2020

  • Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities.  
    Cell, 2020 (in press).  
    Jia N, Wang J, Shi W, Du L, et al., Tick Genome and Microbiome Consortium, Zhao F & Cao WC.  
  • [PubMed]
  • Visualization of circular RNAs and their internal splicing events from transcriptomic data.
    Bioinformatics, 2020, Jan 17:btaa033.
    Zheng Y & Zhao F.
  • [PubMed]
  • CircAltas: an integrated resource of one million highly confident circular RNAs from 1,070 vertebrate transcriptomes.
    Genome Biology, 2020 21:101
    Wu W, Ji P & Zhao F.
  • [PubMed]
  • Accurate quantification of circular RNAs identifies extensive circular isoform switching events.
    Nature Communications, 2020, 11:90.
    Zhang J, Chen S, Yang J & Zhao F.
  • [PubMed]
2019

  • Database Resources of the National Genomics Data Center in 2020.
    Nucleic Acids Res, 2019, doi: 10.1093/nar/gkz913.
    National Genomics Data Center Members and Partners.
  • [PubMed]
  • Argonaute proteins from human gastrointestinal bacteria catalyze DNA-guided cleavage of single- and double-stranded DNA at 37 °C.
    Cell Discovery, 2019, 5:38.
    Cao Y, Sun W, Wang J, Sheng G, Xiang G, Zhang T, Shi W, Li C, Wang Y, Zhao F & Wang H.
  • [PubMed]
  • Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the gastrointestinal tract.
    Gut, 2019, 10.1136/gutjnl-2019-318977.
    Wang J, Jia Z, Zhang B, Peng L & Zhao F.
  • [PubMed]
  • Expanded expression landscape and prioritization of circular RNAs in mammals.
    Cell Reports, 2019, 26:3444-3460.
    Ji P^, Wu W^, Chen S^, Zheng Y, Zhou L, Zhang J, Cheng H, Yan J, Zhang S, Yang P & Zhao F.
  • [PubMed]
  • Mining the hidden treasures from canid genomes.
    National Science Review, 2019, 6(1):124.
    Zhao F.
  • [PubMed]
  • Genetic basis for the establishment of endosymbiosis in Paramecium.
    ISME Journal, 2019, 13(5): 1360-1369.
    He M^, Wang J^, Fan X, Liu X, Shi W, Huang N, Zhao F & Miao M.
  • [PubMed]
  • Reconstruction of full-length circular RNAs enables isoform-level quantification.
    Genome Medicine, 2019, 11:2.
    Zheng Y^, Ji P^, Chen S, Hou L & Zhao F.
  • [PubMed]
2018

  • Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus.
    Gut, 2018, 67:1614-1625.
    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.
  • [PubMed]
  • Single-cell metagenomics: challenges and applications.
    Protein & Cell,, 2018, 9(5):501-510.
    Xu Y & Zhao F.
  • [PubMed]
  • Computational strategies for exploring circular RNAs.
    Trends in Genetics, 2018, 34(5): 389-400.
    Gao Y & Zhao F.
  • [PubMed]
  • Detection and reconstruction of circRNAs from transcriptomic data.
    Methods in Molecular Biology, 2018, 1724:1-8.
    Zheng Y & Zhao F.
  • [PubMed]
  • Prioritization and functional assessment of noncoding variants associated with complex diseases.
    Genome Medicine, 2018, 10:53.
    Zhou L & Zhao F.
  • [PubMed]
2017

  • Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species.
    Molecular Biology Evolution, 2017, 34(9):2214-2228.
    Teng H, Zhang Y, Shi C, Mao F, Cai W, Lu L, Zhao F, Sun Z & Zhang J.
  • [PubMed]
  • Circular RNA identification based on multiple seed matching.
    Briefings in Bioinformatics, 2017, DOI: 10.1093/bib/bbx014.
    Gao Y, Zhang J & Zhao F.
  • [PubMed]
  • Gut microbiota dysbiosis contributes to the development of hypertension.
    Microbiome, 2017, 5:14.
    Li J^, Zhao F^, Wang Y^, Chen J^, Tao J, Tian G, Wu S, Liu W, Cui Q, Geng B, Zhang W, Yang L, Liu X, Zhu B, Yang X & Cai J.
  • [PubMed]
  • The combination of direct and paired link graphs boosts repetitive genome assembly.
    Nucleic Acids Res, 2017, 45 (6): e43.
    Shi W^, Ji P^ & Zhao F.
  • [PubMed]
  • MetaSort untangles metagenome assembly by reducing microbial community complexity.
    Nature Communications, 2017, 8:14306.
    Ji P^, Zhang Y^, Wang J & Zhao F.
  • [PubMed]
2016

  • Species divergence vs functional convergence characterizes crude oil microbial community assembly.
    Frontiers in Microbiology, 2016, 7:1254.
    Nie Y, Zhao J, Tang Y, Guo P, Yang Y, Wu X✉ & Zhao F.
  • [PubMed]
  • A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes.
    Genome Biology, 2016, 17:232.
    Peng G^, Ji P^ & Zhao F.
  • [PubMed]
  • Convergent evolution of rumen microbiomes in high-altitude mammals.
    Current Biology, 2016, 26(14):1873-1879.
    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.
  • [PubMed]
  • RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes.
    Nucleic Acids Res, 2016, 44:e99.
    Zhang Y^, Ji P^, Wang J & Zhao F.
  • [PubMed]
  • Comprehensive identification of internal structure and alternative splicing events in circular RNAs.
    Nature Communications, 2016, 7:12060.
    Gao Y^, Wang J^, Zheng Y^, Zhang J, Chen S & Zhao F.
  • [PubMed]
  • Phage-bacteria interaction network in human oral microbiome.
    Environmental Microbiology, 2016, 18(7):2143-2158.
    Wang J^, Gao Y^ & Zhao F.
  • [PubMed]
2015

  • Comparative mitogenomic analyses reveal cryptic diversity of the bryozoan Bugula neritina Linnaus, 1758, in the Yellow Sea.
    Marine & Freshwater Res, 2015, 67(8):1241-1252.
    Shen X, Tian M, Chu KH, Wang J, Chen S, Liu H, Zhao X & Zhao F✉.
  • [PubMed]
  • The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic (A2O) nitrogen and phosphorus removal reactor using Illumina sequencing.
    J. Environ. Sci, 2015, 35:181-190..
    Tian M, Zhao F, Shen X, Chu K, Wang J, Chen S, Guo Y, Liu H.
  • [PubMed]
  • The value and significance of metagenomics of marine environments.
    Genomics, Proteomics & Bioinformatics, 2015, 13(5):271-274.
    Zhao F & Bajic VB.
  • [PubMed]
  • CRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge.
    Protein & Cell, 2015, 6(7):541-545.
    Zhou H, Zhao H, Zheng J, Gao Y, Zhang Y, Zhao F & Wang J.
  • [PubMed]
  • MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution.
    J. Mol. Cell Biol, 2015, 7(4):299-313.
    Cai W, Mao F, Teng H, Cai T, Zhao F, Wu J, Sun ZS.
  • [PubMed]
  • CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.
    Genome Biology, 2015, 16:4
    Gao Y^, Wang J^ & Zhao F.
  • [PubMed]
  • Phylogenomics of non-model ciliates based on transcriptomic analyses.
    Protein & Cell, 2015, 6(5):373-385.
    Chen X^, Zhao X^, Liu X, Warren A, Zhao F & Miao M.
  • [PubMed]
  • BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection.
    Nucleic Acids Res, 2015, 43 (14):6701-6703.
    Zhao H & Zhao F.
  • [PubMed]
  • Saccharina genomes provide novel insight into kelp biology.
    Nature Communications, 2015, 6: 6986.
    Ye N^, Zhang X^, Miao M^, Fan X^, Zheng Y, Xu D, Wang J, Hou 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.
  • [PubMed]
  • TCRklass: A new K-string-based algorithm for human and mouse TCR repertoire characterization.
    Journal of Immunology, 2015, 194(1):446-454.
    Yang X, Liu D, Lv N, Zhao F, Liu F, Zou J, Chen Y, Xiao X, Wu J, Liu P, Gao J, Hu Y, Shi Y, Liu J, Zhang R, Chen C, Ma J, Gao GF, Zhu B.
  • [PubMed]
2014

  • Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains.
    Protein & Cell, 2014, 5(8):603-615.
    Liu P, Liu D, Yang X, Gao J, Chen Y, Xiao X, Liu F, Zou J, Wu J, Ma J, Zhao F, Zhou X, Gao GF, Zhu B.
  • [PubMed]
2013

  • Ancestry of the Australian Termitivorous Numbat.
    Mol. Biol. Evol, 2013, 30(5):1041- 1045.
    Zemann A, Churakov G, Donellan S, Grützner F, Zhao F, Brosius J, and Schmitz J.
  • [PubMed]
  • Extensive lysine acetylation occurs in evolutionarily conserved metabolic pathways and parasite-specific functions during Plasmodium falciparum in traerythrocytic development.
    Molecular Microbiology, 2013, 89(4): 660-675.
    Miao J, Lawrence M, Jeffers V, Zhao F, Parker D, Ge Y, Sullivan WJ, Cui L.
  • [PubMed]
  • Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota.
    Nature Communications, 2013, 4:2151.
    Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Pan Y, Li J, Zhu L, Wang X, Meng Z, Zhao F, Liu D, Ma J, Qin N, Xiang C, Xiao Y, Li L, Yang H, Wang J, Yang R, Gao GF, Wang J, Zhu B.
  • [PubMed]
  • Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau..
    BMC Genomics, 2013, 14:820.
    Guan X^, Wang J^, Zhao H, Luo X, Liu F & Zhao F.
  • [PubMed]
  • Metagenomic sequencing reveals microbiota and its functional potentials associated with periodontal diseases
    Scientific Reports, 2013, 3: 1843.
    Wang J^, Qi J^, Zhao H, He S, Wei S & Zhao F.
  • [PubMed]
  • Composition based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.
    Nucleic Acids Res, 2013, 41(1):e3..
    Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F & Qi J.
  • [PubMed]
  • HTQC: a fast quality control toolkit for Illumina sequencing data.
    BMC Bioinformatics., 2013 Jan 31;14:33.
    Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F & Zhu B.
  • [PubMed]
2012

  • Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus.
    Mol Phylogenet Evol, 2012 62 (1):206-213.
    Yu T, Li J, Yang Y, Qi L, Chen B, Zhao F, Bao Q, Wu J.
  • [PubMed]
  • Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
    Genomics, 2012 Mar;99(3):178-182.
    Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.
  • [PubMed]
  • Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: The first representative of the suborder Malacostegina.
    Comp Biochem Physiol Part D Genomics Proteomics, 2012, 7(3):248-253.
    Shen X, Tian M, Meng X, Liu H, Cheng H, Zhu C, Zhao F.
  • [PubMed]
  • olarand brown bear genomes reveal ancient admixture and demographic footprints of past climate change.
    PNAS, 2012,109 (36):E2382-E2390.
    Miller W, Schuster SC, Wellch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI,WittekindtNE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, Sage GK, Rode K, Obbard M, Montiel R, Bachmann L, Ingolfsson O, Aars J, Mailund T, Wiig O, Tabot S, Lindqvist C.
  • [PubMed]
2011

  • Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing.
    PLoS ONE , 2011, 5(11): e15519.
    Xu G, Wu J, Hou L, Chen B, Sun Z, Zhao F, Tao Z.
  • [PubMed]
  • A new scheme to identify and visualize structural variations from paired-end mapping data.
    Nucleic Acids Res, 2011, 39: W567-W575.
    Qi J and Zhao F.
  • [PubMed]
  • Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria.
    Functional Genomics and Evolution of Photosynthetic Systems, 2011.
    Bryant DA, Liu Z, Li T, Zhao F, Garcia Costas AM, Klatt CG, Ward DM, Frigaard NU, and Overmann J.
  • [PubMed]
  • Small RNA transcriptome investigation based on next-generation sequencing technology.
    J Genet Genomics, 2011, 38(11):505-513.
    Hou L, Li X, Liu Q, Zhao F, Wu J.
  • [PubMed]
  • Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).
    PNAS, doi/10.1073/pnas. 1102838108.
    Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt, NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya O, Katiyar N, Tomsho LP, Kasson LM, Hardie R, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC.
  • [PubMed]
2010

  • inGAP: an integrated next-genome analysis platform.
    Bioinformatics, 2010, 26(1):127-129.
    Qi J^,Zhao F^, Schuster SC.
  • [PubMed]
  • Sequencing and genetic variation of multidrug resistance plasmids in clinical samples.
    PLoS One, 2010, 5(4): e10141.
    Zhao F^, Bai J^, Wu J, et al.
  • [PubMed]
  • Complete Khoisan and Bantu genomes from southern Africa.
    Nature, 2010 463: 943-947.
    Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM.
  • [PubMed]
  • MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation.
    Nucleic Acids Res, 2010, 38: W732-W736.
    Hou H^, Zhao F^, Hou L, Zhu E, Teng H, et al.
  • [PubMed]
  • mirTools: microRNA profiling and discovery based on high-throughput sequencing.
    Nucleic Acids Res, 2010, 38: W392-W397.
    Zhu E^, Zhao F^, Xu G, Hou H, Hou L, Li X, Sun Z and Wu J.
  • [PubMed]
2009

  • Titochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
    Genome Research, 2009, 19: 213-220.
    Miller W, Drautz D, Janecka J, Lesk A, Ratan A, Tomsho L, Packard M, Zhang Y, McClellan L, Qi J, Zhao F, Gilbert M, Dalen L, Arsuaga J, Ericson P, Huson D, Helgen K, Murphy W, Gotherstrom A, Schuster S.
  • [PubMed]
  • A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.
    BMC Genomics, 2009, 10:136
    Shen X¶, Ma X, Ren J, Zhao F.
  • [PubMed]
  • PGA4genomics for comparative genome assembly based on genetic algorithm optimization.
    Genomics, 2009, 94: 284-286.
    Zhao F¶, Hou H, Bao Q, Wu J¶.
  • [PubMed]
  • FlyPhy: a phylogenetic analysis platform for Drosophila genes and gene families.
    BMC Bioinformatics, 2009, 10:123.
    Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F¶, Li X¶.
  • [PubMed]
  • Extensive homologous recombination in the core genome of Rickettsia.
    Comparative and Functional Genomics,2009 doi:10.1155/2009/510270.
    Wu J, Yu T, Bao Q¶, Zhao F¶.
  • [PubMed]
  • The Repertoire and Evolution of ATP-Binding Cassette Systems in Synechococcus and Prochlorococcus.
    Journal of Molecular Evolution, 2009, 69: 300-310.
    Bu L, Xiao J, Lu L, Xu G, Li J, Zhao F, Li X, Wu J.
  • [PubMed]
2008

  • PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families.
    Bioinformatics, 2008, 24(9): 1217-1220.
    Xu X, Wu J, Xiao J, Tan Y, Bao Q¶, Zhao F¶, and Li X¶.
  • [PubMed]
  • Sequencing the nuclear genome of the extinct woolly mammoth.
    Nature, 2008.456, 387-390.
    Miller W, Drautz D, Ratan A, Pusey B, Qi J, Lesk A, Tomsho L, Packard M, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander E, Knight J, Irzyk G, Fredrikson K, Harkins T, Sheridan S, Pringle T, Schuster S.
  • [PubMed]
  • Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria.
    Journal of Molecular Evolution, 2008. 67, 85-94.
    Wu J, Bai J, Bao Q¶, Zhao F¶.
  • [PubMed]
  • A novel pheromone trail-based genetic algorithm for comparative genome assembly.
    Nucleic Acids Research, 2008, 36:3455-3462.
    Zhao F, Zhao F, Li T, Bryant DA.
  • [PubMed]
2007

  • Combinational biosynthesis of a fluorescent cyanobacterial holo-a-phycocyanin in E. coli.
    Applied Biochemistry and Biotechnology, 2007, 142(1):52-59.
    Guan X, Qin S, Su Z, Zhao F, et al.
  • [PubMed]
  • Expression of β-carotene hydroxylase gene (crtR-B) from the green alga Haematococcus pluvialis in chloroplasts of Chlamydomonas reinhardtii.
    Journal of Applied Phycology, 2007, 19(4): 347-355
    Tan C, Zhao F, Su Z, Liang C, Qin S.
  • [PubMed]
  • Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus.
    Genetica, 2007, 129(3): 291-299.
    Zhao F, Qin S.
  • [PubMed]
  • Evidence for positive darwinian selection of Vip Gene in Bacillus thuringiensis.
    Journal of Genetics and Genomics , 2007 34 (7): 649-660.
    Wu J^, Zhao F^, Bai J, Deng G, Qin S, Bao Q.
  • [PubMed]
  • cTFbase: a database for comparative genomics of transcription factors in cyanobacteria.
    BMC Genomics, 2007, 8: 104.
    Wu J, Zhao F¶, Wang S, Deng G, Wang J, Bai J, Lu J, Qu J and Bao Q¶.
  • [PubMed]
  • Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria.
    BMC Genomics , 2007, 8: 395.
    Zhang X^, Zhao F^, Guan X, Yang Y, Liang C, Qin S.
  • [PubMed]
2006

  • Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics.
    Intl J Biol Sci, 2006 ;2 (4):197-207.
    Liang C^, Zhao F^, Wei W, et al.
  • [PubMed]
  • Genome wide analysis of restriction- modification system in unicellular and filamentous cyanobacteria.
    Physiological Genomics , 2006, 24: 181-190
    Zhao F, Zhang XW, Liang CW, et al.
  • [PubMed]
  • Evolutionary analysis of phycobiliproteins: Implications for their structural and functional relationships.
    Journal of Molecular Evolution , 2006. 63(3):330-40
    ZZhao F, Qin S.
  • [PubMed]