(1) Zuo Z & Zhao F*. Gut microbiota-targeted interventions: from conventional approaches to genetic engineering. Science Bulletin, 2023, 68(12):1231-1234. [PubMed]

(2) Chen L, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma X, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L & Zhao F. A guide to naming eukaryotic circular RNAs. Nature Cell Biology, 2023, 25:1-5. [PubMed]

(3) Chen W, Geng Y, Zhang B, Yan Y*, Zhao F* & Miao M*. STOP or not: genome-wide profiling of reassigned stop codons in ciliates. Molecular Biology and Evolution, 2023, 40(4):msad064. [PubMed]

(4) Chen Y, Zhou S, Li M, Zhao F* & Qi J*. STEEL enables high-resolution delineation of spatiotemporal transcriptomic data. Briefings in Bioinformatics, 2023, 24(2):bbad068. [PubMed]

(5) Li Z, Zhang B, Wang N, Zuo Z, Wei H & Zhao F*. A novel peptide protects against diet-induced obesity by suppressing appetite and modulating the gut microbiota. Gut, 2023, 72:686-698. [PubMed]

(6) Hou L, Zhang J* & Zhao F*. Full-length circular RNA profiling by nanopore sequencing and CIRI-long. Nature Protocols, 2023, 18:1795-1813. [PubMed]

(7) Xiao L & Zhao F*. Microbial transmission, colonization and succession: from pregnancy to infancy. Gut, 2023, 72:772-786. [PubMed]


(1) Wang J, Xiao L, Xiao B, Zhang B, Zuo Z, Ji P, Zheng J, Li X & Zhao F*. Maternal and neonatal viromes indicate the risk of offspring’s gastrointestinal tract exposure to pathogenic viruses of vaginal origin during delivery. mLife, 2022, 1(3):303-310. [PubMed]

(2) Wang X, Pang K, Wang J, Zhang B, Liu Z, Lu S, Xu X, Zhu L, Zhou Z, Niu M, Gao J, Li J, Zhao F* & Wu J*. Microbiota dysbiosis in primary Sjögren’s syndrome and the ameliorative effect of hydroxychloroquine. Cell Reports, 2022, 40(11):111352. [PubMed]

(3) Tang B, Tang L, He W, Jiang X, Hu C, Li Y, Zhang Y, Pang K, Lei Y, Li S, Liu S, Wang S, Yang M, Li Z*, Zhao F* & Yang S*. Correlation of gut microbiota and metabolic functions to the antibody response to the BBIBP-CorV vaccine. Cell Reports Medicine, 2022, 3(10):100752. [PubMed]

(4) He R, Li P, Wang J, Cui B, Zhang F* & Zhao F*. The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation. Gut Microbes, 2022, 14(1):e2100197. [PubMed]

(5) Xiao L, Zhang F & Zhao F*. Large-scale microbiome data integration enables robust biomarker identification. Nature Computational Science, 2022, 2:307-316. [PubMed]

(6) Wu W, Zhang J, Cao X, Cai Z & Zhao F*. Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. Nature Communications, 2022, 13(1):3242. [PubMed]

(7) Zhao Y, Zhang B, Ma Y, Zhao F, Chen J, Jin H, Zhou F, Guan J, Zhao Q, Wang H, Liu Q*, Zhao F* & Wang X*. Colorectal cancer patient-derived 2D and 3D models efficiently recapitulate inter- and intra-tumoral heterogeneity. Advanced Science, 2022, 9(22):e2201539. [PubMed]

(8) Yang J, Hou L, Wang J, Xiao L, Zhang J, Yin N, Yao S, Cheng K, Zhang W, Shi Z, Wang J, Jiang H, Huang N, You Y, Lin M, Shang R, Wei Y*, Zhao Y* & Zhao F*. Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins. Gut, 2022, 71:2451-2462. [PubMed]

(9) Zhang B, Hou L, Qi H, Hou L, Zhang T, Zhao F* & Miao M*. An extremely streamlined macronuclear genome in the free-living protozoan Fabrea salina. Molecular Biology and Evolution, 2022, 39(4):msac062. [PubMed]

(10) Chen S, Cao X, Zhang J, Wu W, Zhang B & Zhao F*. circVAMP3 drives CAPRIN1 phase separation and inhibits hepatocellular carcinoma by suppressing c-Myc translation. Advanced Science, 2022, 9(8):e2103817. [PubMed]

(11) Yu Y, Zhang B, Ji P, Zuo Z, Huang Y, Wang N, Liu C, Liu SJ & Zhao F*. Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8+/- mouse model of ASD-like behavior. Nature Communications, 2022, 13(1):1151. [PubMed]


(1) Zhang J, Hou L, Zuo Z, Zhang X, Xue Y & Zhao F*. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nature Biotechnology, 2021, 39:836-845. [PubMed]

(2) Xiao L, Wang J, Zheng J, Li X & Zhao F*. Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. Genome Biology, 2021, 22:243. [PubMed]

(3) Chen W, Zuo C, Wang C, Zhang T, Lyu L, Qiao Y, Zhao F* & Miao M*. The hidden genomic diversity of ciliated protists revealed by single-cell genome sequencing. BMC Biology, 2021, 19:264. [PubMed]

(4) Zhang J & Zhao F*. Characterizing circular RNAs using nanopore sequencing. Trends in Biochemical Sciences, 2021, 46(9):785-786. [PubMed]

(5) Wang J, Li Z, Ma X, Du L, Jia Z, Cui X, Yu L, Xiao L, Zhang B, Fan H & Zhao F*. Translocation of vaginal microbiota is involved in impairment and protection of uterine health. Nature Communications, 2021, 12:4191. [PubMed]


(1) Jia N, Wang J, Shi W, Du L, Sun Y, et al., Tick Genome and Microbiome Consortium, Zhao F* & Cao WC*. Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities. Cell, 2020, 182(5):1328-1340. [PubMed]

(2) Zhang J, Chen S, Yang J & Zhao F*. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications, 2020, 11:90. [PubMed]

(3) Wu W, Ji P & Zhao F*. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biology, 2020, 21:101. [PubMed]

(4) Zheng Y & Zhao F*. Visualization of circular RNAs and their internal splicing events from transcriptomic data. Bioinformatics, 2020, 36(9):2934-2935. [PubMed]

(5) Wang J, Jia Z, Zhang B, Peng L & Zhao F*. Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the GI tract. Gut, 2020, 69:1355-1356. [PubMed]


(1) Ji P, Wu W, Chen S, et al, Zhao F*. Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Reports, 2019, 26(12),3444-3460. [PubMed]

(2) Zheng Y, Ji P, Chen S, Hou L & Zhao F*. Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Medicine, 2019, 11:2. [PubMed]

(3) He M, Wang J, Fan X, Liu X, Shi W, Huang N, Zhao F* & Miao M*. Genetic basis for the establishment of endosymbiosis in Paramecium. ISME J, 2019, 13(5):1360-1369. [PubMed]


(1) Wang J, Zheng J, Shi W, Du N, Xu X, Zhang Y, Ji P, Zhang F, Jia Z, Wang Y, Zheng Z, Zhang H & Zhao F*. Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus. Gut, 2018, 67:1614-1625. [PubMed]

(2) Gao Y & Zhao F*. Computational strategies for exploring circular RNAs. Trends in Genetics, 2018, 34(5):389-400. [PubMed]

(3) Zhou L & Zhao F*. Prioritization and functional assessment of noncoding variants associated with complex diseases. Genome Medicine, 2018, 10:53. [PubMed]

(4) Xu Y & Zhao F*. Single-cell metagenomics: challenges and applications. Protein & Cell, 2018, 9(5):501-510. [PubMed]

(5) Gao Y, Zhang J & Zhao F*. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics, 2018, 19(5):803-810. [PubMed]


(1) Teng H, Zhang Y, Shi C, Mao F, Cai W, Lu L, Zhao F*, Sun Z* & Zhang J*. Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species. Molecular Biology Evolution, 2017, 34(9):2214-2228. [PubMed]

(2) Ji P, Zhang Y, Wang J & Zhao F*. MetaSort untangles metagenome assembly by reducing microbial community complexity. Nature Communications, 2017, 8:14306. [PubMed]

(3) Shi W, Ji P & Zhao F*. The combination of direct and paired link graphs boosts repetitive genome assembly. Nucleic Acids Res, 2017, 45(6):e43. [PubMed]


(1) Peng G, Ji P & Zhao F*. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biology, 2016, 17:232. [PubMed]

(2) Gao Y, Wang J, Zheng Y, Zhang J, Chen S & Zhao F*. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nature Communications, 2016, 7:12060. [PubMed]

(3) Zhang Y, Ji P, Wang J & Zhao F*. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Res, 2016, 44:e99. [PubMed]

(4) Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, Wang W, Qiu Q, Huang X, Zhou J, Long R*, Zhao F* & Shi P*. Convergent evolution of rumen microbiomes in high-altitude mammals. Current Biology, 2016, 26(14):1873-1879. [PubMed]


(1) Gao Y, Wang J & Zhao F*. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biology, 2015, 16:4. [PubMed]

(2) Zhao H & Zhao F*. BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection. Nucleic Acids Res, 2015, 43(14):6701-6703. [PubMed]

(3) Ye N*, Zhang X, Miao M, Fan X, Zheng Y, Xu D, Wang J, Zhou L, Wang D, Gao Y, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J* & Zhao F*. Saccharina genomes provide novel insight into kelp biology. Nature Communications, 2015, 6:6986. [PubMed]