzn, .D. Scott, Bittinger K, Albenberg L, Valentine JF, Hanson J, Suskind D, Meyer A, Compher CW, Bewtra M, Saxena A, Dobes A, Cohen B, Flynn AD, Fischer M, Saha S, Swaminath A, Yacyshyn B, Scherl E, Horst S, Curtis JR, Braly K, Nessel L, McCauley M, McKeever L, Herfarth H and the DINE-CD Study Group (2021): A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults with Crohn’s Disease. Gastroenterology, 161: 837-852, e9.

Kondo A, Siyuan Ma, Michelle Y. Y. Lee, Vivian Ortiz, Daniel Traum, Jonathan Schug, Benjamin Wilkins, Natalie A. Terry, Lee H, Kaestner, K.H. (2021): Highly multiplexed image analysis of intestinal tissue sections in patients with inflammatory bowel disease. Gastroenterology, 161: 1940-1952.


*Cao Y, Zhang A and Li H (2020): Multi-sample estimation of bacterial composition matrix in metagenomics data. Biometrika, 107:75-92.

Bittinger K, C Zhao, Y Li, E Ford, E Friedman, J Ni, C Kulkarni, J Cai, Y Tian, Q Liu, A Patterson, D Sarkar, Siu Hung Joshua Chan, C Maranas, A Saha-Shah, P Lund, B Garcia, L Mattei, J Gerber, M Elovitz, A Kelly, P DeRusso, D Kim, C Hofstaedter, M Goulian, Li H, F Bushman, B Zemel, Wu G (2020): Bacterial colonization reprograms the neonatal gut metabolome. Nature Microbiology, 5:838-847.

Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim M-S, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, Kachelries K, Erlichman J, Hart JL, Moraskie M, Kim D, Zhang H, Hofstaedter CE, Wu GD, Lewis JD, Zackular JP, Li H , Bittinger K and Baldassano R (2020): Multi-omic analysis of the interaction between Clostridioides difficile infection and pediatric inflammatory bowel disease. Cell Host & Microbe, 28(3):422-433.

Yarmarkovich M, Alvin Farrell, Artemio Sison III, Moreno Di Marco, Pichai Raman, Joshua Parris, Dimitri S Monos, Lee H , Stefan Stevanovic, John M Maris (2020): Immunogenicity and Immune Silence in Human Cancer. Frontiers in Immunology, 11:69.

Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen G (2020): Emerging priorities for microbiome research. Frontiers in Microbiology, 11:136.


Guo Z, Wang W, Cai T, Li H (2019): Optimal estimation of genetic relatedness in high-dimensional linear models. Journal of American Statistical Association, 114: 358-369.

*Cao Y, Lin W, Li H (2019): Large Covariance Estimation for Compositional Data via Composition-Adjusted Thresholding. Journal of American Statistical Association, 114: 759-772.

Cai T, Li H, Ma J, Xia Y (2019): Differential Markov Random Field Analysis with an Application to Detecting Differential Microbial Community Networks. Biometrika, 106(2): 401-416.

Li H (2019):Statistical and Computational Methods in Microbiome and Metagenomics. Handbook in Statistical Genomics, 977-996.

*Lu J, Shi P, Li H (2019): Generalized Linear Models with Linear Constraints for Microbiome Compositional Data. Biometrics, 75: 235-244.

*Sohn M and Li H (2019): Compositional mediation analysis for microbiome studies. Annals of Applied Statistics, 13: 661-681.

Gao B, Liu X, Li H and Cui Y (2019): Integrative analysis of genetical genomics data incorporating network structures. Biometrics, 75(4): 1063-1075.

Gluck C, Qiu C, Han SY, Palmer M, Oark J, Ko YA, Guan Y, Sheng X, Hanson RL, Huang J, Chen Y, Park ASD, Mantzaris I, Verma A, Li H and Susztak K (2019): Kidney cytosine methylation changes can improve renal function decline estimation in patients with diabetic kidney disease. Nature Communications, 10, Article No: 2461.

Cordero P, Narikh VN, E Chin, A Erbilgin, M Gloudemans, C Shang, Y Huang, AC. Chang, KS. Smith, F Dewey , K Zaleta, M Morley, J Brandimarto, N Glazer, A Pavlovic, M Zhao, C Moravec, W H. Tang, J Viterna, C Malloy, S Hannenhalli, Li H , S Ritter, M Li, D Bernstein, A Connolly, H Hakonarson, A J. Lusis, K B. Margulies, A A. Depaoli-Roach, S B. Montgomery, M T. Wheeler, T Cappola, and E A. Ashley (2019): Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure. Nature Communications, 10, Artical number: 2760.

Simon-Soro A, Sohn MB, McGinniss JE, Imai I, Brown MC, Knecht VR, Bailey A, Clarke EL, Cantu E, Li H, Bittinger K, Diamond JM, Christie JD, Bushman FD, Collman RG (2019): Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant. Annals of the American Thoracic Society, 16(11): 1383-1391

McGinniss JE, Imai I, Simon-Soro A, Brown MC, Knecht VR, Frye L, Ravindran PM, Dothard MI, Wadell DA, Sohn MB, Li H, Christie JD, Diamond JM, Haas AR, Lanfranco AR, DiBardino DM, Bushman FD, Collman RG. (2019): Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents. PLoS One, 14(5):e0217306.

Park J, Guan Y, Sheng X, Gluck C, Seasock MJ, Hakimi AA, Qiu C, Oullman J, Verma A, Li H, Palmer M, Susztak K (2019): Functional methylome analysis of human diabetic kidney disease. JCI Insight, 4(11). pii: 128886

Lee JW, Moen EL, Punshon T, Hoen AG, Stewart D, Li H, Karagas MR, Gui J (2019): An integrated Gaussian graphical model to evaluate the impact of exposures on metabolic networks. Computers in Biology and Medicine, 114: 103417.


*Gao Y, Li H (2018): Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. Nature Methods, 15:1041-1044.

Xia Y, Cai TT and Li H (2018): Joint testing and false discovery rate control in high-dimensional multivariate response regression model. Biometrika, 105: 249-269.

*Cao Y, Lin W, Li H (2018): Two-sample tests of high dimensional means for compositional data. Biometrika, 105(1): 115-132.

*Sohn M, Li H (2018): A GLM-Based Latent Variable Ordination Method for Microbiome Samples. Biometrics, 74: 448-457.

Li Z, Lee K, Karagas MR, Madan JC, Hoen AG, O'Malley J, Li H (2018): A multivariate zero-inflated logistic model for microbiome relative abundance data. Statistics in Biosciences, 10(3): 587-608.

Vajravelu R, Scott FI, Mamtani R, Li H, Moore JH, Lewis JD (2018): Medication class enrichment analysis: a novel algorithm to analyze multiple pharmacologic exposures simultaneously using electronic health record data. Journal of the American Medical Informatics Association, 25: 780-789.

Liao M, Xie Y, Mao Y, Lu Z, Tan A, Wu C, Zhang Z, Chen Y, Li T, Ye Y, Yao Z, Jiang Y, Li H, Yang X, Wang Q, Mo Z (2018): Comparative analyses of fecal microbiota in Chinese isolated Yao population, minority Zhuang and rural Han by 16S RNA sequencing. Scientific Reports, 8:1141.

Friedman ES, Li Y, Shen TC, Jiang J, Chau L, Adorini L, Babakhani F, Edwards J, Shapiro D, Zhao C, Carr RM, Bittinger K, Li H, Wu G (2018): FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid. Gastroenterology, 55(6):1741-1752

Pierson SK, Stonestrom AJ, Shilling D, Ruth J, Nabel C, Singh A, Ren Y, Stone K, Li H, van Rhee F and Fajgenbaum DC (2018): Plasma proteomics identifies a "chemokine storm" in idiopathic multicentric Castleman disease. American Journal of Hematology, 93: 902-912.

Sinha R, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso, Joseph Russell Carmical, Andrew T Chan, Anthony Fodor, Mitchell H Gail, Curtis C Harris, Kathy Helzlsouer, Curtis Huttenhower, Rob Knight, Heidi H Kong, Gabriel Y Lai, Diane Leigh Smith Hutchinson, Loic Le Marchand, Li H, Michael J Orlich, Jianxin Shi, Ann Truelove, Mukesh Verma, Emily Vogtmann, Owen White, Walter Willett, Wei Zheng, Somdat Mahabir, Christian Abnet (2018): Next Steps in Studying the Human Microbiome and Health in Prospective Studies, Bethesda, MD May 16 - 17, 2017. Microbiome, 6(1): 210.


*Zhao SD, Cai TT, Cappola TP, Margulies KB, Li H (2017): Sparse simultaneous signal detection for identifying genetically controlled disease genes. Journal of American Statistical Association, 112 (519): 1032-1046.

*Shi P, Li H (2017): A model for paired-multinomial data and its application to analysis of data on a taxonomic tree. Biometrics, 73(4): 1266-1278.

Tang ZZ, Chen G, Alekseyenko AV, Li H (2017): A general framework for association analysis of microbial communities on a taxonomic tree. Bioinformatics, 33(9): 1278-1285.

*Chen EZ, Bushman FD, Li H (2017): A Model-based Approach for Species Abundance Quantification Based on Shotgun Metagenomic Data. Statistics in Biosciences, 9: 13-27.

*Zhao SD, Cai TT and Li H (2017): Optimal detection of weak positive latent dependence between two sequences of multiple tests. Journal of Multivariate Analysis, 160: 169-184.

Ni J, Ting-Chin David Shen, Eric Z. Chen, Aubrey Bailey, Manuela Roggiani, Alexandra Sirota-Madi, Elliot S. Friedman, Lillian Chau, Andrew Lin, Ilana, Nissim, Justin Scott, Abigail Lauder, Christopher Hoffmann, Gloriany Rivas, Lindsey Albenberg, Robert N. Baldassano, Jonathan Braun, Ramnik J. Xavier, Clary B. Clish, Marc Yudkoff, Li H, Mark Goullian, Frederic D. Bushman, James D. Lewis, Gary D. Wu (2017): A Role for Bacterial Urease in Crohn’s Disease and Gut Dysbiosis. Science Translational Medicine, Vol. 9, Issue 416, eaah6888.

Ko Y, Yi H, Qiu C, Huang S, Park J, Ledo N, Kottgen A, Li H, Rader DJ, Pack MA, Brown CD, Susztak K (2017): Genetic-variation-driven gene-expression changes highlight genes with important functions for kidney disease. American Journal of Human Genetics, 100(6): 940-953.

Schoch H, Kreibich AS, Ferri SL, White RS, D Bohorquez, A Banerjee, RG Port, HC Dow, L Cordero, A Pallathra, H Kim, Li H, W Bilker, S Hirano, RT Schultz, K Borgmann-Winter, C-G Hahn, D Feldmeyer, GC Carlson, T Abel and ES Brodkin (2017): Sociability Deficits and Altered Amygdala Circuits in Mice Lacking Pcdh10, an Autism Associated Gene. Biological Psychiatry, 81(3):193-202.

Kamoun M, McCullough KP, Maiers M, Fernandez Vina MA, Li H, Teal V, Leichtman AB, Merion RM (2017): HLA amino acid polymorphisms and kidney allograft survival. Transplantation, 101(5): e170-e177.


*Shi P, Zhang A and Li H (2016): Regression Analysis for Microbiome Compositional Data. Annals of Applied Statistics, 10(2): 1019-1040.

Cai T, Li H, Liu W and Xie J (2016): Joint Estimation of Multiple High-dimensional Precision Matrices. Statistica Sinica, 26(2), 445-464.

Chen EZ and Li H (2016): A two-part mixed-effect model for analyzing longitudinal microbiome compositional data. Bioinformatics, 32 (17): 2611-2617.

Wu GD, Compher C, Chen EZ, Smith SA, Shah R, Bittinger K, Chehoud C, Albernberg LG, Nessel L, Gilroy E, Star J, Weijie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD (2016): Comparative Metabolomics in Vegans and Omnivores Reveal Constraints on Diet-Dependent Gut Microbiota Metabolite Production. Gut, 61(1): 63-72.

Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison H, Sogin M, Li H, Moore JH, Karagas MR (2016): Effects of Cesarean delivery and formula supplementation on the intestinal microbiome of six-week old infants. JAMA Pediatrics, 11: 1-8.

Ferri SL, Kreibich AS, Torre M, Picccoli CT, Dow H, Pallathra AA, Li H, Bilker WB, Gur R, Abel T, and Brodkin ES (2016): Activation of Basolateral Amygdala in Juvenil C57BL/6J Mice During Social Approach Behavior. Neuroscience, 335:184-194.


Li H (2015): Microbiome, Metagenomics and High Dimensional Compositional Data Analysis. Annual Review of Statistics and Its Application, 2:73-94.

*Lin W, Feng R and Li H (2015): Regularization Methods for High-Dimensional Instrumental Variables Regression With an Application to Genetical Genomics. Journal of American Statistical Association, Theory and Methods, 110: 270-288.

Zhao N, Chen J, Carroll IM, Ringel-Kulka T, Epstein MP, Zhou H, Zhou JJ, Ringel Y, Li H and Wu MC (2015): Testing in Microbiome Profiling Studies with the Microbiome Regression-based Kernel Association Test (MiRKAT). American Journal of Human Genetics, 96, 797-807.

Lewis JD, Eric Z. Chen, R.N. Baldassano, A.R. Otley, A.M. Griffiths, D. Lee, K. Bittinger, A. Bailey, E.S. Friedman, C. Hoffmann, L. Albenberg, R. Sinha, C. Compher, E. Gilroy, L. Nessel, A. Grant, C. Chehoud, Li H, G.D. Wu, F.D. Bushman (2015): Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host & Microbe, 18(4): 489-500.

*Wu Q, Won KJ and Li H (2015): Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data. Cancer Informatics, Suppl. 1, 11-22.

*Jeng J, *Wu Q and Li H (2015): A Statistical Method for Identifying Trait-Associated Copy Number Variants. Human Heredity, 79(3-4):147-156.

*Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD and Li H (2015): Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA. Bioinformatics, 31(15):2461-8.

Chen L, Liu H, Kocher JPA, Li H, Chen J (2015): glmgraph: An R Package for Variable Selection and Predictive Modeling of Structured Genomic Data. Bioinformatics, 31(24): 3991-2993.

Zsiros E, Duttagupta P, Dangaj D., Li H, Frank R, Garrabrant T, Hagemann IS, Levine B, June CH, Zhang L, Wang E, Marincola FM, Bedognetti D, Powell DJ, Tanyi J, Feldman MD, Kandalaft LE, Coukos G (2015): The Ovarian Cancer Chemokine Landscape is Conducive to Homing of Vaccine-primed and CD3/CD28 Costimulated T cells Prepared for Adoptive Therapy. Clinical Cancer Research, 22(12): 2840-2850.

Li YR, Zhao SD, Li J, JP Bradfield, Mohebnasab M, Steel L, Kobie J, Abrams DJ, Mentch FD, Glessner JT, Guo Y, Wei Z, Connolly JJ, CJ Cardinale, M Bakay, D Li, S.M. Maggadottir, K.A. Thomas, H. Qui, R.M. Chiavacci, C.E. Kim, F. Wang, J. Snyder, B Flato, O Forre, LA. Denson, S.D. Thompson, M.L. Becker, S.L. Guthery, A. Latiano, E. Perez, E. Resnick, C. Strisciuglio, A. Staiano, E. Miele, M.S. Silverberg, B.A. Lie, M. Punaro, R.K. Russell, D.C. Wilson, M.C. Dubinsky, D.S. Monos, V. Annese, J.E. Munro, C. Wise, H. Chapel, C. Cunningham-Rundles, J.S. Orange, E.M. Behrens, K.E. Sullivan, S. Kugathasan, A.M. Griffiths, J. Satsangi, S.F.A. Grant, P.M.A. Sleiman, T. Finkel, C. Polychronakos, R.N. Baldassano, E.T. Luning Prak, J.A. Ellis, Li H, B.J. Keating, H. Hakonarson (2015): Genetic Sharing and Heritability of Pediatric Age-of-Onset Autoimmune Diseases. Nature Communications, 6:8442 | DOI: 10.1038/ncomms9442.

Li YR, Jin Li, Sihai D. Zhao, J.P. Bradfield, F.D. Mentch, S.M Maggadottir, C. Hou, D.J. Abrams, D. Chang, F. Gao, Y. Guo, Z. Wei, J.J. Connolly, C.J. Cardinale, M. Bakay, J.T. Glessner, D. Li, C. Kao, K.A. Thomas, H. Qiu, R.M.Chiavacci, C.E. Kim, F. Wang, J. Snyder, M.D. Richie, B. Flat??, ??, F??rre, L.A.Denson, S.D. Thompson, M.L. Becker, S.L. Guthery, A. Latiano, E. Perez, E. Resnick, R.K. Russell, D.C. Wilson, M.S. Silverberg, V. Annese, B.A. Lie, M. Punaro, M.C. Dubinsky, D.S. Monos, C. Strisciuglio, A. Staiano, E. Miele, S. Kugathasan, J.A. Ellis, J.E. Munro, K.E. Sullivan, C. Wise, H. Chapel, C. Cunningham-Rundles, S.F.A. Grant, J.S. Orange, P.M.A. Sleiman, E.M. Behrens, A.M. Griffith, J. Satsangi, T.H. Finkel, A. Keinan, E.T. Luning Prak, C. Polychronakos, R.N.Baldassano, Li H, B.J. Keating, H. Hakonarson (2015): Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nature Medicine, 21(9): 1018-1027.

Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Comphter C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu G and Lewis J (2015): Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Inflammatory Bowel Diseases, 21(8):1786-1793.

Jaewook Oh, Iryna F. Sanders, Eric Z. Chen, Li H, John W. Tobias, R. Benjamin Isett, Sindura Penubarthi, Hao Sun, Don A. Baldwin and Nigel W. Fraser (2015): Genome Wide Nucleosome Mapping for HSV-1 shows Nucleosome Free Regions on many Genes. PloS One, 10(2): e0117471. doi:10.1371/journal.pone.0117471.

*Xie J, Cai T, Li H (2015): Correction to the paper "Optimal False Discovery Rate Control for Dependent Data". Statistics and Its Inference, 9(1); 33-35.


*Zhao, S.D., Cai T and Li H (2014): Direct estimation of differential networks. Biometrika, 101(2): 253-268.

*Lin W, Shi P, Feng R and Li H (2014): Variable selection in regression with compositional covariates. Biometrika, 101(4): 785-797.

*Vardhanabhuti S, Jeng J, Wu Y and Li H (2014): Parametric modeling of whole-genome sequencing data for CNV identification. Biostatistics, 15(3): 427-441.

*Zhao, SD, Cai T and Li H (2014): More powerful genetic association testing via a new statistical framework for integrative genomics. Biometrics, 70(4): 881-890.

Hu X, Feng Y, Zhang D., Zhao SD, Greshock J, Hu Z, Zhang Y, Yang L, Wang L-P, Jean S, Li C, Huang Q, Katsaros D, Montone K, Tanyi JL, Lu Y, Boyd J, Nathanson KL, Li H, Mills H, Lin Z (2014): A Functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in human cancer. Cancer Cell, 26(3): 344-357.

*Sun H, *Lin W, Feng R and Li H (2014): Network-regularized high dimensional Cox regression for Analysis of Genomic data. Statistica Sinica, 24, 1433-1459.

He S, Yin J, Li H and Wang X (2014): Graphical Model Selection and Estimation for High Dimensional Tensor Data. Journal of Multivariate Analysis, 128, 165-185.

Hu Y, Liu Y, Mao X, Jia C, Ferguson J, Xue C, Reilly M, Li H, Li M (2014): PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by Modeling Non-Uniform Read Distribution. Nucleic Acids Research, 42(3):e20.

*Wang W, Wei Z and Li H (2014): A change-point model for identifying 3'UTR switching by next-generation RNA sequencing. Bioinformatics, 30(15):2162-2170.

Albenberg LA, Esipova TV, Judge CP, Bittinger K, Chen J, Grunberg S, Baldassano RN, Lewis JD, Li H, Bushman FD, Vinogradov SA, and Wu GD (2014): Oxygen Measurements and Gene Sequencing Reveal a Correlation between Intraluminal Oxygen Gradient and Radial Partitioning of Gut Microbiota. Gastroenterology, 147 (5): 1055-1068.e8.


Li H (2013): Systems Biology Approaches to Epidemiological Studies of Complex Diseases. WIREs Systems Biology and Medicine, 5: 677-686.

*Jeng XJ, Cai TT and Li H (2013): Simultaneous Discovery of Rare and Common Segment Variants. Biometrika, 100(1), 157-172.

Cai TT, Li H, Liu W and *Xie J (2013): Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics. Biometrika, 100(1), 139-156.

*Deng W, Geng Z, Li H (2013): Learning Local Directed Acyclic Graphs Based On Multivariate Time Series Data. Annals of Applied Statistics, 7: 1663-1683.

*Chen J and Li H (2013):Variable Selection for Sparse Dirichlet-Multinomial Regression with An Application to Microbiome Data Analysis. Annals of Applied Statistics, 7(1): 418-442.

*Chen J, Bushman FD, Lewis J, Wu GD and Li H (2013): Structure-Constrained Sparse Canonical Correlation Analysis with an Application to Microbiome Data Analysis. Biostatistics, 14(2): 244-258.

*Xia F, Chen J, Fung WK and Li H (2013): A logistic normal multinormial regression model for microbiome compositional data analysis. Biometrics, 69 (4): 1053-1063.

*Zhi W, Minturn J, Rappaport E, Brodeur G, Li H (2013): Network-based analysis of multivariate gene expression data. Methods in Molecular Biology, 972:121-39.

*Vardhanabhuti S, Li M and Li H (2013): A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-Sample RNA-Seq Data. Statistics in Bioscience, 5(1): 244-258.

Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy B, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WHW, Bushman FD, Lusis AJ, and Hazen SL (2013): Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine, 19: 576-585.

*Yin J and Li H (2013): Adjusting for High-dimensional Covariates in Sparse Precision Matrix Estimation by $\ell_1$-Penalization. Journal of Multivariate Analysis, 116, 365-381.

Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu, GD, Lew JD, Bushman FD (2013): Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents. PLoS One, 8(6): e66019. doi:10.1371/journal.pone.0066019

*Wu Y, Tian L, Pirastu M, Stambolian D and Li H (2013): MATCHCLIP: Locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads. Frontiers in Genetics , 4:157. doi: 10.3389/fgene.2013.00157.


Cai T, Jeng J and Li H (2012): Robust Detection and Identification of Sparse Segments in Ultra-High Dimensional Data Analysis. Journal of Royal Statistical Society, Series B., 74 (5): 773-797.

*Sun H and Li H (2012): Robust Gaussian Graphical Modeling via l1 Penalization. Biometrics, 68: 1197-1206.

*Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD and Li H (2012): Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics, 28(16):2106-13.

Li H (2012): U-statistics in Genetic Association Studies. Human Genetics, 131(9): 1395-1401.

*Yin J and Li H (2012): Model Selection and Estimation in the Matrix Normal Graphical Model. Journal of Multivariate Analysis, 107: 119-140.

*Daye J, Li H and Wei Z (2012): A Powerful Test for Multiple Rare Variants Association Studies that Incorporate Sequencing Qualities. Nucleic Acids Research, 40: e60.

*Daye J, Chen J, Li H (2012): High-dimensional heteroscedastic regression with an application to eQTL data analysis. Biometrics, 68: 316-326.

*Daye J, Xie J, Li H (2012): A Sparse Structured Shrinkage Estimator for Nonparametric Varying-Coefficient Model with an Application in Genomics. Journal of Computational and Graphical Statistics, 21 (1): 110-133.

*He J, Li H, Edmondson A, Rader D and Li M (2012):A Gaussian Copula approach for the analysis of secondary phenotypes in case-control genetic association studies. Biostatistics, 13(03): 497-508.

Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD (2012): Assessing bacterial populations of the lung by comparing replicate samples from the upper and lower respiratory tracts. PloS One, 7(9): e42786.

Fairless A, Dow HC, Kreibich AS, Toree M, Kuruvilla M, Gordon E, Morton EA, Tan J, Berrettini WH, Li H, Abel T and Brodkin ES (2012): Sociability and brain Development in BALB/cJ and C57BL/6J Mice. Behavior Brain Research, 228:299-310.


Huang J, Ma S, Li H and Zhang CH (2011): The Sparse Laplacian Shrinkage Estimator for High-Dimensional Regression. Annals of Statistics, 39(4), 2021-2046.

*Yin J and Li H (2011): A Sparse Conditional Gaussian Graphical Model for Analysis of Genetical Genomics Data. Annals of Applied Statistics , 5(4): 2630-2650.

Lu T, Liang H, Li H , Wu H (2011): High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. Journal of American Statistical Association, 106: 1242-1258.

*Xie J, Cai TT, Li H (2011): Sample Size and Power Analysis for Sparse Signal Recovery in Genome-Wide Association Studies. Biometrika, 98(2), 273-290.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (2011): Linking long-term dietary patterns with gut microbial enterotypes. Science, 334:105-108.

Winter C, Austin RS, Blanvillain-Baufum??? B, Reback MA, Monniaux M, Wu MF, Sang Y, Yamaguchi A, Yamaguchi N, Parker JE, Parcy F, Jensen ST, Li H and Wagner D (2011): LEAFY Target Genes Reveal a Direct Link Between Biotic Stimulus Response and Flower. Developmental Cell, 20: 430-443.

Wang K, SJ. Diskin, H Zhang, EF Attiyeh, C Winter, C Hou, RW Schnepp, M Diamond, K Bosse, PA. Mayes, J Glessner, C Kim, E Frackelton, M Garris, Q Wang, W Glaberson, R Chiavacci, L Nguyen, J Jagannathan, N Saeki, H Sasaki, SFA Grant, A Iolascon, YP Mosse, KA Cole, Li H, M Devoto, PW McGrady, WB London, M Capasson, N Rahman, H Hakonarson & JM Maris (2011): Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Nature, 469: 216-220.

*Chen J, *Xie J and Li H (2011): A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis. Biometrics, 67(1), 299-308.

Wei X, Huang J and Li H (2011): Variable selection and estimation in high-dimensional varying-coefficient models. Statistica Sinica, 21, 1515-1540.

*Xie J, Cai T, Maris, J and Li H (2011): Optimal False Discovery Rate Control for Dependent Data. Statistics and Its Interface, 4(4): 417-430.

Minot S, Rohini S, Chen J, Li H, Keibaugh SA, Wu G, Lewis J and Bushman R (2011): The human gut virome: inter-individual variation and dynamic response to diet. Genome Research, 21:1616-1625.

*Nguyen LB, Diskin SJ, Cappasso M, Wang K, Diamond MA, Glessner J, Kim C, Attiyeh EF, Mosse YP, Cole K, Lolascon A, Devoto M, Hakonarson H, Li H, Maris JM (2011): Phenotype Restricted Genome-Wide Association Study Using a Gene-Centric Approach Identifies Three Low-Risk Neuroblastoma Susceptibility Loci. PLoS Genetics, 7(3): e1002026. doi:10.1371/journal.pgen.1002026.

Dow H, Kaercher K, Sankoorikal G, Pauley E, Lohoff F, Ferraro T, Li H , Brodkin E (2011): Genetic dissection of intermale aggressive behavior in BALB/cJ and A/J mice. Genes, Brain and Behavior, 10:57-68.

Fairless AH, Shah RY, Guthrie AJ, Li H and Brodkin ES (2011): Deconstructing Sociability, an Autism-relevant phenotype, in mouse models. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology. 294: 1713-1725.


*Jeng J, Cai TT and Li H (2010): Optimal sparse segment identification with application in copy number variation analysis. Journal of American Statistical Association, 105 (491): 1156-1166.

*Li C and Li H (2010): Variable Selection and Regression Analysis for Graph-Structured Covariates with an Application to Genomics. Annals of Applied Statistics, 4(3): 1498-1516.

Charlson ES, Jun Chen, Rebecca Custers-Allen, Kyle Bittinger, H Li, Rohini Sinha, Jennifer Hwang, Frederic D. Bushman and Ronald G. Collman (2010): Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One , 5(12): e15216.

*Sun H and Li H (2010): A Bayesian Appraoch for Graph-Constrained Estimation for High-dimensional Regression. International Journal of Systems and Synthetic Biology, 1(2): 255-272.

*Xulvi-Brunet R, Li H (2010): Co-expression Networks: Graph Properties and Topological Comparisons. Bioinformatics, 26: 205-214.

Li H, Wei Z and Maris J (2010): A hidden Markov random field model for genome-wide association studies. Biostatistics, 11: 139-150.

*Li C, Wei Z and Li H (2010): Network-based Empirical Bayes Methods for Linear Models with Applications to Genomic Data. Journal of Biopharmaceutical Statistics, 20: 209-222.

Sleiman P, M Imielinski, JP Bradfield, K Annaiah, S.A.G. Willis-Owen, NM. Rafaels, S Michel, K B???nnelykke, CE. Kim, EC. Frackelton, J. Glessne, C Hou, J Flory, F.G Otieno, E Santa, K Thomas, R.M. Smith, WR. Glaberson, M Garris, RM. Chiavacci, TH Beaty, I Ruczinski, J Allen, JM. Spergel, R Grundmeier, RA. Mathias, JD. Christie, E von Mutius, W.O.C. Cookson, M Kabesch, MF. Moffatt, MM. Grunstein, Li H, KC. Barnes, M Devoto, M Magnusson, S.F.A. Grant, H Bisgaard and H Hakonarson (2010): A locus on 1q31 harboring /DENND1B/ is associated with asthma susceptibility in both Caucasian and African American children. New England Journal of Medicine, 362: 36-44.

Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman F (2010): Sampling and pyrosequencing methods for quantifying bacterial communities in the human gut. BMC Microbiology 10:206.


Diskin SJ, Hou C, JT. Glessner, EF. Attiyeh, M Laudenslager, K Bosse, K Cole, YP. Mosse, A Wood, JE. Lynch, K Pecor, M Diamond, C Winter, K Wang, C Kim, EA. Geiger, PW. McGrady, A.I.F. Blakemore, W.B. London, T.H. Shaikh, J Bradfield, S.F.A. Grant, Li H, M Devoto, E.R. Rappaport, H Hakonarson, J.M. Maris (2009): Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 459: 987-991.

Capasso M, Hou C, Asgharzadeh S, Attiyeh EF, Mosse YP, Diskin SJ, Cole K, Bosse K, Diamond M, Laudenslager M, Winter C, Bradfield JP, Scott RH, Jagannathan J, Glessner JT, Kim C, London, WB, Seeger RC, Li H, Rahman N, Rappaport E, Hakonarson H, Devoto M, Maris J (2009): Common variations in the BARD1 tumor suppressor gene influence susceptibility to high-risk neuroblastoma. Nature Genetics, 41(6): 718-723.

Paulson T, Maley C, Li X, Li H, Sanchez C, Chao D, Odze R, Vaughan T, Blount P, Reid B (2009): Chromosomal instability and copy number alterations in Barrett's esophagus and esophageal adenocarcinoma. Clinical Cancer Research, 15: 3306-3314.

Flory J, P Sleiman, J Christi, K Annaiah, J Bradfield, C Kim, J Glessne, M Imielinski, Li H, E Frackelton, Hou C, G Otieno, K Thomas, R Smith, W Glaberson, M Garris, R Chiavacci, J Allen, J Spergel, R Grundmeier, M Grunstein, M Magnusson, S Grant, K B???nnelykke, H Bisgaard, H Hakonarson (2009): 17q12-21 variants interact with smoke exposure as a risk factor for pediatric asthma but are equally associated with early vs late onset asthma in North-Americans of European Ancestry. Journal of Allergy and Clinical Immunology , 124(3): 605-607.


*Wang L, Li H and Huang J (2008): Variable selection in nonparametric varying-coefficient models for analysis of repeated measurements. Journal of the American Statistical Association, 103: 1556-1569.

*Monni S and Li H (2008): Vertex clustering of graphs using reversible jump MCMC. Journal of Computational and Graphical Statistics, 17(2): 388-409.

*Luan Y, Li H (2008): Group Additive Regression Models for Analysis of Genomic Data. Biostatistics, 9:100-113.

*Wei Z and Li H (2008): A Hidden Spatial-temporal Markov Random Field Model for Network-based Analysis of Time Course Gene Expression Data. Annals of Applied Statistics, 2(1), 408-429.

Kamoun M, Holmes JH, Israni AK, Kearns JD, Teal V, Yang W, Rosasa SE, Joffe MM, Li H , Feldman HI (2008): HLA-A amino acid polymorphism and delayed kidney allograft function. Proceedings of National Academy of Sciences, 105(48): 18883-18888.

*Li C and Li H (2008): Network-constraint regularization and variable selection for analysis of genomic data. Bioinformatics, 24: 1175-1182.

*Wei Z, Li M, Rebbeck T, Li H (2008): U-statistics-based tests for multiple genes in genetic association studies. Annals of Human Genetics, 72:821-833.

Maris JM, Yael PM, Bradfield JP, Hou C, Monni S, Scott RH, Asgharzadeh S, Attiveh EF, Diskin SJ, Laudenslager M, Winter C, Cole K, Glessner JT, Kim C, Frackelton EC, Casalunovo T, Eckert AW, Capasso M, Rappaport EF, McConville C, London WB, Seeger RC, Rahman N, Devoto M, Grant SFA, Li H and Hakonarson H (2008) : A genome-wide association study identifies a susceptibility locus to clinically aggressive neuroblastoma at 6p22. New England Journal of Medicine, 358: 2585-2593.

Fairless AH, Dow H, Toledo MM, Kalkus KA, Edelmann M, Li H , Talbot K, Arnold SE and Brodkin ES (2008): Low Sociability is associated with reduced size of corpus callosum. Brain Research, 1230: 211-217.


*Wei Z, Li H (2007): Nonparametric pathways-based regression models for analysis of genomic data. Biostatistics, 8(2): 265-284.

*Wang L, *Chen G, Li H (2007): Group SCAD regression analysis for microarray time course gene expression data. Bioinformatics, 23: 1486-1494.

*Wei Z and Li H (2007): A Markov Random Field Model for Network-based Analysis of Genomic Data. Bioinformatics, 23: 1537-1544.


*Hong F, Li H (2006): Functional hierarchical models for identifying genes with different time-course expression profiles. Biometrics, 62: 534-544.

Li H and Gui J* (2006): Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks. Biostatistics, 7: 302-317.


*Gui J, Li H (2005): Threshold gradient descent method for censored data regression, with applications in pharmacogenomics. Pacific Symposium on Biocomputing, 10, 272-283.

*Gui J, Li H (2005): Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression Data. Bioinformatics, 21:3001-3008.

Li H , *Luan Y (2005): Boosting proportional hazards models using smoothing Spline, with application to high-dimensional microarray data. Bioinformatics,21:2403-2409.

Heit JA, Sobell JL, Li H , Sommer SS (2005): The Incidence of venous thromboembolism among Factor V Leiden carriers: a community-based cohort study. Journal of Thrombosis and Haemostasis, 3: 305-311.

Seldin MF, Shigeta R, Laiho, Li H , Saila H, Savolainene A, Leirisalo-Repo M, Tuomilehto-Wolf E, Kaarela K, Kauppi M, Alexander HC, Begovich AB, Tuomilehta J (2005): Finnish case-control and family studies support PTPN22 R620W polymorphism as a risk factor in rheumatoid arthritis, but suggest only minimal or no effect in juvenile idiopathic arthritis. Genes and Immunity, 6(8): 720-2.

Yang N, Li H , Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, Seldin MF (2005): Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Human Genetics, 29: 1-11.


*Luan Y, Li H (2004): Model-based methods for identifying periodically regulated genes based on the time course microarray gene expression data. Bioinformatics, 20:332-339.

*Zhong X, Li H (2004): Score tests of genetic association in the presence of linkage based on the additive genetic gamma frailty model. Biostatistics, 5:307-327.

Li H , *Gui J (2004): Partial Cox regression analysis for high-dimensional microarray gene expression data. Bioinformatics, 20:i208-i215.

*Sun W, Li H (2004): Ascertainment-adjusted maximum likelihood estimation for the additive genetic gamma frailty models. Lifetime Data Analysis, 10: 229-245

Seldin MF, Morii T, Collins-Schramm EC, Chima B, Kittles R, Criswell LA, Li H (2004): Putative ancestral origins of chromosomal segments in individual African Americans: Implications for admixture mapping. Genome Research, 14:1076-1084.

*Li L, Li H (2004): Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics, 20:3406-3412.

*Zhang C, K Chen, Seldin M, Li H (2004): A hidden Markov modeling approach for admixture mapping based on case-control data. Genetic Epidemiology, 27:225-239.


Li H , *Luan Y (2003): Kernel Cox regression models for linking gene expression profiles to censored survival data. Pacific Symposium on Biocomputing,8: 65-76.

*Luan Y, Li H (2003): Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics, 19: 474-482.

Krahn LE, Li H , O'Connor MK (2003): Patients who strive to be ill: factitious disorder with physical symptoms. American Journal of Psychiatry, 160:6, 1163-1168.


Li H , *Zhong X (2002): Multivariate survival models induced by genetic frailties, with application to linkage analysis. Biostatistics, 3(1): 57-75.

Li H (2002): The additive genetic gamma frailty model for linkage analysis of diseases with variable age of onset using nuclear families. Lifetime Data Analysis, 8: 315-334

Li H , *Luan Y, *Hong F, *Li Y (2002): Statistical methods for analysis of time-course gene expression data. Frontiers in Bioscience, 7, a90-98, May.

Hsu Li, Li H , Houwing J (2002): A method for incorporating ages at onset in affected sib pair linkage studies. Human Heredity, 54:1-12.

*Zhong X, Li H (2002): An additive genetic gamma frailty model for two-locus linkage analysis using sibship age of onset data. Statistical Applications in Genetics and Molecular Biology, Vol 1, No 1, Article 2.

Collins-Schramm HE, Phillips CM, Operario DJ, Lee JS, Webber JL, Hanson RL, Knowler WC, Cooper R, Li H , Seldin MF (2002): Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. American Journal of Human Genetics,70: 737-750.

Seligman VA, Lum R, Olson JL, Li H , Criswell LA (2002): Demographic differences in the development of lupus nephritis. American Journal of Medicine, 112: 726-29.

Parsa A, Peden E, Lum RF, Seligman VA, Olson JL, Li H , Seldin MF, and Criswell LA (2002): Association of angiotensin converting enzyme polymorphisms with systemic lupus erythematosus and nephritis: analysis of 644 SLE families. Genes and Immunity, 3 (supplement 1), S42-S46.


Li H , *Hong F (2001): Cluster-Rasch models for microarray gene expression data. Genome Biology, research0031.1-0031.13.

Li H (2001): A permutation procedure for the haplotype method for identification of disease-predisposing variants. Annals of Human Genetics, 65:189-196.

Seligman VA, Suarez C, Lum R, Inda SE, Olson J, Li H , Seldin MF, Criswell LA (2001): Ethnic variation in the association of Fcgamma$RIIIA polymorphism with lupus nephritis. Arthritis& Rheumatism, 44: 618-625.

Shields RC, McBane RD, Kuiper JD, Li H , Heit JA (2001): Efficacy and safety of intravenous phytonadione (Vitamin K1) for correction of chronic oral anticoagulation. Mayo Clinic Proceedings, 76:260-266.


Li H , Hsu L (2000): Effects of ages at onset on the power of the affected sib pair and transmission/disequilibrium tests. Annals of Human Genetics, 64:239-254

Li H , Fan JJ (2000): A general test of association for complex diseases with variable age of onset. Genetic Epidemiology, 19: S43-S49.

Collins HE, Li H , Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin MF (2000): A simple and accurate methods for determination of microsatellite total allele content differences between DNA pools. Human Genetics, 106(2): 218-226.

St. Louis EK, Wijdicks EFM, Li H , Atkinson JD (2000): Predictors of poor outcome in patients with a spontaneous cerebellar hematoma. The Canadian Journal of Neurological Sciences, 27: 32-36.

Yanovski J, Diament AL, Sovik KN, Nguyen TT, Li H , Sebring NG, Warden CH (2000): Associations between uncoupling protein 2, body composition, and testing energy expenditure in lean and obese African American, white, and Asian children. American Journal of Clinical Nutrition, 71:1405-12.

Silverman MB, Roche PC, Kho RM, Keeney GL, Li H , Podratz KC (2000): Molecular and cytokinetic pretreatment risk assessment in endometrial carcinoma. Gynecologic Oncology, 77(1):1-7.

Criswell LA, Moser KL, Gaffney PM, Inda S, Lin D, Chen JJ, Li H , Gray-McGuire C, Neas BR, Rich SS, Harley JB, Behrens TW, Seldin MF (2000): PARP alleles and SLE: failure to confirm association with disease susceptibility (letter to editor). Journal of Clinical Investigation, 105:1501-1502.

Zanetta GM; Webb MJ; Li H ; Keeney, GL (2000): Hyperestrogenism: A Relevant Risk Factor for the Development of Cancer from Endometriosis. Gynecologic Oncology, 79(1):18-22.

Krahn LE; Gleber E; Rummans TA; Pileggi TS; Lucas DL; Li H (2000) The effects of electroconvulsive therapy on melatonin. Journal of ECT, 16(4):391-8.

Gershwin ME; Leung PS; Li H ; Seldin MF(2000): Primary biliary cirrhosis and autoimmunity: evaluating the genetic risk. Isr Med Assoc J, Suppl:7-10.


Li H (1999). The additive genetic gamma frailty model for linkage analysis of age-at-onset variation. Annals of Human Genetics, 63:455-468.

Therneau TM, Li H (1999). Computing the Cox model for case cohort designs. Lifetime Data Analysis, 5:99-112.

Gould PM; Bonner JA; Sawyer TE; Deschamps C; Lange CM; Li H (1999): Patterns of failure and overall survival in patients with completely resected T3 N0 M0 non-small cell lung cancer. International Journal of Radiation Oncology, Biology, Physics,45:91-5.

Villeneuve JB, Silverman BM, Alderete B, Cliby WA, Li H , Croghan Gary, Podratz KC, Jenkins RB (1999): Loss of Markers Linked to BRCA1 Proceedes Loss at Important Cell Cycle Regulatory in Epithelial Ovarian Cancer. Genes, Chromosomes and Cancer, 5(1):65-9.

Weiner JS, Sherris D, Kasperbauer J, Lewis J, Li H , Persing D (1999): Relationship of human papillomavirus to Schneiderian papillomas. Laryngoscope, 109(1):21-6.

Heit JA, Minor TA, Andrews JC,Larson DR, Li H , Nichols WL (1999). Determinants of plasma Fibrin D-Dimer Sensitivity for Acute Pulmonary Embolism as Defined by Pulmonary Angiography. Archives of Pathological Laboratory Medicine, 123(3):235-40.

Sawyer TE; Bonner JA; Gould PM; Deschamps C; Lange CM; Li H (1999): Patients with stage I non-small cell lung carcinoma at postoperative risk for local recurrence, distant metastasis, and death: implications related to the design of clinical trials. International Journal of Radiation Oncology, Biology, Physics, 45(2):315-21.

Sawyer TE, Bonner JA, Gould PM, Garces YI, Foote RL, Lange CM, Li H (1999): Predictors of subclinical nodal involvement in clinical stages I and II non-small cell lung cancer: implications in the inoperable and three-dimensional dose-escalation settings. International Journal of Radiation Oncology, Biology, Physics, 43(5):965-70.

Flemming KD, Wijdicks EFM, St. Louis EK, Li H (1999): Predicting deterioration in patients with lobar haemorrhages. Journal of Neurology, Neurosurgery and Psychiatry , 66(5):600-5.

Gibson GE, Li H , Pittelkow MR (1999): Homocysteinemia and Livedoid Vasculitis. Journal of the American Academy of Dermatology, 40(2 Pt 1):279-81 .

Frias AE Jr., Li H , Keeney GL, Podratz KC, Woodruff TK (1999): Preoperative Serum Levels of inhibin A are Independent Prognostic Factors in Postmemopausal Women with Epithelial Ovarian Carcinoma. Cancer, 85(2):465-71.

Bonner JA; Garces YI; Sawyer TE; Gould PM; Foote RL; Deschamps C; Lange CM; Li H (1999): Frequency of noncontiguous lymph node involvement in patients with resectable nonsmall cell lung carcinoma. Cancer, 86:1159-64.

Magtibay PM; Perrone JF; Stanhope CR; Katzmann JA; Keeney GL; Li H (1999). Flow-cytometric DNA analysis of early stage adenocarcinoma of the cervix. Gynecol Oncology, 75(2):242-2474.

Sawyer TE; Bonner JA; Gould PM;Foote RL; Deschamps C; Lange CM; Li H (1999): Factors predicting patterns of recurrence after resection of N1 non-small cell lung carcinoma. Ann Thorac Surg, 68(4):1171-6.


Li H , Thompson EA, Wijsman EA (1998): Semiparametric estimation of major gene effects for age of onset. Genetic Epidemiology, 15:279-298.

Li H , Yang P, Schwartz AG (1998): Analysis of age of onset data from case-control family studies. Biometrics, 54:1030-1039.

Li H , Huang J (1998): Semiparametric linkage analysis using pseudolikelihoods on neighbouring Sets. Annals of Human Genetics, 62:323-336.

Adams KM, Li H , Nelson RL, Ogburn PL Jr, Danilenko-Dixon DR (1998): Sequelae of unrecognized gestational diabetes. American Journal of Obstetrics and Gynecology, 178(6):1321-32.

Erickson D, Grarib H, Li H , van Heerden JA (1998): Treatment of Patients with Toxic Multinodular Goiter. Thyroid, 8: 277-282 .

Limburg M, Wijdicks EFM, Li H (1998): Ischemic Stroke After General Surgical Procedures: Clinical Features, Neuroimaging and Risk Factors. Neurology, 50(4):895-901.

Gould PM, Bonner JA, Sawyer TE, Deschamps C, Lange CM, Li H (1998): Bronchial carcinoid tumors: importance of prognostic factors that influence patterns of recurrence and overall survival. Radiology, 208(1):181-5.

Dinneen S, Maldonado D, Leibson C, Klee G, Li H , Melton J, Rizza R (1998): Effects of a Change in the Diagnostic Criteria for Diabetes on Development of the Disease. Diabetes Care, 21(9): 1408-1413.

Shadid GE, Tinsley JA, Li H , Offord KP, Agerter DC (1998): A Survey of Family Physicians and Psychiatrists: Psychotropic Prescribing Practices and Educational Needs. General Hospital Psychiatry, Medicine and Primary Care, 20:360-367.

St. Louis EK, Wijdicks EFM, Li H (1998): Predictive Neurologic Deterioration in Patients with Cerebellar Hematomas. Neurology, 51: 1364-1369.

Lutz ME, Otley CC, Roenigk RK, Brodland DG, Li H (1998): Cutaneous Reinnervation of Flaps and Grafts of the Face. Archives of Dermatology, 134:1271-1274.


Li H , Thompson EA (1997): Semiparametric estimation of major gene and random familial effects for age of onset. Biometrics, 53:282-293.

Li H , Schaid DJ (1997): GENEHUNTER: Application to analysis of bipolar pedigrees and some extensions. Genetic Epidemiology, 14:659-663.

Schaid DJ, Li H (1997): Genotype relative-risks and association tests for nuclear families with missing parental data. Genetic Epidemiology, 14:1113-1118.

Sawyer TE, Bonner JA, Gould PM, Foote RL, Deschamps C, Trastek VF, Pairolero PC, Allen MS, Lange CM, Li H (1997): Effectiveness of Postoperative Irradiation in Stage IIIA Cancer Based on Regression Tree Analyses of Recurrence Risks. Annals of Thoracic Surgery, 64: 1402-1408.

Sawyer T, Bonner J, Gould P, Foote R, Deschamps C, Trastek V, Pairolero P, Allen M, Shaw E, Marks R, Frytak S, Lange C, Li H (1997): The impact of Surgical Adjuvant Thoracic Radiation Therapy for Patients with Nonsmall Cell Lung Carcinoma with Ipsilateral Mediastinal Lymph Node Involvement. Cancer, 80:1399-408.

Tomac TA, Rummans TA, Pileggi TS, Li H (1997): Safety and Efficacy of Electroconvulsive Therapy in Patients Over Age 85. The American Journal of Geriatric Psychiatry, 5(2):126-30.

Invited Book Chapters

Chen J and Li H (2013): Kernel Methods for Regression Analysis of Microbiome Compositional Data. 2012 ICSA Applied Statistics Symposium Proceedings, pp 191-201, edited by Yi Liu, Mingxiu Hu and Jianchang Lin, Springer Science.

Li H (2013): Genetical Genomics Data: Some Statistical Problems and Solutions. Advances in Statistical Bioinformatics: