2024

(2) Xiao L, Zhou T, Zuo Z, Sun N*, Zhao F*. Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders. Science Bulletin, 2024 10.1016/j.scib.2024.02.001. [PubMed]

(1) Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F*, Gao Y*. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. Advanced Science, 2024 Feb 2:e2308115. [PubMed]


2023

(12) Xiao L, Zuo Z, & Zhao F*. Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies. Genomics, Proteomics & Bioinformatics, 2023;,qzad005. [PubMed]

(11) He R, Zhu J, Ji P & Zhao F*. SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes. Nature Methods, 2023, Dec 4. [PubMed]

(10) Zhou T, Xiao L, Zuo Z*, Zhao F*. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Res, 2023, Oct 11:gkad813. [PubMed]

(9) Wu W, Zhao F*, Zhang J*. circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme. Nucleic Acids Res, 2023, Sep 22:gkad770. [PubMed]

(8) Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F*, Wei F*. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. Microbiome, 2023, 11(1):221. [PubMed]

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

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

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

(4) 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]

(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]

(2) 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]

(1) 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]


2022

(11) 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]

(10) 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]

(9) 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]

(8) 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]

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

(6) 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]

(5) 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]

(4) 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]

(3) 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]

(2) 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]

(1) 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]


2021

(5) 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]

(3) 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]

(2) 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]

(1) 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]


2020

(5) 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]

(4) 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]

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

(2) 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]

(1) 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]


2019

(3) 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) 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) 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]


2018

(5) 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]

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

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

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

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


2017

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


2016

(4) 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]

(3) 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]

(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]

(1) 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]


2015

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

(2) 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]

(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]