Liu, X., Ni, Y., Ye, L., Guo, Z., Tan, L., Li, J., … & Li, R. (2024). Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications. Genome Research, gr-279012.
Tan, L., Guo, Z., Shao, Y., Ye, L., Wang, M., Deng, X., Chen, S., & Li, R. (2024). Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Research, gkae601.
Liu, X., Shao, Y., Guo, Z., Ni, Y., Sun, X., Leung, A. Y. H., & Li, R. (2024). Giraffe: a tool for comprehensive processing and visualization of multiple long-read sequencing data. CSBJ, 2024.
Guo, Z., Ni, Y., Tan, L., Shao, Y., Ye, L., Chen, S., & Li, R. (2024). Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing. NAR Genomics and Bioinformatics, 6(2), lqae052.
Tan, L., Guo, Z., Wang, X., Kim, D. Y., & Li, R. (2024). Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications. Msystems, e01163-23.
Wang, X., Liu, X., Tan, L., Jahangiri, L., Cai, W., & Li, R. (2024). Chromosome level genome assembly and transcriptome analysis of E11 cells infected by tilapia lake virus. Fish & Shellfish Immunology, 148, 109505.
Ye, L., Liu, X., Ni, Y., Xu, Y., Zheng, Z., Chen, K., … & Li, R#, Chen, S#. (2024). Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10. 4.1 nanopore sequencing. Microbiological Research, 283, 127666.
Ren, X., Shao, Y., Zhang, Y., Ni, Y., Bi, Y., & Li, R. (2023). Primerdiffer: a python command line module for large-scale primer design in haplotype genotyping. Bioinformatics, btad188.
Liu, X., Ni, Y., Wang, D., Ye, S., Yang, M., Sun, X., Leung, A.Y.H#. and Li, R#., (2023). Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing. Scientific Data, 10(1), p.532.
Si, W., Ni, Y., Jiang, Q., Tan, L., Sparagano, O., Li, R#., & Yang, G#. (2023). Nanopore sequencing identifies differentially methylated genes in the central nervous system in experimental autoimmune encephalomyelitis. Journal of Neuroimmunology, 578134.
Ni, Y., Liu, X., Simeneh, Z. M., Yang, M., & Li, R. (2023). Benchmarking of Nanopore R10. 4 and R9. 4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing. Computational and Structural Biotechnology Journal, 21, 2352-2364.
Tan L,Zhang Y, Kim D#, Li R#. Insect-Specific Chimeric Viruses Potentiated Antiviral Responses and Inhibited Pathogenic Alphavirus Growth in Mosquito Cells. Microbiology Spectrum (2022): e03613-22.
Li R#, Ren X#, Ding Q, Bi Y, Xie D, Zhao Z: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development. Genome Res 2020, 30:287-298.
Zhang S#, Li R#, Zhang L, Chen S, Xie M, Yang L, Xia Y, Foyer CH, Zhao Z, Lam HM: New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs. Nucleic Acids Res 2020, 48:7700-7711. (#co-first author).
Ren X#, Li R#, Wei X, Bi Y, Ho VWS, Ding Q, Xu Z, Zhang Z, Hsieh CL, Young A, et al: Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni. Nucleic Acids Res 2018, 46:1295-1307. (#co-first author).
Sun J#, Mu H#, Ip JCH#, Li R#, Xu T, Accorsi A, Sanchez Alvarado A, Ross E, Lan Y, Sun Y, et al: Signatures of Divergence, Invasiveness, and Terrestrialization Revealed by Four Apple Snail Genomes. Mol Biol Evol 2019, 36:1507-1520. (#co-first author).
Li R, Ren X, Bi Y, Ding Q, Ho VWS, Zhao Z: Comparative mitochondrial genomics reveals a possible role of a recent duplication of NADH dehydrogenase subunit 5 in gene regulation. DNA Res 2018, 25:577-586.
Ding Q#, Li R#, Ren X, Chan L-y, Ho VW, Xie D, Ye P, Zhao Z: Genomic architecture of 5S rDNA cluster and its variations within and between species. BMC genomics 2022, 23:1-20. (#co-first author).
Zou H#, Shi M#, Li R#, Zhang X, Lu W: Comparative transcriptome and methylome analysis of the hindbrain in olive flounder (Paralichthys olivaceus) considering individual behavior-type and oxygen metabolism. Comp Biochem Physiol Part D Genomics Proteomics 2021, 38:100799. (#co-first author).
Wang D, Zheng L, Cheng BY, Sin CF, Li R, Tsui SP, Yi X, Ma AC, He BL, Leung AY, Sun X. Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukemia. Oncogene. 2023 Feb 4:1-0.
Ye L, Dong N, Xiong W, Li J, Li R, Heng H, Chan EWC, Chen S: High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly. Frontiers in microbiology 2022, 13.
Wong M-K, Ho VWS, Huang X, Chan L-Y, Xie D, Li R, Ren X, Guan G, Ma Y, Hu B: Initial characterization of gap phase introduction in every cell cycle of C. elegans embryogenesis. Frontiers in cell and developmental biology 2022:2013.
Song D, Liu Y, Yao Y, Liu F, Tao W, Zhou X, Li R, Zhang X, Li X: Melatonin improves bisphenol A-induced cell apoptosis, oxidative stress and autophagy impairment via inhibition of the p38 MAPK signaling pathway in FLK-BLV cells. Environ Toxicol 2022, 37:1551-1562.
Ding Q, Ren X, Li R, Chan L, Ho VWS, Bi Y, Xie D, Zhao Z: Highly efficient transgenesis with miniMos in Caenorhabditis briggsae. G3 (Bethesda) 2022.
Zhang Y, Yu J, Tan L, Wang X, Li R, Kim DY: Complete genetic dissection and cell type-specific replication of old world alphaviruses, getah virus (GETV) and sagiyama virus (SAGV). J Microbiol 2021, 59:1044-1055.
Sun J, Li R, Chen C, Sigwart JD, Kocot KM: Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes. Philos Trans R Soc Lond B Biol Sci 2021, 376:20200160.
Lin ZY, Xie YC, Nong WY, Ren XL, Li RS, Zhao ZY, Hui JHL, Yuen KWY: Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization. Nucleic Acids Research 2021, 49:9174-9193.
Lan Y, Sun J, Chen C, Sun Y, Zhou Y, Yang Y, Zhang W, Li R, Zhou K, Wong WC, et al: Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis. Nat Commun 2021, 12:1165.
Ip JC, Xu T, Sun J, Li R, Chen C, Lan Y, Han Z, Zhang H, Wei J, Wang H, et al: Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. Mol Biol Evol 2021, 38:502-518.
Sun J, Chen C, Miyamoto N, Li R, Sigwart JD, Xu T, Sun Y, Wong WC, Ip JCH, Zhang W, et al: The Scaly-foot Snail genome and implications for the origins of biomineralised armour. Nat Commun 2020, 11:1657.
Yang L, Perrera V, Saplaoura E, Apelt F, Bahin M, Kramdi A, Olas J, Mueller-Roeber B, Sokolowska E, Zhang W, Li R, et al: m(5)C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants. Curr Biol 2019, 29:2465-2476 e2465.
Bi Y, Ren X, Li R, Ding Q, Xie D, Zhao Z: Specific Interactions Between Autosome and X Chromosomes Cause Hybrid Male Sterility in Caenorhabditis Species. Genetics 2019, 212:801-813.
Li X, Cong R, Yao W, Jia Y, Li R, Sun Z, Li X, Zhao R: Glucocorticoid receptor is involved in the differential expression of hepatic 3β‐hydroxysteroid dehydrogenase between barrows and boars at finishing stage. Animal Science Journal 2018, 89:158-166.
Li R, Ren X, Bi Y, Zhao Z: Mitochondrial genome of Caenorhabditis nigoni (Rhabditida: Rhabditidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016, 27:3107-3108.
Li R#, Ren X#, Bi Y, Ho VWS, Hsieh C-L, Young A, Zhang Z, Lin T, Zhao Y, Miao L: Specific downregulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression. Genome research 2016:gr. 204479.204116.
Li R, Jia Y, Pan S, Li X, Song H, Zhao R: Glucocorticoid Receptor Mediates the Effect of High-Fat Diet on Mitochondrial Oxidative Phosphorylation in Mouse Liver. DNA Cell Biol 2016, 35:51-58.
Li R, Hsieh CL, Young A, Zhang Z, Ren X, Zhao Z: Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome. Sci Rep 2015, 5:10814.
Li RS, Jia YM, Zou HF, Zhao RQ: Breed-specific expression of DROSHA, DICER and AGO2 is regulated by glucocorticoid-mediated miRNAs in the liver of newborn piglets. Animal Genetics 2014, 45:817-826.
Li R, Zou H, Jia Y, Zhao R: Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets. BMC Vet Res 2013, 9:87.
Zou H#, Li R#, Jia Y, Yang X, Ni Y, Cong R, Soloway PD, Zhao R: Breed-dependent transcriptional regulation of 5’-untranslated GR (NR3C1) exon 1 mRNA variants in the liver of newborn piglets. PLoS One 2012, 7:e40432.
Li R, Sun Q, Jia Y, Cong R, Ni Y, Yang X, Jiang Z, Zhao R: Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and large white pigs. PLoS One 2012, 7:e38716.