Publication

Statistical Methodology Papers (Google Scholar)

*indicates a student under my supervision

Lam Tran, Gen Li, Lan Luo, Hui Jiang (2024+). A fast solution to the lasso problem with equality constraints. Journal of Computational and Graphical Statistics, accepted. Code
Lap Sum Chan*, Gen Li (2024). Zero is not absence: censoring-based differential abundance analysis for microbiome data. Bioinformatics, 40(2): btae071. Code
Tianchen Xu*, Kun Chen, Gen Li (2024). Tensor regression for incomplete observations with application to longitudinal studies. The Annals of Applied Statistics, 18(2): 1195-1212. Code
Zhiwen Fang, Gen Li, Wendong Li, Xiaolong Pu, Dongdong Xiang (2024). Distributed eQTL analysis with auxiliary information. Journal of Statistical Planning and Inference, 228: 34–45.
Gen Li, Yan Li*, Kun Chen (2023). It's all relative: regression analysis with compositional predictors. Biometrics, 79(2): 1318-1329. Code
Yan Li*, Gen Li, Kun Chen (2022). Principal amalgamation analysis for microbiome data. Genes, 13(7): 1139. Code
Tianchen Xu*, Kun Chen, Gen Li (2022). The more data, the better? Demystifying deletion-based methods in linear regression with missing data. Statistics and Its Interface, 15(4): 515-526.
Xiaokang Liu, Xiaomei Cong, Gen Li, Kendra Maas, Kun Chen (2022). Multivariate log-contrast regression with sub-compositional predictors: testing the association between preterm infants’ gut microbiome and neurobehavioral outcomes. Statistics in Medicine, 41(3): 580-594.
Xing Gao, Sungwon Lee, Gen Li, Sungkyu Jung (2021). Covariate-driven factorization by thresholding for multi-block data. Biometrics, 77(3): 1011-1023.
Tianchen Xu*, Ryan T. Demmer, Gen Li (2021). Zero-inflated Poisson factor model with application to microbiome read counts. Biometrics, 77(1): 91-101. Code
Jihui Lee*, Gen Li, James D. Wilson (2020). Varying-coefficient models for dynamic networks. Computational Statistics & Data Analysis, 152: 107052. Code
Gen Li (2020). Generalized co-clustering analysis via regularized alternating least squares. Computational Statistics & Data Analysis, 150: 106989. Code
Zhe Sun, Wanli Xu, Xiaomei Cong, Gen Li, Kun Chen (2020). Log-contrast regression with functional compositional predictors: linking preterm infant’s gut microbiome trajectories to neurobehavioral outcome. The Annals of Applied Statistics, 14(3): 1535-1556. Code
Huichen Zhu*, Gen Li, Eric F. Lock (2020). Generalized integrative principal component analysis for multi-type data with block-wise missing structure. Biostatistics, 21(2):302-318. Code
Irina Gaynanova, Gen Li (2019). Structural learning and integrative decomposition of multi-view data. Biometrics, 75(4): 1121-1132. Code
Jihui Lee*, Gen Li, William F. Christensen, Gavin Collins, Matthew Seeley, Anton E. Bowden, David T. Fullwood, Jeff Goldsmith (2019). Functional data analyses of gait data measured using in-shoe sensors. Statistics in Biosciences, 11(2): 288–313.
Gen Li, Xiaokang Liu, Kun Chen (2019). Integrative multi-view regression: bridging group-sparse and low-rank models. Biometrics, 75(2): 593-602. Code, Supp
Gen Li, Jianhua Z. Huang, Haipeng Shen (2018). Exponential family functional data analysis via a low-rank model. Biometrics, 74(4): 1301-1310. Code, Supp
Gen Li, Jianhua Z. Huang, Haipeng Shen (2018). To wait or not to wait: Two-way functional hazards model for understanding waiting in call centers. Journal of the American Statistical Association, 113(524): 1503-1514. Code, Supp
Gen Li, Irina Gaynanova (2018). A general framework for association analysis of heterogeneous data. The Annals of Applied Statistics, 12(3): 1700-1726. Code, Supp
Chongliang Luo, Jian Liang, Gen Li, Fei Wang, Changshui Zhang, Dipak K. Dey, Kun Chen (2018). Leveraging mixed and incomplete outcomes via reduced-rank modeling. Journal of Multivariate Analysis, 167: 378-394. Code
Gen Li, Andrey A. Shabalin, Ivan Rusyn, Fred A. Wright, Andrew B. Nobel (2018). An empirical Bayes approach for multiple tissue eQTL analysis. Biostatistics, 19(3): 391-406. Code, Supp
Eric F. Lock, Gen Li (2018). Supervised multiway factorization. Electronic Journal of Statistics, 12(1): 1150-1180. Code
Gen Li, Dereje Jima, Fred A. Wright, Andrew B. Nobel (2018). HT-eQTL: Integrative eQTL analysis in a large number of human tissues. BMC Bioinformatics, 19(1): 95. Code
Gen Li, Sungkyu Jung (2017). Incorporating covariates into integrated factor analysis for multi-view data. Biometrics, 73(4): 1433-1442. Code, Supp
Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei (2017). QRank: A novel quantile regression tool for eQTL discovery. Bioinformatics, 33(14): 2123-2130. Code
Gen Li, Haipeng Shen, Jianhua Z. Huang (2016). Supervised sparse and functional principal component analysis. Journal of Computational and Graphical Statistics, 25(3): 859-878. Code, Supp
Gen Li, Dan Yang, Andrew B. Nobel, Haipeng Shen (2016). Supervised singular value decomposition and its asymptotic properties. Journal of Multivariate Analysis, 146: 7-17. Code, Supp
Gen Li, Guohua Zou, Xinyu Zhang (2012). Model selection for high-dimensional data: a review. Chinese Journal of Applied Statistics and Management, 180(4): 74-92.

Application Papers (PubMed)

Kristopher Opron, Lesa A. Begley, John R. Erb-Downward, Gen Li, Neil E. Alexis, Igor Barjaktarevic, R. Graham Barr, Eugene Bleecker, Richard Boucher, Russell P. Bowler, Stephanie A. Christenson, Alejandro P. Comellas, Gerard Criner, Christopher B. Cooper, David Couper, Craig J. Galban, MeiLan K. Han, Annette Hastie, Charles Hatt, Eric A. Hoffman, Robert J. Kaner, Mehmet Kesimer, Jerry A. Krishnan, David C. Lafon, Fernando J. Martinez, Victor E. Ortega, Stephen P. Peters, Robert Paine III, Nirupama Putcha, Prescott G. Woodruff, Gary B. Huffnagle, Jeffrey L. Curtis, Yvonne J. Huang (2024+). Loss of airway phylogenetic diversity is associated with clinical and pathobiological markers of disease development in COPD. American Journal of Respiratory and Critical Care Medicine, accepted.
Christopher Flora, Mary Olesnavich, Yu Zuo, Erin Sandford, Rashmi Madhukar, Michelle Rozwadowski, Kavya Sugur, Andrew Ly, Ata Alpay Canbaz, Audra Shedeck, Gen Li, Marcus J. Geer, Gregory A. Yanik, Monalisa Ghosh, David G. Frame, Challice L. Bonifant, Tania Jain, Jason S. Knight, Sung Won Choi, Muneesh Tewari (2024). Longitudinal plasma proteomics in CAR T–cell therapy patients implicates neutrophils and NETosis in the genesis of CRS. Blood Advances, 8(6): 1422-1426.
Deesha Bhaumik, Elizabeth Salzman, Elyse Davis, Freida Blostein, Gen Li, Katherine Neiswanger, Daniel McNeil, Mary Marazita, Betsy Foxman (2024). Plaque microbiome in caries-active and caries-free teeth by dentition. JDR Clinical & Translational Research, 9(1): 61-71.
Marcell Costa de Medeiros, Stephanie The, Emily Bellile, Nickole Russo, Ligia Schmitd, Erika Danella, Priyanka Singh, Rajat Banerjee, Christine Bassis, George R. Murphy III, Maureen A. Sartor, Isabelle Lombaert, Thomas M. Schmidt, Avi Eisbruch, Carol Anne Murdoch-Kinch, Laura Rozek, Greg Wolf, Gen Li, Grace Y. Chen, Nisha J. D’Silva (2023). Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer. Microbiome, 11(1): 268.
Lisa A. Carmody, Linda M. Kalikin, Donald R. VanDevanter, Gen Li, Kristopher Opron, Richard H. Simon, Lindsay J. Caverly, John J. LiPuma (2022). Changes in airway bacterial communities occur soon after initiation of antibiotic treatment of pulmonary exacerbations in cystic fibrosis. Journal of Cystic Fibrosis, 21(5): 766-768.
Siddharth S. Madapoosi, Charmion Cruickshank-Quinn, Kristopher Opron, John R. Erb-Downward, Lesa A. Begley, Gen Li, Igor Barjaktarevic, R. Graham Barr, Alejandro P. Comellas, David Couper, Christopher B. Cooper, Christine Freeman, Meilan Han, Robert J. Kaner, Wassim Labaki, Fernando J. Martinez, Victor E. Ortega, Stephen P. Peters, Robert Paine, Prescott Woodruff, Jeffrey L. Curtis, Gary B. Huffnagle, Kathleen A. Stringer, Russell P. Bowler, Charles R. Esther Jr, Nichole Reisdorph, Yvonne J. Huang (2022). Lung microbiota and metabolites collectively associate with clinical outcomes in milder stage COPD. American Journal of Respiratory and Critical Care Medicine, 206(4): 427-439.
Yao Shen, Jasvinder Singh, Bindeshwar Sah, Zhongming Chen, Wootae Ha, Christine Henzler, Tao Su, Lilian Xie, Yibin Deng, Gen Li, Hua Guo, Hanina Hibshooshi, Liang Liu (2022). The histone demethylase HR suppresses breast cancer development through enhanced CELF2 tumor suppressor activity. Cancers, 14(19): 4648.
Hiroko Matsumoto, Elaine L. Larson, Shay I.Warren, Bradley T. Hammoor, Lisa Bonsignore-Opp, Michael J. Troy, Kody K. Barrett, Brendan Steriano, Gen Li, Mary Beth Terry, Benjamin D. Roye, Lawrence Lenke, David Skaggs, Michael Glotzbecker, John Flynn, David P. Roye, Michael G. Vitale (2022). A clinical risk model for surgical site infection following pediatric spine deformity surgery. The Journal of Bone & Joint Surgery, 104(4): 364-375.
Patrick Ho, George W. Moran, Vinson Wang, Gen Li, Renu K. Virk, Christopher B. Anderson (2022). The effect of tumor grade heterogeneity on recurrence in non-muscle invasive bladder cancer. Urologic Oncology: Seminars and Original Investigations, 40(2): 60.e11-60.e16.
Brendan K. Wallace, Gen Li, James M. McKiernan, G. Joel DeCastro, Christopher B. Anderson (2021). Radical cystectomy in a cohort of octogenarians managed in the ERAS era. Urologic Oncology: Seminars and Original Investigations, 39(5): 299.e1-299.e6.
Michael Smigelski, Brendan K. Wallace, Jun Lu, Gen Li, Christopher B. Anderson (2021). Differences in use of aggressive therapy for localized prostate cancer in New York City. Clinical Genitourinary Cancer, 19(1): e55-e62.
Minjae Kim, Gen Li, Sumit Mohan, Zachary A. Turnbull, Ravi P. Kiran, Guohua Li (2021). Intraoperative data enhance the detection of high risk acute kidney injury patients when added to a baseline prediction model. Anesthesia & Analgesia, 132(2): 430-441.
Shawn J. Mendonca, Sun-Ming J. Pan, Gen Li, Steven B. Brandes (2021). Real world practice patterns favor minimally invasive methods over ureteral reconstruction in the initial treatment of severe blunt ureteral trauma - a national trauma data bank analysis. The Journal of Urology, 205(2): 470-476.
Cooper R. Benson, Gen Li, Steven B. Brandes (2021). Long term outcomes of one-stage augmentation anterior urethroplasty: a systematic review and meta-analysis. International Brazilian Journal of Urology, 47(2): 237-250.
Roy N. Alcalay, Pavlina Wolf, Ming Sum, Ruby Chiang, Karolina Helesicova, Xiaokui Kate Zhang, Kalpana Merchant, Samantha J. Hutten, Clemens Scherzer, Chelsea Caspell-Garcia, Cornelis Blauwendraat, Tatiana Foroud, Kelly Nudelman, Ziv Gan Or, Tanya Simuni, Lana M. Chahine, Oren Levy, Dandi Zheng, Gen Li, Sergio Pablo Sardi, The Parkinson’s Progression Markers Initiative (2020). Longitudinal measurements of glucocerebrosidase activity in Parkinson’s patients. Annals of Clinical and Translational Neurology, 7(10): 1816-1830.
Kathleen M. Capaccione, Gen Li, Mary M. Salvatore (2020). Pulmonary embolism rate in patients infected with SARS-CoV-2. Blood Research, 55(4): 275-278.
Hyunjoong Kim, KM Capaccione, Gen Li, Lyndon Luk, Reginald Widemon, Ozair Rahman, Volkan Beylergil, Ryan Mitchell, Belinda M. D’Souza, Jay S. Leb, Shifali Dumeer, Stuart Bentley-Hibbert, Michael Liu, Sachin Jambawalikar,John HM Austin, Mary Salvatore (2020). The role of initial ER chest X-ray in triaging patients with suspected COVID-19 during the pandemic. Emergency Radiology, 27(6): 617-621.
Christopher R. Haas, Gen Li, Elias S. Hyams, Ojas Shah (2020). Delayed decompression of obstructing stones with urinary tract infection is associated with increased odds of death. The Journal of Urology, 204(6): 1256-1262.
Joseph M. Caputo, Michael B. Smigelski, Elisabeth M. Sebesta, Gen Li, Matthew P. Rutman, Kimberly L. Cooper (2020). Increased time between scheduling date and appointment date results in increased no-show rates in the academic urology practice. Urology Practice, 7(6): 461-466.
The GTEx Consortium (2020). The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science, 369(6509): 1318-1330.
Monica Pernia, Liberato Salvatore, Andrew Einstein , Gen Li, Ramona Jayasena, Reginald Widemon, Hyunjoong William Kim, KM Capaccione, Mary M. Salvatore (2020). D-dimer in COVID-19 patients. Annals of Pulmonology, 4(1): 39-44.
Cooper R. Benson, Stephanie Thompson, Gen Li, Denise Asafu-Adjei, Steven B. Brandes (2020). Bladder and ureteral injuries during benign hysterectomy: an observational cohort analysis in New York State. World Journal of Urology, 38(8): 2049-2054.
Joseph M. Caputo, George Moran, Benjamin Muller, Alison T. Keller, Gen Li, Christopher B. Anderson (2020). The management of newly-diagnosed non-muscle invasive bladder cancer in veterans integrated services network 02 of the veterans health administration. Military Medicine, 185(1-2): 276-281.
Elisabeth M. Sebesta, Anika March, Christopher Sayegh, Gen Li, Michelle Love, Gina M. Badalato, Marcy Ferdschneider, Kimberly L. Cooper (2020). Reducing over-prescribing of antibiotics for suspected urinary tract infections in a health sciences campus student health service. Neurourology and Urodynamics, 39(1): 220-224.
Denise Asafu-Adjei, Clark Judge, Christopher Deibert, Gen Li, Doron Stember, Peter J. Stahl (2020). Systematic review of the impact of varicocele grade on response to surgical management. The Journal of Urology, 203(1): 48-56.
Christopher B. Anderson, Michael Lipsky, Subhadra V. Nandula, Christopher E. Freeman, Thomas Matthews, Caitlin E. Walsh, Gen Li, Matthias Szabolcs, Mahesh M. Mansukhani, James M. McKiernan, Vundavalli V. Murty (2020). Cytogenetic analysis of 130 renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations. Genes, Chromosomes and Cancer, 59(1): 6-12.
Ryan Demmer, Pauline Trinh, Michael Rosenbaum, Gen Li, Charles LeDuc, Rudolph Leibel, Antonio González, Rob Knight, Bruce Paster, Paolo Colombo, Moise Desvarieux, Panos Papapanou, David Jacobs (2019). Subgingival microbiota and longitudinal glucose change: results from ORIGINS. Journal of Dental Research, 98(13): 1488-1496.
Kevin Chua, Gen Li, Peter J. Stahl, Elias S. Hyams (2019). Receiving industry payments is associated with prescribing habits of tadalafil. Urology Practice, 6(5): 282-288.
Kevin Chua, Gen Li, Matthew P. Rutman, Elias S. Hyams (2019). Alpha blocker and 5-alpha reductase inhibitor prescribing habits among urologists and primary care physicians. Urology Practice, 6(4), 262-268.
Nancy S. Green, Deogratias Munube, Paul Bangirana, Linda Rosset Buluma, Bridget Kebirungi, Robert Opoka, Ezekiel Mupere, Philip Kasirye, Sarah Kiguli, Annet Birabwa, Michael S. Kawooya, Samson K. Lubowa, Rogers Sekibira, Edwards Kayongo, Heather Hume, Mitchell Elkind, Weixin Peng, Gen Li, Caterina Rosano, Philip LaRussa, Frank J. Minja, Amelia Boehme, Richard Idro (2019). Burden of neurological and neurocognitive impairment in pediatric sickle cell anemia in Uganda (BRAIN SAFE): a cross-sectional study. BMC Pediatrics, 19(1): 381.
Justin T. Matulay, Solomon L. Woldu, Amy Lim, Vikram M. Narayan, Gen Li, Ashish M. Kamat, Christopher B. Anderson (2019). The impact of squamous histology on survival in patients with muscle-invasive bladder cancer. Urologic Oncology: Seminars and Original Investigations, 37(6): 353.e17-353.e24 .
Robyn D. Gartrell, Douglas K. Marks, Emanuelle M. Rizk, Margaret H. Bogardus, Camille Gerard, Luke Barker, Yichun Fu, Camden E. Esancy, Gen Li, Jiayi Ji, Shumin Rui, Marc S. Ernstoff, Bret Taback, Sarabjot Pabla, Rui Chang, Sandra Lee, John Krolewsky, Carl Morrison, Yvonne M. Saenger (2019). Validation of melanoma immune profile (MIP), a prognostic immune gene prediction score for stage II-III melanoma. Clinical Cancer Research, 25(8): 2494-2502.
Ashley N. Gonzalez, Michael J. Lipsky, Gen Li, Matthew P. Rutman, Kimberly L. Cooper, David M. Weiner, Gina Badalato, Guarionex J. Decastro, Sven Wenske, James M. McKiernan, Christopher B. Anderson (2019). The prevalence of bladder cancer during cystoscopy for asymptomatic microscopic hematuria. Urology, 126: 34-38.
Benjamin Rohaut, Kevin W. Doyle, Alexandra S. Reynolds, Kay Igwe, Caroline Couch, Adu Matory, Batool Rizvi, David Roh, Angela Velasquez, Murad Megjhani, Soojin Park, Sachin Agarwal, Christine M. Mauro, Gen Li, Andrey Eliseyev, Vincent Perlbarg, Sander E. Connolly, Adam Brickman, Jan Claassen (2019). Deep structural brain lesions associated with consciousness impairment early after haemorrhagic stroke. Scientific Reports, 9, 4174.
Kevin Chua, Gen Li, Kimberly Cooper, Elias S. Hyams (2019). Urologists use uoroquinolones more frequently in states with high resistance. International Journal of Urology, 26(3): 433-434.
Patrick M. Mazza, George W. Moran, Gen Li, Dennis J. Robins, Justin T. Matulay, Harry W. Herr, Guarionex J. Decastro, James M. McKiernan, Christopher B. Anderson (2018). Conservative management following clinical complete response to neoadjuvant chemotherapy of muscle-invasive bladder cancer: contemporary outcomes of a multi-institutional cohort study. The Journal of Urology, 200(5): 1005-1013.
Wanda Anslemo, Emanuela Branchetti, Juan B. Grau, Gen Li, Salma Ayoub, Eric K. Lai, Nancy Rioux, Artak Tovmasyan, Jacqueline H. Fortier, Micheal S. Sacks, Ines Batinic-Haberle, Stanley L. Hazen, Robert J. Levy, Giovanni Ferrari (2018). Porphyrin-based SOD mimic MnTnBuOE-2-PyP5+ inhibits mechanisms of aortic valve remodeling in human and murine models of aortic valve sclerosis. Journal of the American Heart Association, 7(20): e007861 .
John B. Doyle, Rohit R. Raghunathan, Ilana Cellum, Gen Li, Justin S. Golub (2018). Longitudinal tracking of sound exposure and hearing aid usage through objective data logs. Otolaryngology-Head and Neck Surgery, 159(1): 110-116.
Elizabeth J. Millings, Maria Caterina De Rosa, Sarah Fleet, Kazuhisa Watanabe, Richard Rausch, Dieter Egli, Gen Li, Charles A. Leduc, Yiying Zhang, Stuart G. Fischer, Rudolph L. Leibel (2018). ILDR2 has a negligible role in hepatic steatosis. PLoS ONE, 13(5): e0197548.
Ezra J. Margolin, Justin T. Matulay, Gen Li, Xiaosong Meng, Brian Chao, Varun Vijay, Hayley Silver, Timothy N. Clinton, Laura-Maria Krabbe, Solomon L. Woldu, Nirmish Singla, Aditya Bagrodia, Vitaly Margulis, William C. Huang, Marc A. Bjurlin, Ojas Shah, Christopher B. Anderson (2018). Discordance between ureteroscopic biopsy and final pathology for upper tract urothelial carcinoma. The Journal of Urology, 199(6): 1440-1445.
Robyn D. Gartrell, Douglas K. Marks, Thomas D. Hart, Gen Li, Danielle R. Davari, Alan Wu, Zoe Blake, Yan Lu, Kayleigh N. Askin, Anthea Monod, Camden L. Esancy, Edward C. Stack, Dan Tong Jia, Paul M. Armenta, Yichun Fu, Daisuke Izaki, Bret Taback, Raul Rabadan, Howard L. Kaufman, Charles G. Drake, Basil A. Horst, Yvonne M. Saenger (2018). Quantitative analysis of immune infiltrates in primary melanoma. Cancer Immunology Research, 6(4): 481-493.
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu (2017). Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through integrative omics analyses. Scientific Reports, 7, 42646.
George W. Moran, Gen Li, Dennis J. Robins, Justin T. Matulay, James M. McKiernan, Christopher B. Anderson (2017). Systematic review and meta-analysis on the efficacy of chemotherapy with transurethral resection of bladder tumors as definitive therapy for muscle invasive bladder cancer. Bladder Cancer, 3(4): 245-258.
GTEx Consortium (2017). Genetic effects on gene expression across human tissues. Nature, 550(7675): 204-213.
The GTEx Consortium (2015). The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348(6235): 648-660.

Book Chapter

Gen Li (2020). Expression quantitative trait loci analysis in multiple tissues. In Xinghua Mindy Shi (Eds), eQTL Analysis: Methods and Protocols, Methods in Molecular Biology, volume 2082, Springer Nature.