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, doi: 10.1093/nar/gkw165.
Gao Y, Wang J & Zhao F*. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biology. 2015, 16:4
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.
Wang J, Gao Y & Zhao F*. Phage-bacteria interaction network in human oral microbiome. Environmental Microbiology. 2015 DOI: 10.1111/1462-2920.12923
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S* and Zhao F*. Metagenomic sequencing reveals microbiota and its functional potentials associated with periodontal disease. Sci. Rep. 2013, 3, 1843.
Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F* and Qi J*. Composition based classification of short metagenomic sequences elucidates landscapes of taxonomic and functional enrichment. Nucleic Acids Res 2013, 41(1):e3.
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 Mar 30.
Qi J* and Zhao F*. A new scheme to identify and visualize structural variations from paired-end mapping data. Nucleic Acids Res 2011, 39: W567-W575
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 sequencing. Nucleic Acids Res 2010, 38: W392-W397.
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 annotation. Nucleic Acids Res 2010, 38: W732-W736.
Zhao F, Bai J, Wu J, et al., Sequencing and genetic variation of multidrug resistance plasmids in clinical samples.PLoS One 2010, 5(4): e10141.
Qi J^, Zhao F^, Schuster SC. inGAP: an integrated next-gen genome analysis platform. Bioinformatics 2010 26(1):127-129.
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.
Zhao F*, Hou H, Bao Q, Wu J*. PGA4genomics for comparative genome assembly based on genetic algorithm optimization. Genomics 2009, 94: 284-286.
Zhao F, Zhao F, Li T, Bryant DA. A novel pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Research 2008, 36:3455-3462.