Beijing Institute of Genomics
Center of Genomics and Bioinformatics, Chinese Academy of Sciences
Beijing 101300, China
Tel: +86-10-82995357; Fax: +86-10-82995373
E-mail: junyu@big.ac.cn
http://sourcedb.cas.cn/sourcedb_big_cas/zw/zjrc/yjy/200907/t20090724_2194384.html
Area of expertise: Genome sequence; structure; prediction; functional genomics; large scale genome analysis; comparative genome; annotation; expressed sequence tag
Co-editor until: Dec. 31, 2010

• Hu J, Zhao X, Zhang Z, Yu J (2007) Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Res. Microbiol. 158, 363-370.
• Song S, Qu H, Chen C, Hu S, Yu J (2007) Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data. BMC Plant Biol. 7, 49.
• Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4, 259-263.
• Tian X, Zheng J, Hu S, Yu J (2007) The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: a genome-wide investigation of indica rice. J. Mol. Evol. 64, 299-307.
• Zhang Z, Deng Y, Tan J, Hu S, Yu J, Xue Q (2007) A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res. 14, 37-45.
• Chen C, Tang J, Dong W, Wang C, Feng Y, Wang J, Zheng F, Pan X, Liu D, Li M, Song Y, Zhu X, Sun H, Feng T, Guo Z, Ju A, Ge J, Dong Y, Sun W, Jiang Y, Wang J, Yan J, Yang H, Wang X, Gao GF, Yang R, Wang J, Yu J (2007) A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS One 2, e315.
• Zhao X, Zhang Z, Yan J, Yu J (2007) GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem. Biophys. Res. Commun. 356, 20-25.
• Yan J, Liu Y, Tang H, Zhang Q, Huo Z, Hu S, Yu J (2006) Mutations at 17 STR loci in Chinese population. Forensic Sci. Int. 162, 53-54.
• Zhao XQ, Hu JF, Yu J (2006) Comparative analysis of eubacterial DNA polymerase III alpha subunits. Genomics Proteomics Bioinformatics. 4, 203-211.
• Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J (2007) Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 35, D376-D380.
• Zhang Z, Yu J (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics Bioinformatics. 4, 173-181.
• Yu J, Ni P, Wong GK (2006) Comparing the whole-genome-shotgun and map-based sequences of the rice genome. Trends Plant Sci. 11, 387-391.
• Sood R, English MA, Jones M, Mullikin J, Wang DM, Anderson M, Wu D, Chandrasekharappa SC, Yu J, Zhang J, Paul Liu P (2006) Methods for reverse genetic screening in zebrafish by resequencing and TILLING. Methods 39, 220-227.
• Zhang Z, Li J, Yu J (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol. Biol. 6, 44.
• Garcia-Espa?a A, Chung PJ, Zhao X, Lee A, Pellicer A, Yu J, Sun TT, Desalle R (2006) Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and function. Mol. Phylogenet. Evol. 41, 355-367.
• Zhang B, Liu Q, Yin W, Zhang X, Huang Y, Luo Y, Qiu P, Su X, Yu J, Hu S, Yan G (2006) Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tags. BMC Genomics 7, 152.
• Zhu QY, Qin ED, Wang W, Yu J, Liu BH, Hu Y, Hu JF, Cao WC (2006) Fatal infection with influenza A (H5N1) virus in China. N. Engl. J. Med. 354, 2731-2732.
• Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA (2006) The DNA sequence, annotation and analysis of human chromosome 3. Nature 440, 1194-1198.
• Su Z, Wang J, Yu J, Huang X, Gu X (2006) Evolution of alternative splicing after gene duplication. Genome Res. 16, 182-189.
• Ma Z, Yu J, Kang L (2006) LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7, 11.
• Tian X, Zheng J, Hu S, Yu J (2006) The rice mitochondrial genomes and their variations. Plant Physiol. 140, 401-410.
• Kou Z, Lei FM, Yu J, Fan ZJ, Yin ZH, Jia CX, Xiong KJ, Sun YH, Zhang XW, Wu XM, Gao XB, Li TX (2005) New genotype of avian influenza H5N1 viruses isolated from tree sparrows in China. J. Virol. 79, 15460-15466.
• Tang J, Xia H, Li D, Cao M, Tao Y, Tong W, Zhang X, Hu S, Wang J, Yu J, Yang H, Zhu L (2005) Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions. Mol. Genet. Genomics 274, 467-476.
• Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK, Wang J (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput. Biol. 1, e43.
• Bao J, Lee S, Chen C, Zhang X, Zhang Y, Liu S, Clark T, Wang J, Cao M, Yang H, Wang SM, Yu J (2005) Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiol. 138, 1216-1231.
• Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott J, Samudrala R, Wang J, Yang H, Yu J, Kristiansen K, Wong GK, Wang J (2005) Origin and evolution of new exons in rodents. Genome Res. 15, 1258-1264.
• Wernersson R, Schierup MH, J?rgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornsh?j H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L (2005) Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 6, 70.
• Li SY, Chen C, Zhang HQ, Guo HY, Wang H, Wang L, Zhang X, Hua SN, Yu J, Xiao PG, Li RS, Tan X (2005) Identification of natural compounds with antiviral activities against SARS-associated coronavirus. Antiviral Res. 67, 18-23.
• Tong Z, Zhou D, Song Y, Zhang L, Pei D, Han Y, Pang X, Li M, Cui B, Wang J, Guo Z, Qi Z, Jin L, Zhai J, Du Z, Wang J, Wang X, Yu J, Wang J, Huang P, Yang H, Yang R (2005) Pseudogene accumulation might promote the adaptive microevolution of Yersinia pestis. J. Med. Microbiol. 54, 259-268.
• Chen W, Yan M, Yang L, Ding B, He B, Wang Y, Liu X, Liu C, Zhu H, You B, Huang S, Zhang J, Mu F, Xiang Z, Feng X, Wen J, Fang J, Yu J, Yang H, Wang J (2005) SARS-associated coronavirus transmitted from human to pig. Emerg. Infect. Dis. 11, 446-448.
• Chiu CH, Tang P, Chu C, Hu S, Bao Q, Yu J, Chou YY, Wang HS, Lee YS (2005) The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res. 33, 1690-1698.
• Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38.
• Wang J, He X, Ruan J, Dai M, Chen J, Zhang Y, Hu Y, Ye C, Li S, Cong L, Fang L, Liu B, Li S, Wang J, Burt DW, Wong GK, Yu J, Yang H, Wang J (2005) ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 33, D438-D441.
• Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R, Feng T, Ye C, Lu C, Wang J, Li S, Wong GK, Yang H, Wang J, Xiang Z, Zhou Z, Yu J (2005) SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res. 33, D399-D402.
• Kang L, Chen X, Zhou Y, Liu B, Zheng W, Li R, Wang J, Yu J (2004) The analysis of large-scale gene expression correlated to the phase changes of the migratory locust. Proc. Natl. Acad. Sci. USA 101, 17611-17615.
• Yu J co-first authored in International Chicken Polymorphism Map Consortium. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 431, 717-722.
• Yu J co-first authored in International Chicken Genome Sequencing Consortium. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 431, 695-716.
• Yu J co-first authored in Biology Analysis Group (2004) A draft sequence of the genome of the domesticated silkworm Bombyx mori. Science 310, 1938-1940.
• Zhou D, Han Y, Song Y, Tong Z, Wang J, Guo Z, Pei D, Pang X, Zhai J, Li M, Cui B, Qi Z, Jin L, Dai R, Du Z, Bao J, Zhang X, Yu J, Wang J, Huang P, Yang R (2004) DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation. J. Bacteriol. 186, 5138-5146.
• Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GK (2004) Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature 431, 1038-1039.
• Tang L, Zhu Q, Qin E, Yu M, Ding Z, Shi H, Cheng X, Wang C, Chang G, Zhu Q, Fang F, Chang H, Li S, Zhang X, Chen X, Yu J, Wang J, Chen Z (2004) Inactivated SARS-CoV vaccine prepared from whole virus induces a high level of neutralizing antibodies in BALB/c mice. DNA Cell Biol. 23, 391-394.
• Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Wang J, Yu J, Yang H, Zhu L (2004) A comparison of rice chloroplast genomes. Plant Physiol. 135, 412-420.
• Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X, Zhang Y, Ni P, Zhang J, Li S, Wang J, Wong GK, Zhao H, Yu J, Yang H, Wang J (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res. 32, D377-D382.