| Year |
Citation |
Score |
| 2022 |
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. 39. PMID 35325184 DOI: 10.1093/molbev/msac062 |
0.314 |
|
| 2021 |
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. 19: 264. PMID 34903227 DOI: 10.1186/s12915-021-01202-1 |
0.327 |
|
| 2020 |
Yue L, Li J, Zhang B, Qi L, Li Z, Zhao F, Li L, Zheng X, Dong X. The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode. Nucleic Acids Research. PMID 32857850 DOI: 10.1093/Nar/Gkaa702 |
0.313 |
|
| 2020 |
Zheng X, Liu W, Dai X, Zhu Y, Wang J, Zhu Y, Zheng H, Huang Y, Dong Z, Du W, Zhao F, Huang L. Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation. Environmental Microbiology. PMID 32627268 DOI: 10.1111/1462-2920.15154 |
0.391 |
|
| 2020 |
Wu W, Ji P, Zhao F. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biology. 21: 101. PMID 32345360 DOI: 10.1186/S13059-020-02018-Y |
0.36 |
|
| 2020 |
Zhang J, Chen S, Yang J, Zhao F. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications. 11: 90. PMID 31900416 DOI: 10.1038/S41467-019-13840-9 |
0.306 |
|
| 2019 |
Ji P, Wu W, Chen S, Zheng Y, Zhou L, Zhang J, Cheng H, Yan J, Zhang S, Yang P, Zhao F. Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals. Cell Reports. 26: 3444-3460.e5. PMID 30893614 DOI: 10.1016/J.Celrep.2019.02.078 |
0.328 |
|
| 2019 |
Zheng Y, Ji P, Chen S, Hou L, Zhao F. Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Medicine. 11: 2. PMID 30660194 DOI: 10.1186/S13073-019-0614-1 |
0.324 |
|
| 2019 |
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. The Isme Journal. PMID 30647459 DOI: 10.1038/S41396-018-0341-4 |
0.384 |
|
| 2019 |
Zhao F. Mining the hidden treasures from canid genomes National Science Review. 6: 124-124. DOI: 10.1093/Nsr/Nwy087 |
0.368 |
|
| 2018 |
Shi W, Qi H, Sun Q, Fan G, Liu S, Wang J, Zhu B, Liu H, Zhao F, Wang X, Hu X, Li W, Liu J, Tian Y, Wu L, et al. gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. Nucleic Acids Research. PMID 30365027 DOI: 10.1093/Nar/Gky1008 |
0.301 |
|
| 2018 |
Zhou L, Zhao F. Prioritization and functional assessment of noncoding variants associated with complex diseases. Genome Medicine. 10: 53. PMID 29996888 DOI: 10.1186/S13073-018-0565-Y |
0.326 |
|
| 2018 |
Sheng Y, He M, Zhao F, Shao C, Miao M. Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti. Molecular Phylogenetics and Evolution. PMID 29908995 DOI: 10.1016/J.Ympev.2018.06.025 |
0.358 |
|
| 2018 |
Xu Y, Zhao F. Single-cell metagenomics: challenges and applications. Protein & Cell. PMID 29696589 DOI: 10.1007/S13238-018-0544-5 |
0.409 |
|
| 2018 |
Zheng Y, Zhao F. Detection and Reconstruction of Circular RNAs from Transcriptomic Data. Methods in Molecular Biology (Clifton, N.J.). 1724: 1-8. PMID 29322436 DOI: 10.1007/978-1-4939-7562-4_1 |
0.307 |
|
| 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 and Evolution. PMID 28482038 DOI: 10.1093/Molbev/Msx157 |
0.32 |
|
| 2017 |
Gao Y, Zhang J, Zhao F. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics. PMID 28334140 DOI: 10.1093/Bib/Bbx014 |
0.324 |
|
| 2017 |
Ji P, Zhang Y, Wang J, Zhao F. MetaSort untangles metagenome assembly by reducing microbial community complexity. Nature Communications. 8: 14306. PMID 28112173 DOI: 10.1038/Ncomms14306 |
0.394 |
|
| 2016 |
Peng G, Ji P, Zhao F. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biology. 17: 232. PMID 27855707 DOI: 10.1186/S13059-016-1094-X |
0.351 |
|
| 2016 |
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. 7: 12060. PMID 27350239 DOI: 10.1038/Ncomms12060 |
0.313 |
|
| 2016 |
Xu T, Qin S, Hu Y, Song Z, Ying J, Li P, Dong W, Zhao F, Yang H, Bao Q. Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 27330141 DOI: 10.1093/Dnares/Dsw023 |
0.424 |
|
| 2016 |
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 : Cb. PMID 27321997 DOI: 10.1016/J.Cub.2016.05.012 |
0.371 |
|
| 2016 |
Zhang Y, Ji P, Wang J, Zhao F. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Research. PMID 26984526 DOI: 10.1093/Nar/Gkw165 |
0.428 |
|
| 2015 |
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. Journal of Environmental Sciences (China). 35: 181-90. PMID 26354707 DOI: 10.1016/J.Jes.2014.12.027 |
0.305 |
|
| 2015 |
Wang J, Gao Y, Zhao F. Phage-bacteria interaction network in human oral microbiome. Environmental Microbiology. PMID 26036920 DOI: 10.1111/1462-2920.12923 |
0.318 |
|
| 2015 |
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, ... ... Zhao F, et al. Saccharina genomes provide novel insight into kelp biology. Nature Communications. 6: 6986. PMID 25908475 DOI: 10.1038/Ncomms7986 |
0.432 |
|
| 2015 |
Chen X, Zhao X, Liu X, Warren A, Zhao F, Miao M. Phylogenomics of non-model ciliates based on transcriptomic analyses. Protein & Cell. 6: 373-85. PMID 25833385 DOI: 10.1007/S13238-015-0147-3 |
0.375 |
|
| 2015 |
Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biology. 16: 4. PMID 25583365 DOI: 10.1186/S13059-014-0571-3 |
0.315 |
|
| 2015 |
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, et al. TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization. Journal of Immunology (Baltimore, Md. : 1950). 194: 446-54. PMID 25404364 DOI: 10.4049/Jimmunol.1400711 |
0.337 |
|
| 2014 |
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. 5: 603-15. PMID 24866699 DOI: 10.1007/S13238-014-0060-1 |
0.308 |
|
| 2013 |
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Scientific Reports. 3: 1843. PMID 23673380 DOI: 10.1038/Srep01843 |
0.323 |
|
| 2013 |
Zemann A, Churakov G, Donnellan S, Grützner F, Zhao F, Brosius J, Schmitz J. Ancestry of the Australian termitivorous numbat. Molecular Biology and Evolution. 30: 1041-5. PMID 23429857 DOI: 10.1093/Molbev/Mst032 |
0.365 |
|
| 2013 |
Teng H, Cai W, Zeng K, Mao F, You M, Wang T, Zhao F, Sun Z. Genome-wide identification and divergent transcriptional expression of StAR-related lipid transfer (START) genes in teleosts. Gene. 519: 18-25. PMID 23415839 DOI: 10.1016/J.Gene.2013.01.058 |
0.398 |
|
| 2013 |
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. 14: 33. PMID 23363224 DOI: 10.1186/1471-2105-14-33 |
0.336 |
|
| 2013 |
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 microorganisms. Nucleic Acids Research. 41: e3. PMID 22941634 DOI: 10.1093/Nar/Gks828 |
0.339 |
|
| 2012 |
Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the United States of America. 109: E2382-90. PMID 22826254 DOI: 10.1073/Pnas.1210506109 |
0.371 |
|
| 2012 |
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. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. 7: 248-53. PMID 22503287 DOI: 10.1016/J.Cbd.2012.03.003 |
0.407 |
|
| 2012 |
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. 99: 178-82. PMID 22226708 DOI: 10.1016/J.Ygeno.2011.12.003 |
0.397 |
|
| 2012 |
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 Prochlorococcus. Molecular Phylogenetics and Evolution. 62: 206-13. PMID 22040764 DOI: 10.1016/J.Ympev.2011.09.013 |
0.388 |
|
| 2011 |
Zhou L, Li X, Liu Q, Zhao F, Wu J. Small RNA transcriptome investigation based on next-generation sequencing technology Journal of Genetics and Genomics. 38: 505-513. PMID 22133681 DOI: 10.1016/J.Jgg.2011.08.006 |
0.32 |
|
| 2011 |
Carpi G, Cagnacci F, Wittekindt NE, Zhao F, Qi J, Tomsho LP, Drautz DI, Rizzoli A, Schuster SC. Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks. Plos One. 6: e25604. PMID 22022422 DOI: 10.1371/Journal.Pone.0025604 |
0.359 |
|
| 2011 |
Qi J, Zhao F. inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Research. 39: W567-75. PMID 21715388 DOI: 10.1093/Nar/Gkr506 |
0.3 |
|
| 2011 |
Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America. 108: 12348-53. PMID 21709235 DOI: 10.1073/Pnas.1102838108 |
0.374 |
|
| 2010 |
Wittekindt NE, Padhi A, Schuster SC, Qi J, Zhao F, Tomsho LP, Kasson LR, Packard M, Cross P, Poss M. Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics. Plos One. 5: e13432. PMID 20976145 DOI: 10.1371/Journal.Pone.0013432 |
0.365 |
|
| 2010 |
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Research. 38: W392-7. PMID 20478827 DOI: 10.1093/Nar/Gkq393 |
0.329 |
|
| 2010 |
Hou H, Zhao F, Zhou L, Zhu E, Teng H, Li X, Bao Q, Wu J, Sun Z. MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. Nucleic Acids Research. 38: W732-6. PMID 20444865 DOI: 10.1093/Nar/Gkq302 |
0.385 |
|
| 2010 |
Zhao F, Bai J, Wu J, Liu J, Zhou M, Xia S, Wang S, Yao X, Yi H, Lin M, Gao S, Zhou T, Xu Z, Niu Y, Bao Q. Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae. Plos One. 5. PMID 20405037 DOI: 10.1371/Journal.Pone.0010141 |
0.337 |
|
| 2010 |
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, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795 |
0.417 |
|
| 2010 |
Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics (Oxford, England). 26: 127-9. PMID 19880367 DOI: 10.1093/Bioinformatics/Btp615 |
0.377 |
|
| 2009 |
Zhao F, Hou H, Bao Q, Wu J. PGA4genomics for comparative genome assembly based on genetic algorithm optimization. Genomics. 94: 284-286. PMID 19573591 DOI: 10.1016/J.Ygeno.2009.06.006 |
0.414 |
|
| 2009 |
Zhao F, Qi J, Schuster SC. Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. Genome Research. 19: 1384-92. PMID 19508981 DOI: 10.1101/Gr.091363.109 |
0.411 |
|
| 2009 |
Wu J, Yu T, Bao Q, Zhao F. Evidence of Extensive Homologous Recombination in the Core Genome of Rickettsia Comparative and Functional Genomics. 2009: 510270-510270. PMID 19478958 DOI: 10.1155/2009/510270 |
0.426 |
|
| 2009 |
Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X. FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. Bmc Bioinformatics. 10: 123. PMID 19393099 DOI: 10.1186/1471-2105-10-123 |
0.395 |
|
| 2009 |
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 esculenta. Bmc Genomics. 10: 136. PMID 19327168 DOI: 10.1186/1471-2164-10-136 |
0.422 |
|
| 2009 |
Shen X, Sun M, Wu Z, Tian M, Cheng H, Zhao F, Meng X. The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes. Gene. 437: 1-8. PMID 19268697 DOI: 10.1016/J.Gene.2009.02.014 |
0.402 |
|
| 2009 |
Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, et al. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research. 19: 213-20. PMID 19139089 DOI: 10.1101/Gr.082628.108 |
0.399 |
|
| 2008 |
Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 456: 387-90. PMID 19020620 DOI: 10.1038/Nature07446 |
0.411 |
|
| 2008 |
Wu J, Bai J, Bao Q, Zhao F. Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria. Journal of Molecular Evolution. 67: 85-94. PMID 18551331 DOI: 10.1007/S00239-008-9127-Z |
0.358 |
|
| 2008 |
Zhao F, Zhao F, Li T, Bryant DA. A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Research. 36: 3455-62. PMID 18445633 DOI: 10.1093/Nar/Gkn168 |
0.411 |
|
| 2008 |
Xu X, Wu J, Xiao J, Tan Y, Bao Q, Zhao F, Li X. PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. Bioinformatics (Oxford, England). 24: 1217-20. PMID 18337260 DOI: 10.1093/Bioinformatics/Btn092 |
0.359 |
|
| 2007 |
Yang Y, Qin S, Zhao F, Chi X, Zhang X. Comparison of envelope-related genes in unicellular and filamentous cyanobacteria. Comparative and Functional Genomics. 25751. PMID 18253473 DOI: 10.1155/2007/25751 |
0.384 |
|
| 2007 |
Guan X, Qin S, Zhao F, Zhang X, Tang X. Phycobilisomes linker family in cyanobacterial genomes: Divergence and evolution International Journal of Biological Sciences. 3: 434-445. PMID 18026567 DOI: 10.7150/Ijbs.3.434 |
0.39 |
|
| 2007 |
Zhang X, Zhao F, Guan X, Yang Y, Liang C, Qin S. Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria. Bmc Genomics. 8: 395. PMID 17971218 DOI: 10.1186/1471-2164-8-395 |
0.346 |
|
| 2007 |
Wu J, Zhao F, Bai J, Deng G, Qin S, Bao Q. Adaptive Evolution of cry Genes in Bacillus thuringiensis: Implications for Their Specificity Determination Genomics, Proteomics & Bioinformatics. 5: 102-110. PMID 17893075 DOI: 10.1016/S1672-0229(07)60020-5 |
0.333 |
|
| 2007 |
Wu J, Zhao F, Wang S, Deng G, Wang J, Bai J, Lu J, Qu J, Bao Q. cTFbase: a database for comparative genomics of transcription factors in cyanobacteria. Bmc Genomics. 8: 104. PMID 17439663 DOI: 10.1186/1471-2164-8-104 |
0.385 |
|
| 2006 |
Zhang X, Zhao F, Qin S, Yan B. Cloning, expression and characterization of phycoerythrin gene from Ceramium boydenn. Dna Sequence : the Journal of Dna Sequencing and Mapping. 17: 129-35. PMID 17076255 DOI: 10.1080/10425170600724907 |
0.359 |
|
| 2006 |
Liang C, Zhao F, Wei W, Wen Z, Qin S. Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics. International Journal of Biological Sciences. 2: 197-207. PMID 16967101 DOI: 10.7150/Ijbs.2.197 |
0.392 |
|
| 2006 |
Zhao F, Qin S. Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus. Genetica. 129: 291-9. PMID 16897463 DOI: 10.1007/S10709-006-0010-9 |
0.308 |
|
| 2006 |
Zhao F, Qin S. Evolutionary analysis of phycobiliproteins: Implications for their structural and functional relationships Journal of Molecular Evolution. 63: 330-340. PMID 16830096 DOI: 10.1007/S00239-005-0026-2 |
0.322 |
|
| 2005 |
Zhao F, Zhang X, Liang C, Wu J, Bao Q, Qin S. Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria. Physiological Genomics. 24: 181-90. PMID 16368872 DOI: 10.1152/Physiolgenomics.00255.2005 |
0.413 |
|
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