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Zheng Y & Zhao F. Detection and reconstruction of circRNAs from transcriptomic data. Methods in Molecular Biology, 2017

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

Gao Y, Zhang JZhao F. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics 2017, DOI: 10.1093/bib/bbx014.

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. Gut microbiota dysbiosis contributes to the development of hypertension.  Microbiome, 2017, 5:14.

Zhou L & Zhao F. Prioritization and functional assessment of noncoding variants associated with complex diseases. 2017 (submitted)

Ji P^Zhang Y^, Wang J Zhao FMetaSort untangles metagenome assembly by reducing microbial community complexity. Nature Communications 2017, 8:14306.


Nie Y, Zhao J, Tang Y, Guo P, Yang Y, Wu X & Zhao FSpecies divergence vs functional convergence characterizes crude oil microbial community assembly. Frontiers in Microbiology 2016, 7:1254.

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.

Peng G^, Ji P^ & Zhao FA novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biology 2016, 17:232.

Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, Wang W, Qiu Q, Huang X, Zhou J, Long RZhao F, Shi PConvergent evolution of rumen microbiomes in high-altitude mammals. Current Biology  2016, 26(14):1873-1879.

Zhang Y^, Ji P^, Wang J Zhao FRiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Res 2016, 44:e99.

Gao Y^Wang J^Zheng Y^Zhang J, Chen S Zhao FComprehensive identification of internal structure and alternative splicing events in circular RNAs. Nature Communications 2016, 7:12060.

Wang J^, Gao Y^ & Zhao F. Phage-bacteria interaction network in human oral microbiome.  Environmental Microbiology 2016, 18(7):2143-2158.


Shen X, Tian M, Chu KH, Wang J, Chen S, Liu H, Zhao X Zhao FComparative mitogenomic analyses reveal cryptic diversity of the bryozoan Bugula neritina Linnaus, 1758, in the Yellow Sea. Marine & Freshwater Res. 2015, 67(8):1241-1252.

Tian M, Zhao F, Shen X, Chu K, Wang J, Chen S, Guo Y, Liu H. 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.

Zhao F & Bajic VB. The value and significance of metagenomics of marine environments.  Genomics, Proteomics & Bioinformatics 2015, 13(5):271-274.

Zhou H, Zhao H, Zheng J, Gao Y, Zhang Y, Zhao F & Wang JCRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge. Protein & Cell. 2015, 6(7):541-545.

Cai W, Mao F, Teng H, Cai T, Zhao F, Wu J, Sun ZS. MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolutionJ. Mol. Cell Biol. 2015, 7(4):299-313.

Gao Y^, Wang J^ Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identificationGenome Biology 2015, 16:4

Chen X^, Zhao X^, Liu X, Warren A, Zhao FMiao M. Phylogenomics of non-model ciliates based on transcriptomic analyses. Protein & Cell 2015, 6(5):373-385.

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

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.


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. Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains.  Protein & Cell 2014, 5(8):603-615.

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. TCRklass: A new K-string-based algorithm for human and mouse TCR repertoire characterization. Journal of Immunology 2015, 194(1):446-454.


Zemann A, Churakov G, Donellan S, Grützner F, Zhao F, Brosius J, and Schmitz J. Ancestry of the Australian Termitivorous Numbat. Mol. Biol. Evol. 2013, 30(5):1041- 1045.

Miao J, Lawrence M, Jeffers V, Zhao F, Parker D, Ge Y, Sullivan WJ, Cui L. 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.

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. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiotaNature Communications 2013, 4:2151.

Guan X^, Wang J^, Zhao H, Luo X, Liu F & Zhao F. Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau. BMC Genomics 2013, 14:820.

Wang J^, Qi J^, Zhao H, He S, Wei SZhao F. Metagenomic sequencing reveals microbiota and its functional potentials associated with periodontal diseasesScientific Reports 2013, 3: 1843.

Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F & Qi J. Composition based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganismsNucleic Acids Res 2013, 41(1):e3.

Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F & Zhu B. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics. 2013 Jan 31;14:33. 


Yu T, Li J, Yang Y, Qi L, Chen B, Zhao F, Bao Q, Wu J. Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and ProchlorococcusMol Phylogenet Evol. 2012 62 (1):206-213.

Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J. Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer. Genomics. 2012 Mar;99(3):178-182. 

Shen X, Tian M, Meng X, Liu H, Cheng H, Zhu C, Zhao F. 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.

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. Polarand brown bear genomes reveal ancient admixture and demographic footprints of past climate changePNAS 2012,109 (36):E2382-E2390


Xu G, Wu J, Zhou L, Chen B, Sun Z, Zhao F, Tao ZCharacterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencingPLoS ONE 2011, 5(11): e15519.

Qi J and Zhao F. A new scheme to identify and visualize structural variations from paired-end mapping dataNucleic Acids Res 2011, 39: W567-W575

Bryant DA, Liu Z, Li T, Zhao F, Garcia Costas AM, Klatt CG, Ward DM, Frigaard NU, and Overmann J. 2011. Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria. In: Advances in Photosynthesis and Respiration, Vol. 33, Functional Genomics and Evolution of Photosynthetic Systems, (Burnap, R. L. and Vermaas, W., eds.), Springer, Dordrecht, The Netherlands.

Zhou L, Li X, Liu Q, Zhao F, Wu J. Small RNA transcriptome investigation based on next-generation sequencing technologyJ Genet Genomics. 2011, 38(11):505-513.

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. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). 2011 PNAS doi/10.1073/pnas. 1102838108


Qi J^,Zhao F^, Schuster SC. inGAP: an integrated next-gen genome analysis platform. Bioinformatics,  2010, 26(1):127-129.

Zhao F^, Bai J^, Wu J, et al., Sequencing and genetic variation of multidrug resistance plasmids in clinical samplesPLoS One 2010, 5(4): e10141.

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. Complete Khoisan and Bantu genomes from southern AfricaNature 2010 463: 943-947.

Hou H^, Zhao F^, Zhou L, Zhu E, Teng H, et al. MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotationNucleic Acids Res 2010, 38: W732-W736.

Zhu E^, Zhao F^, Xu G, Hou H, Zhou L, Li X, Sun Z and Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencingNucleic Acids Res 2010, 38: W392-W397.


Zhao F, Qi J, Schuster SC. Tracking the past: Interspersed repeats in an extinct afrotherian mammal, Mammuthus primigenius. Genome Research 2009 19(8):1384-1392.

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. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).  Genome Research  2009, 19: 213-220.

Shen X, Ma X, Ren J, Zhao F. A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculentaBMC Genomics 2009, 10:136

Zhao F, Hou H, Bao Q, Wu J. PGA4genomics for comparative genome assembly based on genetic algorithm optimization.  Genomics 2009, 94: 284-286.

Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X. FlyPhy: a phylogenetic analysis platform for Drosophila genes and gene familiesBMC Bioinformatics 2009, 10:123

Wu J, Yu T, Bao Q, Zhao F. Extensive homologous recombination in the core genome of Rickettsia.  Comparative and Functional Genomics 2009 doi:10.1155/2009/510270

Bu L, Xiao J, Lu L, Xu G, Li J, Zhao F, Li X, Wu J. The Repertoire and Evolution of ATP-Binding Cassette Systems in Synechococcus and ProchlorococcusJournal of Molecular Evolution 2009, 69: 300-310.


Xu X, Wu J, Xiao J, Tan Y, Bao Q, Zhao F, and Li X. PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene familiesBioinformatics 2008, 24(9): 1217-1220.

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. Sequencing the nuclear genome of the extinct woolly mammoth. 2008, Nature 456, 387-390.

Wu J, Bai J, Bao Q, Zhao F. Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteriaJournal of Molecular Evolution 2008. 67, 85-94.

Zhao F, Zhao F, Li T, Bryant DA. A novel pheromone trail-based genetic algorithm for comparative genome assemblyNucleic Acids Research 2008, 36:3455-3462.


Guan X, Qin S, Su Z, Zhao F, et al. Combinational biosynthesis of a fluorescent cyanobacterial holo-a-phycocyanin in E. coliApplied Biochemistry and Biotechnology. 2007, 142(1):52-59.

Tan C, Zhao F, Su Z, Liang C, Qin S. Expression of β-carotene hydroxylase gene (crtR-B) from the green alga Haematococcus pluvialis in chloroplasts of Chlamydomonas reinhardtiiJournal of Applied Phycology 2007, 19(4): 347-355

Zhao F, Qin S. Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus.  Genetica 2007, 129(3): 291-299.

Wu J^, Zhao F^, Bai J, Deng G, Qin S, Bao Q. 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, Wang S, Deng G, Wang J, Bai J, Lu J, Qu J and Bao Q. cTFbase: a database for comparative genomics of transcription factors in cyanobacteriaBMC Genomics 2007, 8: 104.

Zhang X^, Zhao F^, Guan X, Yang Y, Liang C, Qin S. Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteriaBMC Genomics 2007, 8: 395.


Liang C^, Zhao F^, Wei W,  et al. Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomicsIntl J Biol Sci. 2006 ;2 (4):197-207.

Zhao F, Zhang XW, Liang CW, et al. Genome wide analysis of restriction- modification system in unicellular and filamentous cyanobacteriaPhysiological Genomics 2006, 24: 181-190

Zhao F, Qin S. Evolutionary analysis of phycobiliproteins: Implications for their structural and functional relationshipsJournal of Molecular Evolution 2006. 63(3):330-40

Before 2005

Zhao F, Tang ZH, Lin F et al. High cell density fermentation of a recombinant E.coli producing an anti-S180 tumor recombinant protein (rAPC)High Technol Lett 2003 13(2): 29-33. (in Chinese)

Tan C, Qin S, Zhang Q, Jiang P, Zhao F. Establishment of a micro-particle bombardment transformation system for Dunaliella salinaJ Microbiology, 2005, 43: 361-365.