于军 (Jun Yu)
教授，副所长，美国纽约大学博士
E-mail: junyu@big.ac.cn
学习及工作经历：
78年考入吉林大学化学系生物化学专业，
83年考入中科院生物物理所并获CUSBEA奖学金，次年赴美国纽约大学医学院攻读博士。
90获得全美泌尿科疾病基金博士奖，任纽约大学医学院泌尿系研究助理教授。
93年参与国际人类基因组计划，在美国华盛顿大学基因组中心工作。
98年回国后与同事共同创建了中国科学院遗传研究所人类基因组中心和北京基因组研究所。先后参与并主持了国际人类基因组计划（包括中国部分），超级杂交水稻基因组计划，家蚕基因组计划等重大科学研究项目。目前担任国家重大科学计划转录组研究首席科学家。一直从事基因组学、生物信息学和人类遗传学等研究。迄今已在包括《Nature》、《Science》和《PLoS Biology》等主要国际杂志发表科学论文逾百篇，发表科学专著二十余本（章），包括《分子细胞学和分子医学大百科全书》。先后获得国家自然科学基金委“杰出青年奖”，中国科学院“百人计划（国外杰出人才）”，香港求是科技基金会 “求是杰出科技成就奖”。
2003年度中国科学院杰出科技成就奖。
2002年，被国际著名的《科学美国人》杂志评选为首届年度全球科研领袖。担任《Genomics，Proteomics and Bioinformatics》主编，《Genomics》和《Journal of Comparative Plant Genomics》副主编。
专业工作：
于军博士84年起从事上皮细胞分化研究，用细胞生物学和分子生物学手段研究、鉴定并命名了一系列膀胱上皮细胞特有的分化标志性亚细胞结构（不对称单位膜）、蛋白质和基因（尿路膜板块基因系列UPI、II、III等），在Journal of Cell Biology, Journal of Biological Chemistry和Journal of Cell Science等专业杂志发表论文十余篇。93年起为“人类基因组计划”的大规模测序阶段的到来做技术准备工作，与黄家树博士共同建立“多酶全解物理图谱”制作技术，并将该技术用于大规模DNA测序实践。先后在Genome Research, PNAS, Genomics等专业杂志发表相关论文数十余篇。97年起研究基因组学基本理论和生物信息学方法。98年开始基因多态性和单核苷酸多态性(SNP)研究，用重新测序的方法验证EST和基因编码区SNP的分布特点，研究结果在Nature Genetics发表。曾测定数百基因的SNP，发现一类基因的低频率（<10%）多态性可能是基因产物的适应性造成，与人类的迁徙和生活环境相关。98年起主持了“人类基因组计划北京部分（1%计划）”、“中国杂交水稻基因组计划”、“家蚕基因组计划”、“鸡基因组多态性研究计划”等多项基因组研究计划。目前的研究工作主要有四个方面：（1）基因组比较分析与基因组进化研究，对象包括原核生物、单细胞真核生物和动植物基因组；（2）基因组稳定性与基因变异规律研究，主要内容为DNA修复机制、细胞周期和细胞凋亡相关基因的表达与调控；（3）以细胞为基础的转录组分析和方法学探索，研究对象为哺乳动物和人类不同组织的干细胞、分化细胞和肿瘤细胞；（4）表型可塑性研究动物模型的建立，发现相关调控基因并以线粒体的参与功能性介入为主要研究对象。
历届研究生情况：
在读博士生(含联合培养)：
2006年：5名
2005年：7名
2004年：6名
在读硕士生(含联合培养)：合计7人
拟招研究生：
2008年拟招收4名硕博生，欢迎数学、生物学、计算机编程等背景的学生报名。
主要论文论著：
SELECTED PEER-REVIEWED ORIGINAL RESEARCH PUBLICATIONS: (*First-author equivalent, ‡Corresponding author, and [Cover Story])
1. Binbin Wang, Yong-Biao Zhang, Feng Zhang, Xumin Wang, Hongbin Lin, Ning Wan, Haiyu Weng, Zhenqing Ye, Panpan Wang, Tingting Wu, Lili Zhang, Xin Li, Longfei Cheng, Jing Wang Jiangwei Yan, Duen-Mei Wang, Xu Ma, Jun Yu. ‡ (2011) On the Origin of Tibetans and their Genetic Basis in Adapting High-Altitude Environments. PLoS One 6(2): e17002.
2. Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu. ‡ (2011) Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biology Direct 6:13.
3. Qingshu Meng, Kaifu Chen, Lina Ma, Songnian Hu and Jun Yu. ‡ (2011) A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. Journal of Genetics and Genomics 38:63–70.
4. Jianhong An, Haolei Wan, Xiangtian Zhou, Dan-Ning Hu, Ledan Wang, Lili Hao, Dongsheng Yan, Fanjun Shi, Zhonglou Zhou, Jiao Wang, Songnian Hu, Jun Yu‡, Jia Qu. (2011) A Comparative Transcriptomic Analysis of Uveal Melanoma and Normal Uveal Melanocyte. PLoS ONE 6(1): e16516.
5. Jun Wang, Jianguo Zhang, Ruiqiang, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu, Jason McDermott, Ram Samudrala, Siqi Liu, Jian Wang, Huanming Yang, Jun Yu,‡ Gane Ka-Shu Wong. (2010) Evolutionary Transients in the Rice Transcriptome. Geno Proteo & Bioinfo 8(4)223-228.
6. Wanfei Liu, Dawei Huang, Kan Liu, Songnian Hu, Jun Yu, Gang Gao, and Shuhui Song (2010). Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae. Geno Proteo & Bioinfo 8(4): 229-237.
7. Lili Hao, Xiaomeng Ge, Hao-Lei Wan, Songnian Hu, Martin J Lercher, Jun Yu‡ and Wei-Hua Chen. (2010) Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evolutionary Biology 10:316.
8. Haiyan Guo, WeiWei Wang, Ning Yang, BaoLin Guo, Sun Zhang, RuiJin Yang, Yuan Ye, JunLin Yu, SongNian Hu, QiShi Sun and Jun Yu. ‡ (2010) DNA barcoding provides distinction between Radix Astragali and its adulterants. Science in China Series C Life Sciences 53: 53 No.8: 992–999.
9. Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Wei Gong, Lingfang Zhang, Jianing Geng, Bing Zhang, Xiaomin Yu, Jin Yang, Songnian Huand Jun Yu‡. (2010) A Comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 2010 Nov;96(5):259-65. Published online August 3, 2010.
10. Meng Yang, Xiaowei Zhang, Yuxin Yin, Guiming Liu, Kaifu Chen, Quanzheng Yun, Duojun Zhao, Ibrahim S. Al-Mssallem, and Jun Yu. ‡ The chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5(9): e12762.
11. Zhang Zhang and Jun Yu. ‡ (2010) Modeling genome compositional dynamics based on GC and purine contents. Biology Direct 5:63.
12. Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, and Jun Yu.‡ (2010) Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans. Geno Proteo & Bioinfo 8:92–102.
13. Ximiao He, Shu Tao, Jing Jin, Songnian Hu, and Jun Yu.‡ (2010) The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome. Geno Proteo & Bioinfo 8:81–91.
14. Xiaoguang Zhou, Lufeng Ren, Qingshu Meng, Yuntao Li, Yude Yu, and Jun Yu. ‡ (2010) The next-generation sequencing technology and application. Protein & Cell 1:520–536.
15. Meng Yang, Shuhui Song, Xiangjun Tian, Zhizhuang Zhao, Songnian Hu, and Jun Yu‡. (2010). A comprehensive analysis of protein phosphatases in rice and Arabidopsis. Plant Systematics and Evolution 289:111–126.
16. YANG Yue, GONG Wei, WANG Weiwei, YU Xiaomin, HU Songnian, YU Jun. ‡ (2010). The Alterations of Energy Metabolism-related Protein Patterns in Brown Adipose Tissue of Rats during Cold-induced Thermogenesis. Progress in Biochemistry and Biophysics 37:1108–1119.
17. Peng Cui, Qiang Lin, Chengqi Xin, Lu Han, Lili An, Yulan Wang, Zhishang Hu, Feng Ding, Lingfang Zhang, Songnian Hu‡, Haiying Hang‡, and Jun Yu‡. (2010). Hydroxyurea-induced Global Transcriptional Suppression in Mouse ES Cells. Carcinogenesis 31:1661–1668.
18. Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu and Yanchun Liang. (2010). PMirP: A pre-microRNA prediction method based on structure–sequence hybrid features. Journal Artificial Intelligence in Medicine 49:127–132.
19. Qi-Long Qin, Xi-Ying Zhang , Xu-Min Wang, Gui-Ming Liu, Xiu-Lan Chen, Bin-Bin Xie, Hong-Yue Dang, Bai-Cheng Zhou, Jun Yu and Yu-Zhong Zhang. (2010). The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11:247.
20. Jiang Zhu, Fuhong He, Dapeng Wang, Kan Liu, Dawei Huang, Jingfa Xiao, Jiayan Wu, Songnian Hu and Jun Yu. ‡ (2010) A novel role for minimal introns: routing mRNAs to the cytosol. PLoS One 5(4): e10144.
21. Yimei Cai, Xiaomin Yu, Qing Zhou, Caixia Yu, Haiyan Hu, Jiucheng Liu, Hongbin Lin, Jin Yang, Bing Zhang, Peng Cui, Songnian Hu and Jun Yu. ‡ (2010). Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 10:405–415.
22. Dapeng Wang, Yubin Zhanga, Zhang Zhang, Jiang Zhu and Jun Yu. ‡ (2010). KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Geno Proteo &Bioinfo. 8:77–80.
23. XiaoGuang Zhou, Ren LuFeng, Li YunTao, Zhang Meng, Yu YuDe and Yu Jun. ‡ (2010). The next-generation sequencing technology: A technology review and future perspective. Science in China Series C Life Sciences 53(1) 1–14.
24. Liguo Wang, Yuanxin Xi, Jun Yu, Liping Dong, Laising Yen, Wei Li. (2010). A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq. PLoS ONE 5(1): e8529.
25. Cui Peng, Lingfang Zhang, Qiang Lin, Feng Ding, Chengqi Xin, Xiangdong Fang, Songnian Hu, Jun Yu. ‡ (2010). A novel mechanism of epigenetic regulation: Nucleosome-space occupancy. Biochem Biophys Res Com 391:884–889.
26. Cui Peng, Huitao Liu, Qiang Lin, Feng Ding, Guoyin Zhuo, Songnian Hu, DongCheng Liu, Wenlong Yang, Kehui Zhan, Aimin Zhang, and Jun Yu. ‡ (2009). A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai) and fast evolving mitochondrial genes in higher plants. Journal of Genetics 88:209–307.
27. Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu. (2009). Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees. Geno Prot & Bioinfo 7:107–115.
28. Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu. ‡ (2009). How Do Variable Substitution Rates Influence Ka and Ks Calculations? Geno Prot & Bioinfo 7:116–127.
29. Jingfa Xiao and Jun Yu. ‡ (2009). On the Genetic Code and Its Origin. Science in China Series C 39(8):717–726.
30. Xiaomin Yu,Qing Zhou, Yimei Cai, Qibin Luo, Hongbin Lin, Songnian Hu,Jun Yu. ‡ (2009). A Discovery of Novel microRNAs in the Silkworm (Bombyx mori) Genome. Genomics 94:438–444.
31. Jun Yu as a listed author f the Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium. (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature 460: 345–351 (16 July 2009) | doi:10.1038/nature08140.
32. Jun Li, Zhang Zhang, Søren Vang, Jun Yu, Gane Ka-Shu Wong, Jun Wang. (2009) Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol 68(4):414-23. Epub 2009 Mar 24.
33. Dapeng Wang, Haolei Wan, Song Zhang, and Jun Yu.‡ (2009) Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biology Direct 2009, 4:20.
34. Gang Wei, Yong Tao, Guozhen Liu, Chen Chen, Renyuan Luo, Hongai Xia, Qiang Gan, Haipan Zeng, Zhike Lu, Yuning Han, Guisheng Song, Honglin Xu, Xiaoli Wei, Mengliang Cao, Huafeng Deng, Longping Yuan, Jun Yu,‡ Zhen Zhu, Lihuang Zhu. (2009) A transcriptomic analysis of super-hybrid rice LYP9 and its parental cultivars. Proc Natl Acad Sci USA 106:7695–7701.(Elected to be the Top10 Scientific News in Basic Research in China, 2009)
35. Jingui Zhu, Yongqiao Sun, Faqing Zhao, Jun Yu, Roger Craig and Songnian Hu. (2009) Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms. BMC Genomics 10:117.
36. Liang Yang and Jun Yu. ‡ (2009) A Comparative Analysis of Divergently-Paired Genes (DPGs) of Drosophila and Vertebrate Genomes. BMC Evolutionary Biology 9:55.
37. Feng Ding, Petrus Tang, Mei-Hua Hsu, Peng Cui, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. (2009) Genome Evolution Driven by Host Adaptations Results in a More Virulent and Antimicrobial-Resistant Streptococcus pneumoniae Serotype 14. BMC Genomics 10:158.
38. Weihua Chen, Xiaomeng Ge, Weiwei Wang, Jun Yu,‡ and Songnian Hu. (2009). A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana. BMC Genomics 10:52.
39. Ji R, Cui P, Ding F, Geng J, Gao H, Zhang H, Yu J, Hu S, Meng H. (2009) Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Anim Genet 2009, 40(4):377–382.
40. Liguo Wang, Lili Hao, Xianran Li, Songnian Hu, Song Ge, Jun Yu.‡ (2009) SNP deserts of cultivated Asian rice: genomic regions under domestication. J Evol Biol 22:51–761.
41. Zejuan Li, Roger T. Luo, Shuangli Mi, Miao Sun, Ping Chen, Jingyue Bao, Mary Beth Neilly,Nimanthi Jayathilaka, Deborah S. Johnson, Lili Wang, Catherine Lavau, Yanming Zhang, Charles Tseng, Xiuqing Zhang, Jian Wang, Jun Yu, Huanming Yang, San Ming Wang, Janet D. Rowley, Jianjun Chen, and Michael J. Thirman. (2009) Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias. Cancer Res 2009; 69: (3).
42. Shuhui Song, Yuefeng Huang, Xuan Wang, Gang Wei, Weiwei Wang, Xiaomeng Ge, Songnian Hu, Yanchun Liang, and Jun Yu.‡ (2009) HRGD: a Database for Heterosis-associated Genes. Plant Mol Biol. 69:255–260.
43. Wang F, Xiao J, Pan L, Yang M, Zhang G, Jin S, Yu J.‡ (2008) A Systematic Survey of Mini-Proteins in Bacteria and Archaea. PLoS ONE 3(12): e4027. doi:10.1371/journal.pone.0004027.
44. Xiaomeng Ge, Weihua Chen, Shuhui Song, Weiwei Wang, Songnian Hu, Jun Yu.‡ (2008) Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines. BMC Plant Biol. 8:114.
45. Zhenqing Ye, Songnian Hu, Jun Yu.‡ (2008) Adaptive clustering algorithm for community detection in complex networks. Phys. Rev. E 78, 046115.
46. Jiang Zhu, Fuhong He, Songnian Hu and Jun Yu. ‡ (2008) Reevaluating the nature of housekeeping gene. Trends in Genetics 24:481–484.
47. Kaifu Chen, Qingshu Meng, Lina Ma, Qingyou Liu, Petrus Tang, Chungshung Chiu, Songnian Hu, Jun Yu.‡ (2008). A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res. 36:6228–36.
48. Xiaomin Yu, Qing Zhou, Sungchou Li, Qibin Luo, Wenchang Lin, Huan Chen, Yue Yang, Songnian Hu, Jun Yu.‡ (2008)Computational and experimental identification of microRNAs in the silkworm (Bombyx mori). PLoS ONE 3(8): e2997.
49. Weiwei Wang, Bo Meng, Xiaomeng Ge, Xiaomin Yu, Yue Yang, Liguo Wang, Songnian Hu, Siqi Liu, Jun Yu.‡ (2008) Proteomic Profiling of Rice Embryos from a Hybrid Rice Cultivar and Its Parental Lines. Proteomics 8:4808–4821.
50. Fengping Wang, Jianbin Wang, Huahua Jian, Bing Zhang,Shengkang Li, Feng Wang, Xiaowei Zeng, Lei Gao, Douglas Hoyt Bartlett, Jun Yu, Songnian Hu, and Xiang Xiao. (2008) Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3. PLoS ONE 3(4): e1937.
51. TONG XiaoMei, CHEN Fang, YU Jun, HUA Sang, ASAN Ciren, LUOSANG JiangBai, WANG Wei, YU Liang, ZHENG XiaoGuang, WANG Jian. (2008). Phylogenetic identification and microbial diversity in snow of the summit (8201 m) of Cho Oyu Mountain in Tibet. Chinese Science Bulletin 53: 3317–3323.
52. Luo Q, Zhou Q, Yu X, Lin H, Hu S, Yu J‡ (2008) Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum. J Genet Genomics35:349–55.
53. Jiang Zhu, Fuhong He, Jing Wang and Jun Yu.‡ (2008) How many human genes can be defined as house-keeping with current expression data? BMC Genomics 9:172.
54. Liping Wei‡ and Jun Yu.‡ (2008) Bioinformatics in China: A Personal Perspective. PLoS Comp Biol 4(4): e1000020.
55. Jiang Zhu, Fuhong He, Jing Wang, and Jun Yu. ‡ (2008) Modeling Transcriptome Based on Transcript-Sampling Data. PLoS ONE 3(2): e1659.
56. Xiangtian Zhou, Weiwei Wang, Fan Lu, Songnian Hu, Liqin Jiang, Dongsheng Yan, Xiaowei Zhang, Xiaomin Yu, Jun Yu, Jia Qu. (2007) A comparative gene expression profile of the whole eye from human, mouse, and guinea pig. Molecular Vision 13:2214–2221.
57. Jingfa Xiao and Jun Yu.‡ (2007) A Scenario on the Stepwise Evolution of the Genetic Code. Geno Prot & Bioinfo 5: 143–151.
58. Ye Feng, Chih-Jung Chen, Lin-Hui Su, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. Evolution and pathogenesis of Staphylococcus aureus: lessons learned from genotyping and comparative genomics. FEMS Microbiology Reviews 32:23 –37.
59. Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jorgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshoj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M. (2007) Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 8(4):R45.
60. Weiwei Wang, Bo Meng, Weihua Chen, Xiaomeng Ge, Siqi Liu, and Jun Yu.‡ (2007) A proteomic study on postdiapaused embryonic development of brine shrimp (Artemia franciscana). Proteomics 7:3580–3591.
61. Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., Belmont, J.W., Boudreau, A., Hardenbol, P., Leal, S.M., Pasternak, S., Wheeler, D.A., Willis, T.D., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Zhao, H., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Shen, Y., Sun, W., Wang, H., Wang, Y., Wang, Y., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.-F., Galver, L.M., Fan, J.-B., Gunderson, K., Murray, S.S., Oliphant, A.R., Chee, M.S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J.-F., Phillips, M.S., Roumy, S., Sallée, C., Verner, A., Hudson, T.J., Kwok, P.-Y., Cai, D., Koboldt, D.C., Miller, R.D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L.-C., Mak, W., You, Q.S., Tam, P.K.H., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C.P., Delgado, M., Dermitzakis, E.T., Gwilliam, R., Hunt, S., Morrison, J., Powell, D., Stranger, B.E., Whittaker, P., Bentley, D.R., Daly, M.J., De Bakker, P.I.W., Barrett, J., Chretien, Y.R., Maller, J., McCarroll, S., Patterson, N., Pe'Er, I., Price, A., Purcell, S., Richter, D.J., Sabeti, P., Saxena, R., Schaffner, S.F., Sham, P.C., Varilly, P., Stein, L.D., Krishnan, L., Smith, A.V., Tello-Ruiz, M.K., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Lin, S., Abecasis, G.R., Guan, W., Li, Y., Munro, H.M., Qin, Z.S., Thomas, D.J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L.R., Clarke, G., Evans, D.M., Morris, A.P., Weir, B.S., Johnson, T.A., Mullikin, J.C., Sherry, S.T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., MacEr, D.R., Suda, E., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Burton, J., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Willey, D.L., Chen, Z., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., Wang, H., An, D., Fu, H., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Jamieson, R., Stewart, J. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861.
62. Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., McCarroll, S.A., Gaudet, R., Schaffner, S.F., Lander, E.S., Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., Belmont, J.W., Boudreau, A., Hardenbol, P., Leal, S.M., Pasternak, S., Wheeler, D.A., Willis, T.D., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Zhao, H., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Shen, Y., Sun, W., Wang, H., Wang, Y., Wang, Y., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.-F., Galver, L.M., Fan, J.-B., Gunderson, K., Murray, S.S., Oliphant, A.R., Chee, M.S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J.-F., Phillips, M.S., Roumy, S., Sallée, C., Verner, A., Hudson, T.J., Kwok, P.-Y., Cai, D., Koboldt, D.C., Miller, R.D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L.-C., Mak, W., You, Q.S., Tam, P.K.H., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C.P., Delgado, M., Dermitzakis, E.T., Gwilliam, R., Hunt, S., Morrison, J., Powell, D., Stranger, B.E., Whittaker, P., Bentley, D.R., Daly, M.J., De Bakker, P.I.W., Barrett, J., Chretien, Y.R., Maller, J., McCarroll, S., Patterson, N., Pe'Er, I., Price, A., Purcell, S., Richter, D.J., Saxena, R., Sham, P.C., Stein, L.D., Krishnan, L., Smith, A.V., Tello-Ruiz, M.K., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Lin, S., Abecasis, G.R., Guan, W., Li, Y., Munro, H.M., Qin, Z.S., Thomas, D.J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L.R., Clarke, G., Evans, D.M., Morris, A.P., Weir, B.S., Johnson, T.A., Mullikin, J.C., Sherry, S.T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., MacEr, D.R., Suda, E., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Burton, J., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Willey, D.L., Chen, Z., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., Wang, H., An, D., Fu, H., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Jamieson, R., Stewart, J. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918.
63. Shu-hui Song, Hong-Zhu Qu, Chen Chen, Song-Nian Hu, Jun Yu.‡ (2007) Differential Gene Expression in an Elite Hybrid Rice Cultivar (Oryza sativa, L): a Global Transcription Analysis Based on SAGE Data. BMC Plant Biology 7:49.
64. Jiangwei Yan, Hui Tang, Yacheng Liu, Wanshan Ma, Yin Liu, Qingxia Zhang, Junwei Gao, Zhangping Jiao, Leipeng Shang, Yuting Jing, Songnian Hu, Jun Yu.‡ (2007) Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groups. Legal Medicine9:330–331.
65. Jun Yu. (2007) An Evolutionary Scenario for the Origin of Genetic Code. Communications of Chinese-American Society of Chemistry, Fall Issue of 2007.pp3–7.
66. Jianfei Hu, Xiaoqian Zhao and Jun Yu.‡ (2007) Replication-associated purine asymmetry (PAS) may contribute to strand-biased gene distribution (SGD). Genomics 90:186–194.
67. Jianfei Hu, Xiaoqian Zhao, Zhang Zhang, Jun Yu.‡ (2007) The Compositional Dynamics of the Guanine and Cytosine Content in Prokaryotic Genomes. Research in Microbiology 158:363–370.
68. Peng Cui, Rimutu Ji, Feng Ding, Dan Qi, Hongwei Gao, He Meng, Jun Yu, Songnian Hu and Heping Zhang. (2007) A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae. BMC Genomics 8:241.
69. Jun Yu. (2007) A content-centric organization of the genetic code. Geno Prot & Bioinfo 5:1–6.
70. Tian Xiangjun, Jing Zheng, Songnian Hu, Jun Yu.‡ (2007) The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowing plants: a genome-wide investigation on indica rice. Journal of Molecular Evolution 64(3): 299.
71. Zhonghua Zhang, Yajun Deng, Jun Tan, Songnian Hu, Jun Yu, Qingzhong Xue. (2007) A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Research 14:37–45.
72. Chen C, Tang J, Dong W, Wang C, Feng Y, Wang J, Zheng F, Pan X, Liu D, Ming L, Song Y, Zhu X, Sun X, 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(3): e315.
73. Xiaoqian Zhao, Zhang Zhang, Jiangwei Yan, Jun Yu.‡ (2007) GC Content Variability of Eubacterial Genomes Is Governed by the Alpha Subunit of DNA Polymerase III. Biochem Biophys Res Com 356:20–25.
74. Jun Yu, G.K. Wong, S. Liu, J. Wang, H. Yang. (2007) A comprehensive crop genome project: the superhybrid rice genome project in China. Philos Trans R Soc Lond B Biol Sci 362(1482):1023–34.
75. Jiangwei Yan, Yacheng Liu, Hui Tang, Qingxia Zhang, Zhenyi Huo, Songnian Hu, Jun Yu. (2006) Mutations at 17 STR loci in Chinese population. Forensic Science International 162:53–54.
76. Zhang Zhang, Jun Li, Jun Wang, Gane Ka-Shu Wong, Jun Yu.‡ (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Geno Prot & Bioinfo 4:259–263.
77. Xiaoqian Zhao, Jianfei Hu, Jun Yu.‡ (2006) Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits. Geno Prot & Bioinfo 4: 203–211.
78. Shuhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu‡, and Jian Wang. (2006) Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Research Database Issue. D1–D5.
79. Zhang Zhang and Jun Yu‡. (2006) Evaluation of six methods for estimation synonymous and nonsynonymous substitution rates. Geno Prot & Bioinfo 4:173–181.
80. Jun Yu, Peixiang Ni, Gane Ka-Shu Wong. (2006). Comparing the whole-genome-shotgun and map-based sequences of the rice genome. Trends in Plant Sciences. 11:387–391.
81. WANG Fu-Qiang, ZHENG Gui-Zhen, ZHAO Ying, HE Jian-Gong, YU Jun.‡ (2006) Molecular cloning and characterization of a glutathione S-transferase gene repressed by phenylacetic acid from Penicillium chrysogenum. Progress in Biochemistry and Biophysics.33:1–8.
82. Raman Sood, Milton A. English, MaryPat Jones , James Mullikin, Duen-Mei Wang, Maria Anderson, Dongying Wu, Settara C. Chandrasekharappa, Jun Yu, Jinghui Zhang, P. Paul Liu. (2006) Methods for reverse genetic screening in zebra by resequencing and TILLING. Methods 39 220–227.
83. Zhang Zhang, Jun Li, Jun Yu.‡ (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evolutionary Biology 6:44.
84. Antonio Garcia-España, Pei-Jung Chung, Xiaoqian Zhao, Andy Lee, Angel Pellicer, Jun Yu, Tung-Tien Sun and Rob DeSalle. (2006) Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: Implications for Uroplakin structure and function. Molecular Phylogenetics and Evolution 41(2):355-67. Epub. 11 May 2006.
85. Bing Zhang, Qinghua Liu, Wei Yin, Xiaowei Zhang, Yijun Huang, Yingfeng Luo, Pengxin Qiu, Xinwen Su, Jun Yu, Songnian Hu and Guangmei Yan. (2006) Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tags. BMC Genomics 7:152.
86. 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(25):2731–2.
87. 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(7088):1194-8.
88. SU, Zhixi, Wang Jianmin, Yu Jun, Huang Xiaoqiu, Gu Xun. (2006) Evolution of alternative splicing after gene duplication. Genome Res 16: 182–189. (F1000: 3.0)
89. Zongyuan Ma, Jun Yu, Le Kang. (2006) LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7:11.
90. SU Zhixi, DONG Xinjiao, ZHANG Bing, ZENG Yanwu, FU Yan, YU Jun, & HU Songnian. (2006) Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes. Science in China: Series C Life Sciences 49 (1): 1-11.
91. Zhao H, Li Q, Li J, Zeng C, Hu S, Yu J‡ (2006) The study of neighboring nucleotide composition and transition/transversion bias. Science in China Series C Life Sciences 49(4): 395.
92. Xiangjun Tian, Jing Zheng, Songnian Hu, Jun Yu‡. (2006) The Rice (Oryza sativa L.) Mitochondrial Genomes and Their Variations. Plant Physiology 140:401–410.
93. Deng YJ, Li YZ, Yu XG, Li L, Wu DY, Zhou J, Man TY, Yang G, Yan JW, Cai DQ, Wang J, Yang HM, Li SB, Yu J.‡ (2005) Preliminary DNA identification for the tsunami victims in Thailand. Geno Prot & Bioinfo 3:143–157.
94. Jun Yu as one of the listed authors of the International HapMap Consortium.[Cover Story](2005) A haplotype map of the human genome. Nature 437:1299-1320.
95. 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(24):15460–15466.
96. Hui Zhao, Qi-Zhai Li, Chang-Qing Zeng, Huan-Ming Yang, and Jun Yu‡. (2005) Neighboring-Nucleotide Effects on the Mutation Pattern of Rice Genome. Geno Prot & Bioinfo 3(3):158-168.
97. Jiabin Tang, Hong’ai Xia, Dayong Li, Mengliang Cao, Yong Tao, Wei Tong, Xiuqing Zhang, Songnian Hu, Jian Wang, Jun Yu‡, Huanming Yang‡, Lihuang Zhu‡. (2005) Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions. Mol Gen Genomics 274:467-476.
98. Shu-Qing Xu, Ying-zhou Yang, Jun Zhou, Guo-En Jing, Yun-tian Chen, Jun Wang, Huanming Yang, Jian Wang, Jun Yu, Xiaoguang Zheng, Ri-Li-Ge. (2005) A mitochondrial genome sequence of the Tibetea Antilope (Pentholops hodgsonii). Geno Prot & Bioinfo 3: 5–17.
99. Li R, Ye J, Li S, Wang J, Han Y, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang. (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4): e43. (F1000: 3.0)
100. JingYue Bao, Sanggyu Lee, Chen Chen, XiuQing Zhang, Yu Zhang, SiQi Liu, Terry Clark, Jian Wang, MengLiang Cao, HuanMing Yang, San Ming Wang, and Jun Yu‡. (2005) Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars. Plant Physiology 138: 1216–1231.
101. Wen Wang, Hongkun Zheng, Shuang Yang, Haijing Yu, Jun Li, Huifeng Jiang, Jianning Su, Lei Yang, Jianguo Zhang, Jason McDermott, Ram Samudrala, Jian Wang, Huanming Yang, Jun Yu, Karsten Kristiansen, Gane Ka-Shu Wong, and Jun Wang. (2005) Origin and evolution of new exons in rodents Genome Res 15:1258–1264. (F1000: 3.0)
102. Rasmus Wernersson, Mikkel H Schierup, Frank G Jorgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Staerfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshoj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K-S Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Soren Brunak, Huanming Yang and Lars Bolund. (2005) Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 6:70.
103. 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.
104. Randall, T. A., R. A. Dwyer, E. Huitema, K. Beyer, C. Cvitanich, H. Kelkar, A. M. V. Ah Fong, K. Gates, S. Roberts, E. Yatzkan, T. Gaffney, M. Law, A. Testa, T. Torto-Alalibo, M. Zhang, L. Zheng, E. Mueller, J. Windass, A. Binder, P. R. J. Birch, U. Gisi, F. Govers, N. A. Gow, F. Mauch, P. van West, M. E. Waugh, J. Yu, T. Boller, S. Kamoun, S. T. Lam, and H. S. Judelson. (2005) Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi. Molecular Plant-Microbe Interactions (MPMI) 18:229–243.
105. Wang Jing, Zhang Meng, Wu Qingfa, Chen Zhu, Qiang Boqin, Yu Jun, Yang Huanming. (2005) “Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis. Science in China: Series C Life Sciences 48(4): 311–29.
106. 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 54:259–68.
107. 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 11:446–8.
108. Jiang, F., Chen Chen, Yanjun Deng, Jun Yu, Songnian Hu. (2005) Analysis of porcine MHC expression profile. Chinese Science Bulletin 50:880–890.
109. Cheng-Hsun Chiu, Petrus Tang, Chishih Chu, Songnian Hu, Qiyu Bao, Jun Yu, Yun-Ying Chou, Hsin-Shih Wang, and Ying-Shiung Lee. (2005) The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen Nucleic Acids Res 33: 1690–1698.
110. Jun Yu‡, Wang J, Lin W, Li S, Li H, et al. [Cover Story] (2005) The Genomes of Oryza sativa: A History of Duplications Rice genomes. PLoS Biol 3:e38. (F1000: 9.6) (The Scientist: Hot Paper in Genomics, January, 2007)
111. 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:D438–41.
112. Wang, Jing, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, and Jun Yu‡. (2005) SilkDB: a knowledgebase for silkworm biology and genomics. Nuclear Acid Res 33:D399–D402.
113. HAN Yujun, NI Peixiang, LÜ Hong, YE Jia, HU Jianfei, CHEN Chen, HUANG Xiangang, CONG Lijuan, LI Guangyuan, WANG Jing, GU Xiaocheng, YU Jun, LI Songgang. (2005) Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis. Science in China Series C-Life Sciences 48(3):300–6.
114. Jun Yu‡and Gane Ka-Shu Wong (2005) Genome Biology: the second modern synthesis. Geno Prot & Bioinfo 3:3–4.
115. Bing Zhang, Wu Jin, Yanwu Zeng, Zhixi Su, Songnian Hu, Jun Yu. ‡ (2004) EST-based Analysis of Gene Expression in the Porcine Brain. Geno Prot & Bioinfo 2(4):237–44.
116. Kang, L., XiangYong Chen, Yan Zhou, BoWan Liu, Wei Zheng, RuiQiang Li, Jun Wang, J. Yu. (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.
117. Jun Yu* co-first authored in International Chicken Polymorphism Map Consortium. [Cover Story] (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 431:717–722.
118. Jun Yu co-authored in International Chicken Genome Sequencing Consortium. [Cover Story] (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 431:695–716.
119. Jun Yu* co-first authored in Xia, Qingyou et al. (2004) A draft sequence of the genome of the domesticated silkworm Bombyx mori). Science 310:1938–1940.
120. Jun Yu as one of the listed authors and co-PI of the Chinese effort, International Human Genome Sequencing Consortium. [Cover Story] (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945.
121. 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 186:5138–46.
122. Wang, Jun, Jianguo Zhang, Hongkun Zheng, Jun Li, Dongyuan Liu, Heng Li, Ram Samudrala, Jun Yu, Gane Ka-Shu Wong. (2004) Mouse transcriptome: neutral evolution of “non-coding” complementary DNAs. Nature 431: 1038–1039.
123. Tang, Lin, Zhu Qingyu, Qin Ede, Yu Man, Ding Zhifen, Shi Huiying, Cheng Xiaojie, Wang Caiping, Chang Guohui, Zhu Qiang, Fang Fang, Chang Haiyan, Li Shuangli, Zhang Xumin, Chen Xishu, Yu Jun, Wang Jian, Chen Ze. (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.
124. Jiang, Songshan, Jordan Gitlin, Fang-Ming Deng, Feng-Xia Liang, Andy Lee, Anthony Atala, Stuart B. Bauer, Garth D. Ehrlich, Sally A. Feather, Judith D. Goldberg, Judith A. Goodship, Timothy H.J. Goodship, Monika Hermanns, Fen Ze Hu, Katrin E. Jones, Sue Malcolm, Cathy Mendelsohn, Robert A. Preston, Alan B. Retik, Francis X. Schneck, Victoria Wright, Xiang Y. Ye, Adrian S. Woolf, Xue-Ru Wu, Harry Ostrer, Ellen Shapiro, Jun Yu, and Tung-Tien Sun. (2004)Lack of major involvement of human uroplakin genes in vesicoureteral reflux: Implications for disease heterogeneity.Kidney International 66: 10–19.
125. Li, Zhongyi, Bingyan Huang, Lynette Rampling, Jun Wang, Jun Yu, Matthew Morell, Sadequr Rahman. (2004) Detailed comparison between the wheat chromosome group 7 short arms and the rice chromosome arms 6S and 8L with special reference to genes involved in starch biosynthesis Functional & Integrative Genomics 4: 231–240.
126. Li, Chengdao, Peixiang Ni, Michael Francki, Adam Hunter, Yong Zhang, David Schibeci, Heng Li, Allen Tarr, Jun Wang, Mehmet Cakir, Jun Yu, Matthew Bellgard, Reg Lance and Rudi Appels. (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison Functional & Integrative Genomics 4: 84–93.
127. Tang, Jiabin, Hong’ai Xia, Mengliang Cao, Xiuqing Zhang, Wanyong Zeng, Songnian Hu, Wei Tong, Jun Wang, Jian Wang, Jun Yu‡, Huanming Yang, and Lihuang Zhu. (2004) A Comparison of Rice Chloroplast Genomes. Plant Physiology 135: 412–420.
128. Li Yan, Chunqing Luo, Wei Li, Zhao Xu, Changqing Zeng, Shenli Bi, Jun Yu, Jun Wu, Huanming Yang. (2004). Structure-Based Preliminary Analysis of Immunity and Virulence of SARS Coronavirus. Viral Immunology 17: 528–534.
129. Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D, Qin H, Pang X, Han Y, Zhai J, Li M, Cui B, Qi Z, Jin L, Dai R, Chen F, Li S, Ye C, Du Z, Lin W, Wang J, Yu J, Yang H, Wang J, Huang P, Yang R. (2004) Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res 11:179–97.
130. Zhao W, Jing Wang, Ximiao He, Xiaobing Huang, Mingtao Dai, Shulin Wei, Yongzhi Jiao, Jian Fu, Chen Ye, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang. (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res 32: D377–D382.
131. Tang, Lin, Wang Jian, Qin Ede, Zhu Qingyu, Yu Man, Ding Zhifen, Shi Huiying, Cheng Xiaojie, Wang Caiping, Chang Guohui, Li Shuangli, Zhang Xumin, Chen Xishu, Yu Jun and Chen Ze. (2003) Preparation, characterization and preliminary in vivo studies of inactivated SARS-CoV vaccine Chinese Science Bulletin48: 2621–2625.
132. Xu, Jing, Jianfei Hu, Jing Wang,Yujun Han, Yongwu Hu, Jie Wen, Yan Li, Jia Ji, Jia Ye, Zizhang Zhang, Wei Wei, Songgang Li, Jun Wang, Jian Wang, Jun Yu, and Huanming Yang. (2003) Genome organization of the SARS-CoV. Geno Prot & Bioinfo 1: 226–235.
133. Hu, Jianfei, Jing Wang, Jing Xu, Wei Li, Yujun Han, Yan Li, Jia Ji, Jia Ye, Zhao Xu, Zizhang Zhang, Wei Wei, Songgang Li, Jun Wang, Jian Wang, Jun Yu,and Huanming Yang. (2003) Evolution and variation of the SARS-CoV genome. Geno Prot & Bioinfo 1: 216–225.
134. Liu, Guozhen, Shaohui Hu, Yongwu Hu, Peng Chen, Jianning Yin, Jie Wen, Jingqiang Wang, Liang Lin, Jinxiu Liu, Bo You, Ye Yin, Shuting Li, Hao Wang, Yan Ren, Jia Ji, Xiaoqian Zhao, Yongqiao Sun, Xiaowei Zhang, Jianqiu Fang, Jian Wang, Siqi Liu, Jun Yu, Heng Zhu, and Huanming Yang. (2003) The C-terminal portion of the nucleocapsid protein demonstrating SARS-CoV antigenicity. Geno Prot & Bioinfo 1: 193–197.
135. Bi, Shengli, E’de Qin, Zuyuan Xu, Wei Li, Jing Wang, Yongwu Hu, Yong Liu, Shumin Duan, Jianfei Hu, Yujun Han, Jing Xu, Yan Li, Yao Yi, Yongdong Zhou, Wei Lin, Jie Wen, Hong Xu, Ruan Li, Zizhang Zhang, Haiyan Sun, Jingui Zhu, Man Yu, Baochang Fan, Qingfa Wu, Wei Lin, Lin Tang, Bao’an Yang, Guoqing Li, Wenming Peng, Wenjie Li, Tao Jiang, Yajun Deng, Bohua Liu, Jianping Shi, Yongqiang Deng, Wei Wei, Hong Liu, Zongzhong Tong, Feng Zhang, Yu Zhang, Cui’e Wang, Yuquan Li, Jia Ye, Yonghua Gan, Jia Ji, Xiaoyu Li, Xiangjun Tian, Fushuang Lu, Gang Tan, Ruifu Yang, Bin Liu, Siqi Liu, Songgang Li, Jun Wang, Jian Wang, Wuchun Cao, Jun Yu, Xiaoping Dong, and Huanming Yang. (2003) Complete genome sequences of SARS-CoV: the BJ group (Isolates BJ01-BJ04). Geno Prot & Bioinfo 1: 180–192.
136. Wang, Jingqiang, Jie Wen, Jingxiang Li, Jianning Yin, Qingyu Zhu, Hao Wang, Yongkui Yang, E’de Qin, Bo You, Wei Li, Xiaolei Li, Shengyong Huang, Ruifu Yang, Xumin Zhang, Ling Yang, Ting Zhang, Ye Yin, Xiaodai Cui, Xiangjun Tang, Luoping Wang, Bo He, Lianhua Ma, Tingting Lei, Changqing Zeng, Jianqiu Fang, Jun Yu, Jian Wang, Huanming Yang, Matthew B. West, Aruni Bhatnagar, Youyong Lu, Ningzhi Xu, and Siqi Liu. (2003) Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus.Clinical Chemistry 49: 1989–1996.
137. Wang J., Li ST, Zhang Y, Zheng HK, Xu Z, Ye J, Yu J, and Wong GKS. (2003) Vertebrate gene predictions and the problem of large genes Nature Reviews Genetics 4: 741–749.
138. Wong, Gane Ka-Shu, Zhiyong Yang, Douglas A. Passey, Miho Kibukawa, Marcia Paddock, Chun-Rong Liu, Lars Bolund, and Jun Yu‡. (2003) A population threshold for functional polymorphisms Genome Res 13: 1873–1879.
139. Woo PC, Zhen H, Cai JJ, Yu J, Lau SK, Wang J, Teng JL, Wong SS, Tse RH, Chen R, Yang H, Liu B, Yuen KY. (2003) The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett 555:469–77.
140. Qin, E’de, Xionglei He, Wei Tian, Yong Liu, Wei Li, Jie Wen, Jingqiang Wang, Baochang Fan, Qingfa Wu, Guohui Chang, Wuchun Cao, Zuyuan Xu, Ruifu Yang, Jing Wang, Man Yu, Yan Li, Jing Xu, Bingyin Si, Yongwu Hu, Wenming Peng, Lin Tang, Tao Jiang, Jianping Shi, Jia Ji, Yu Zhang, Jia Ye, Cui’e Wang, Yujun Han, Jun Zhou, Yajun Deng, Xiaoyu Li, Jianfei Hu, Caiping Wang, Chunxia Yan, Qingrun Zhang, Jingyue Bao, Guoqing Li, Weijun Chen, Lin Fang, Changfeng Li, Meng Lei, Dawei Li, Wei Tong, Xiangjun Tian, Jin Wang, Bo Zhang, Haiqing Zhang, Yilin Zhang, Hui Zhao, Xiaowei Zhang, Shuangli Li, Xiaojie Cheng, Xiuqing Zhang, Bin Liu, Changqing Zeng, Songgang Li, Xuehai Tan, Siqi Liu, Wei Dong, Jun Wang, Gane Ka-Shu Wong, Jun Yu, Jian Wang, Qingyu Zhu, and Huanming Yang. [Cover Story] (2003) A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China Geno Prot & Bioinfo 1: 101–107.
141. Qin, E’De, Zhu Qingyu, Yu Man, Fan Baochang, Chang Guohui, Si Bingyin, Yang Bao’An, Peng Wenming, Jiang Tao, Liu Bohua, Deng Yongqiang, Liu Hong, Zhang Yu, Wang Cui’E, Li Yuquan, Gan Yonghua, Li Xiaoyu, Lü Fushuang, Tan Gang, Cao Wuchun, Yang Ruifu, Wang Jian, Li Wei, Xu Zuyuan, Li Yan, Wu Qingfa, Lin Wei, Han Yujun, Li Guoqing, Li Wenjie, Lü Hong, Shi Jianping, Tong Zongzhong, Zhang Feng, Li Songgang, Liu Bin, Liu Siqi, Dong Wei, Wang Jun, Gane K-S Wong, Yu Jun, and Yang Huanming. [Cover Story] (2003) A complete sequence and comparative analysis of a SARS associated virus (Isolate BJ01) Chinese Science Bulletin 48: 941–948.
142. Zhou, Yan, Jiabin Tang, Michael G. Walker, Xiuqing Zhang, Jun Wang, Songnian Hu, Huayong Xu, Yajun Deng, Jianhai Dong, Lin Ye, Li Lin, Jun Li, Xuegang Wang, Hao Xu, Yibin Pan, Wei Lin, Wei Tian, Jing Liu, Liping Wei, Siqi Liu, Huanming Yang, Jun Yu, Jian Wang. (2003) Gene Identification and Expression Analysis of 86,136 Expressed Sequence Tags (EST) from the Rice Genome. Geno Prot & Bioinfo 1: 26–42.
143. Sultana, Razia, Chang-En Yu, Jun Yu, Jeffery Munson, Donghui Chen, Wenhui Hua, Annette Estes, Fanny Cortes, Flora de la Barra, Dongmei Yu, Syed T. Haider, Barbara J. Trask, Eric D. Green, Wendy H. Raskind, Christine M. Disteche, Ellen Wijsman, Geraldine Dawson, Daniel R. Storm, Gerard D. Schellenberg, Enrique C. Villacres. (2002) Identification of a Novel Gene on Chromosome 7q11.2 Interrupted by a Translocation Breakpoint in a Pair of Autistic Twins. Genomics 80:129–134.
144. Yu, Jun*, Zhiyong Yang, Miho Kibukawa, Marcia Paddock, Douglas A. Passey, and Gane Ka-Shu Wong. (2002) Minimal introns are not “junk”. Genome Res 12:1185–1189. (F1000: 3.0)
145. Wong, Gane Ka-Shu, Jun Wang, Douglas A. Passey, and Jun Yu‡.[Cover Story] (2002) Codon-Usage Gradients in Gramineae Genomes. Genome Res 12:851–856. (F1000: 6.0)
146. Bao, Qiyu, Yuqing Tian, Wei Li, Zuyuan Xu, Jian Yang, Songnian Hu, Wei Dong, Yanjiong Chen, Yanfen Xue, Yi Xu, Xiaoqin Lai, Li Huang, Zhenyu Xuan, Huarong Tan, Runsheng Chen, Jian Wang, Jun Yu, Huanming Yang. (2002) A complete sequence of Thermoanaerobacter tengcongensis genome. Genome Res 12:689–700.
147. Zhang, Xiuqing, Huanming Yang, Jun Yu, Cong Chen, Guangyu Zhang, Jingyue Bao, Yutao Du, Miho Kibukawa, Zhijie Li, Jun Wang, Songnian Hu, Wei Dong, Jian Wang, Niels Gregersen, Erik Niebuhrd and Lars Bolund. (2002) Genomic organization, alternative splicing and comparative analysis of the human nucleoporin 155 (NUP155) gene. Gene288:9–18.
148. Wang, Jun, Gane Ka-Shu Wong, Jian Wang, Peixiang Ni, Yujun Han, Xiangang Huang, Jianguo Zhang, Chen Ye, Yong Zhang, Jianfei Hu, Kunlin Zhang, Xin Xu, Lijuan Cong, Hong Lu, Xide Ren, Xiaoyu Ren, Dan Dai, Jun He, Lin Tao, Douglas A. Passey, Huanming Yang, Jun Yu, and Songgang Li. (2002) RePS: a sequence assembler that masks exact 20-mer repeats identified from the shotgun dataset. Genome Res 12:817–823.
149. Jun Yu, et al. [Cover Story] (2002) A draft sequence assembly of the rice (Oryza sativa ssp. indica) genome. Science 296:79–93. (F1000: 9.8)
150. Wong, G.K.-S., D.A. Passey, and J. Yu‡. (2001) Most of the human genome is transcribed. Genome Res 11:1975–1977. (F1000: 6.0)
151. Jun Yu, et al. [Cover Story] (2001) A draft sequence of the rice (Oryza sativa ssp. indica) genome. Chinese Science Bulletin 46:1937–1942.
152. Z. Tan, S. Jiang, Z. Lin, B. Zhang, J. Yu, G. Feng and L. He. (2001) Identification of SNPs in human gamma aminobutyric acid A receptor gamma2 gene. Int J Mol Med 8:205–209.
153. Jun Yu as one of the listed authors and co-PI of the Chinese effort, the International Human Genome Sequencing Consortium. [Cover Story] (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921.
154. Jiang S., J. Yu, J. Wang, Z. Tan, H. Xue, G. Feng, L. He, H. Yang. (2001) Complete genomic sequence of 195 kb of human DNA containing the gene GABA-g2. DNA Seq 11:373–82.
155. Gane Ka-Shu Wong, Douglas A Passey, Yingzong Huang, Zhiyong Yang, and Jun Yu‡. (2000) Is “junk” DNA mostly intron DNA? Genome Res 10: 1672–1678.
156. Yang, Z., G. K-S. Wong, M.A. Eberle, M. Kibukawa, D.A. Passey, W.R. Hughes, L. Kruglyak, and J. Yu‡. (2000) Sampling SNPs. Nature Genetics26:13–14.
157. Huang, G. M., W. V. Ng, J. Farkas, L. He, H. A. Liang, D. Gordon, J. Yu, and L. Hood. (1999) Prostate cancer expression profiling by cDNA sequencing analysis. Genomics 59:178–186.
158. Yu, J. *, G. K.-S Wong, E.D. Thayer, and M.V. Olson. (1997) Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing. Proc Natl Acad Sci USA 94:5225–5230.
159. Jun Yu and G.K.-S. Wong. (1997) The Mappers’ Touch Song. Genome Res 7:666–668.
160. Gillett, W., L. Hanks, G.K.-S Wong, J. Yu, R. Lim, and M.V. Olson. (1996) Assembly of high-resolution restriction maps based on multiple-complete-digests of a redundant set of overlapping clones. Genomics 33:389–408.
161. Wu, X.-R., J. Lin, T. Walz, M. Hner, J. Yu, U. Aebi, T.-T. Sun. (1994) Mammalian uroplakins: A group of highly conserved urothelial differentiation-related membrane proteins. J Biol Chem 269:13716–13724.
162. Ryan, A.M., J. E. Womack, J. Yu, J.-H. Lin, X.-R. Wu, T.-T. Sun. (1994) Rapid Communication: PstI, HindIII and TaqI restriction fragment length polymorphisms in the bovine Uroplakin IB gene. J Anim Sci 72:1909.
163. Yu, J*, J.-H. Lin, X.-R. Wu and T.-T. Sun. (1994) Uroplakin Ia and Ib, two major differentiation products of bladder epithelium, belong to a family of four transmembrane domain (4TM) proteins. J Cell Biol 125:171–182.
164. Ryan, A.M., J. E. Womack, J. Yu, J.-H. Lin, X.-R. Wu, T.-T. Sun. (1994) Rapid Communication: BamHI and TaqI restriction fragment length polymorphisms in the bovine Uroplakin IA gene. J Anim Sci 72:1908.
165. Ryan, A.M., J.E. Womack, J. Yu, J.-H. Lin, X.-R. Wu, T.-T. Sun, V. Clarke, P. D'Eustachio. (1993) Chromosomal locations of Uroplakins of cattle and mice. Mammal Genome 4:656–661.
166. Yu J., M. Manabe and T.-T. Sun. (1992) Identification of 85-100 kD glycoprotein as a cell surface marker for an advanced stage of urothelial differentiation: association with the inter-plaque ("Hinge") area. J Epithel Biol 1:4–12.
167. Pang, Y.-Y. S., A. Schermer, J. Yu and T.-T. Sun. (1992) Suprabasal changes and subsequent formation of distribution of disulfide-stabilized homo- and heterodimers of keratins during esophageal epithelial differentiation. J Cell Sci 104:727–740.
168. Surya, B., J. Yu, M. Manabe and T.-T. Sun. (1990) Assessing the differentiation state of cultured bovine urothelial cells: elevated synthesis of stratification-related K5 and K6 keratins and persistent expression of Uroplakin I. J Cell Sci 97:419–432.
169. Wu, X.-R., M. Manabe, J. Yu and T.-T Sun (1990) Large scale purification and immunolocalization of bovine uroplakins I, II and III: molecular markers of urothelial differentiation. J Biol Chem 265:19170–19179.
170. Yu, J., M. Manabe, X.-R. Wu, C. Xu, B. Surya and T.-T. Sun (1990) Uroplakin I: a 27-kD protein associated with the asymmetric unit membrane of mammalian urothelium J Cell Biol 111:1207–1216.
PUBLISHED BOOKS, BOOK CHAPTERS, INVITED REVIEWS, AND PROCEEDINGS (selected)
