Ho NT, Li F, Wang S, and Kuhn L. metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models, BMC Bioinformatics, 2019.

Cook RR, Fulcher JA, Tobin NH, Li F, Lee D, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM, and Gorbach PM. Effects of HIV viremia on the gastrointestinal microbiome of young men who have sex with men, AIDS, 2019.

Blazenovic I, Oh YT, Li F, Ji J, Nguyen AK, Wancewicz B, Bender JM, Fiehn O, and Youn HJ. Effects of Gut Bacteria Depletion and High‐Na+ and Low‐K+ Intake on Circulating Levels of Biogenic Amines, Molecular Nutrition & Food Research, 2018.

Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM, and Kuhn L. Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations, Nature Communications, 2018.

Bender JM, Li F, Adisetiyo H, Lee D, Zabih S, Hung L, Wilkinson TA, Pannaraj PS, She RC, Dien-Bard J, Tobin NH, and Aldrovandi GM. Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies, Microbiome, 2018.

Fulcher JA, SK Hussain, Cook R, Li F, Tobin NH, Ragsdale A, Shoptaw S, Gorbach PM, and Aldrovandi GM. Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection, J Infect Dis, 2018.

Kordy K, Romeo AC, Lee DJ, Li F, Zabih S, Saavedra M, Cunningham NH, Tobin NH, and Aldrovandi GM. Combination antibiotics improves disease activity and alters microbial communities in children with ulcerative colitis, J Pediatr Gastroenterol Nutr, 2018.

Tobin NH, Woodward C, Zabih S, Lee DJ, Li F, and Aldrovandi GM. A method for targeted 16S sequencing of human milk samples, J Vis Exp, 2018.

Lee HR, Li F, Choi UY, Yu HR, Aldrovandi GM, Feng P, Gao SJ, Hong YK, and Jung J. Deregulation of HDAC5 by vIRF3 plays an essential role in the Kaposi Sarcoma-associated herpesvirus-induced lymphangiogenesis, mBio, 2018.

Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez P, Bittinger K, Bailey A, Bushman FD, Sleasman JW, and Aldrovandi GM. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome, JAMA Pediatr, 2017.

Bender JM, Li F, Martelly S, Byrt E, Rouzier V, Leo M, Tobin NH, Pannaraj PS, Adisetiyo H, Santiskulvong C, Wang S, Autran C, Bode L, Fitzgerald D, Kuhn L, and Aldrovandi GM. Maternal HIV infection influences the microbiome of HIV-uninfected infants, Sci Transl Med, 2016.

Fang X, Xu M, Fang Q, Tan H, Zhou J, Li Z, Li F, and Yang S. Real-time utilization of metagenomics sequencing in the diagnosis and treatment monitoring of an invasive adenovirus B55 infection and subsequent herpes simplex virus encephalitis in an immunocompetent young adult, Open Forum Infect Dis, 2018.

Yang S, Hemarajata P, Hindler J, Li F, Adisetiyo H, Aldrovandi GM, Sebra R, Kasarskis A, MacCannell D, Didelot X, Russell D, Rubin Z, and Humphries RM. Evolution and transmission of carbapenem-resistant Klebsiella pneumoniae expressing the blaOXA-232 gene during an institutional outbreak associated with endoscopic retrograde cholangiopancreatography, Clin Infect Dis, 2017.

Yang S, Hemarajata P, Hindler J, Ward K, Adisetiyo H, Li F, Aldrovandi GM, Green NM, Russell D, Rubin Z, and Humphries RM. Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing, Diagn Microbiol Infect Dis, 2016.

Ruan A, Tobin NH, Mulligan K, Rollie A, Li F, Sleasman JW, and Aldrovandi GM. Macrophage activation in HIV-infected adolescent males contributes to differential bone loss by sex: adolescent trials network study 021, J Acquir Immune Defic Syndr, 2016.

Li N, Yousefi M, Nakauka-Ddamba A, Li F, Vandivier LE, Parada K, Woo DH, Wang S, Naqvi AS, Rao S, Tobias J, Cedeno RJ, Minuesa G, Katz Y, Barlowe TS, Valvezan A, Shankar S, Deering RP, Klein PS, Jensen ST, Kharas MG, Gregory BD, Yu Z, and Lengner CJ. The Msi family of RNA-binding proteins function redundantly as intestinal oncoproteins, Cell Rep, 2015.

Wang S, Li N, Yousefi M, Nakauka-Ddamba A, Li F, Parada K, Rao S, Minuesa G, Katz Y, Gregory BD, Kharas MG, Yu Z, and Lengner CJ. Transformation of the intestinal epithelium by the MSI2 RNA-binding protein, Nat Commun, 2015.

Vandivier LE, Li F, and Gregory BD. High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes, Methods Mol Biol, 2015.

Stein P, Rozhkov NV, Li F, Cardenas FL, Davydenk O, Vandivier LE, Gregory BD, Hannon GJ, and Schultz RM. Essential role for endogenous siRNAs during meiosis in mouse oocytes, PLoS Genet, 2015.

Silverman IM*, Li F*, Alexander A, Goff L, Trapnell C, Rinn JL, and Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome, Genome Biol, 2014.

Ihara M, Meyer-Ficca ML, Leu NA, Rao S, Gregory BD, Li F, Zalenskaya IA, Schultz RM, and Meyer RG. Paternal poly(ADP-ribose) metabolism regulates retention of inheritable sperm histones and early embryonic gene expression, PLoS Genet, 2014.

Elliott R, Li F, Dragomir I, Chua MW, Gregory BD, and Weiss SR. Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice, PLoS One, 2013.

Vandivier LE, Li F, Zheng Q, Willmann MR, Chen Y, and Gregory BD. Arabidopsis mRNA secondary structure correlates with protein function and domains, Plant Signal Behav, 2013.

Silverman IM*, Li F*, and Gregory BD. Review: Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants, Plant Science, 2013.

Li F, Zheng Q, Vandivier LE, M.R. Willmann, Chen Y, and Gregory BD. Regulatory impact of RNA secondary structure across the Arabidopsis thaliana transcriptome, Plant Cell, 2012.

Li F, Ryvkin P, Childress M, Valladares O, Gregory BD, and Wang LS. SAVoR: a server for sequencing annotation and visualization of RNA structures, Nucleic Acids Res, 2012.

Li F*, Zheng Q*, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang LS, and Gregory BD. Global analysis of RNA secondary structure in two metazoans, Cell Rep, 2012.

Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, and Gregory BD. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis, PLoS Genet, 2010.

Yang Y, Jang G, Yang X, Wang Q, He S, Li S, Quach C, Zhao S, Li F, Yuan Z, Lee HR, Zhong H, and Liang C. Central role of autophagic UVRAG in melanogenesis and the suntan response, PNAS, 2018.

Ha VL, Luong A, Li F, Casero D, Malvar J, Kim YM, Bhatia R, Crooks GM, and Parekh C. The T-ALL related gene BCL11B regulates the initial stages of human T-cell differentiation, Leukemia, 2017.

Yang Y, He S, Wang Q, Li F, Kwak M, Chen S, O’Connell D, Zhang T, Priooz SD, Jeon Y, Chimge N, Frenkel B, Choi Y, Aldrovandi GM, Oh B, Zan Y, and Liang C. Autophagic UVRAG promotes UV-induced photolesion repair by activation of the CRL4DDB2 E3 ligase, Mol Cell, 2016.

Li F, Thiele I, Jamshidi N, and Palsson BO. Identification of potential pathway mediation targets in Toll-like receptor signaling, PLoS Comput Biol, 2009.