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News & Events |
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| | In press |
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Niu D.K. and Jiang, L. (2013) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and Biophysical Research Communications, in press. |
| | 2012-11-25 Publication |
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Guo, S.G., Zhang, J.G., Sun, H.H.,..., Tan, T., Pang E.L., Lin K.,..., Fei, Z.J. and Xu, Y. (2012) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics, doi:10.1038/ng.2470. [Online PDF] |
| | 2012-09-18 Publication |
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Yan Zhang and Kui Lin (2012). A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. BMC Evolutionary Biology, doi:10.1186/1471-2148-12-174. [Online PDF] |
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2012-02-13
Publication
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Erli Pang, Tao Tan and Kui Lin (2012). Promiscuous domains: facilitating stability of the yeast protein-protein interaction network.Mol. BioSyst.,doi:10.1039/C1MB05364G.[Online PDF] |
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2011-12-10 新闻
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庞尔丽老师在福建农林师范大学做学术报告
12月10号，庞尔丽老师等代表生物信息实验室前往福建农林师范大学进行了为期3天的学术交流。在交流期间，双方就科研上的一些问题进行了深入探讨。庞老师做了题为“酵母蛋白互作位点预测及互作网络分析"的报告，受到了大家的一致好评。与此同时
，福建农林师范大学的何教授及其学生也做了相关报告。
会后，在何教授的带领下，庞老师等参观了实验室建设，为进一步的交流奠定了基础。
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2011-11-17 新闻
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林魁教授赴日参加学术交流
11月6日－17日，应日本早稻田大学大学院情报生产系统研究科(Graduate School of Information, Production and Systems, Waseda University)古月敬之(Jinglu HU)教授的邀请，林魁博士和博士研究生张彦同学赴日进行了学术交流并参加了日方主办的国际研讨会。早稻田大学是日本最著名的私立大学之一，其大学院情报生产系统研究科位于福冈县北九州市学术研究城内。
在11月9日－11日研讨会期间，林老师与来自早稻田大学、马来西亚大学、上海交通大学、复旦大学、东南大学等学校的师生就进化算法、机器学习等进行了交流与讨论。张彦同学做了关于“基于共线性特征推断大肠杆菌基因组树”的工作介绍。7、8日和12-16日，林老师和张彦同学与古月敬之教授的实验室师生就各自的研究方向进行了深入的交流。林老师介绍了他们在植物基因组注释与比较分析、微生物群落基因组学分析以及蛋白质与蛋白质相互作用网络的构建与分析方面的工作；古月敬之教授介绍了他们在支持向量机与回归、分布估计算法等相关机器学习算法研究以及生物信息学应用等方面的工作。双方重点探讨了将来在生物信息学方面的合作研究事宜。生物信息学作为一门交叉学科，需要生物学、计算机科学以及数学和统计等不同领域的研究人员共同参与。我们希望此次交流将促进双方进一步的学术合作研究。
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2011-11-02 Publication
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Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, and Kui Lin (2011). RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics,doi:10.1186/1471-2164-12-540. [Online
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2011-03-17
News |
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PhD Opportunities in Computer Science of Royal
Holloway, University of London.[Online
PDF] |
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2010-10-01
Publication
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Niu DK
and Cao JL (2010). Nucleosome deposition and DNA methylation may
participate in the recognition of premature termination codon in
non-sense-mediated mRNA decay.FEBS Letters,584:
3509-3512. [Online
PDF] |
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2010-10-01
Publication
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Zhang
LY, Yang YF and Niu DK (2010). Evaluation of models of the
mechanisms underlying intron loss and gain in Aspergillus
fungi.Journal of
Molecular Evolution,doi:10.1007/s00239-010-9391-6.
[Online
PDF] |
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2010-09-08 News
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热烈祝贺2009届博士生吴晓梅同学的博士论文“酵母基因组蛋白质相互作用网络的构建与动态分析”被评选为2010年北京市优秀博士学位论文
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2010-07-16 Accepted
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Pang, E.L. and Lin, K.* (2010) Yeast protein–protein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels.
Molecular BioSystems,DOI: 10.1039/C0MB00038H.
[Online PDF]
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2010-01-29 Publication
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Fu, C., Li, J. and Wang, E.* (2009) Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression.
Molecular BioSystems, 5: 1809-1816.
[Online PDF]
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2010-01-18 Seminar
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应林魁教授邀请，中国农业大学蛋白质生物信息学实验室张子丁教授及学生来我院进行研究生学术交流和学术报告。
报告时间: 2010年1月18日 星期一 9:00
报告地点: 北师大生科院生物信息学教室（生地楼机房）
点击详细信息
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2009-11-11 Publication
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Huang, S.W., Li, R.Q., Zhang, Z.H., Li, L., Gu, X.F., Fan, W., Lucas, W.J., Wang, X.W., Xie, B.Y., Ni, P.X., Ren, Y.Y., Zhu, H.M., Li, J., Lin, K., Jin, W.W., Fei, Z.J., Li, G.C., Stabu, J., Kilian, A., Vossen, E.A., Wu, Y., Guo, J., He, J., Jia, Z.Q., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W.B., Wang, M.W., Huang, Q.F., Li, B., Xuan, Z.L., Cao, J.J., Asan, Wu, Z.G., Zhang, J.B., Cai, Q.L., Bai, Y.Q., Zhao, B.W., Han, Y.H., Li, Y., Li, X.F., Wang, S.H., Shi, Q.X., Liu, S.Q., Cho, W.K., Kim, J.Y., Xu, Y., Uszynska, K.H., Miao, H., Cheng, Z.C., Zhang, S.P., Wu, J., Yang, Y.H., Kang, H.X., Li, M., Liang, H.Q., Ren, X.L., Shi, Z.B., Wen, M., Jian, M., Yang, H.L., Zhang, G.J., Yang, Z.T., Chen, R., Liu, S.F., Li, J.W., Ma, L.J., Liu, H., Zhou, Y., Zhao, J., Fang, X.D., Li, G.Q., Fang, L., Li, Y.R., Liu, D.Y., Zheng, H.K., Zhang, Y., Qin, N., Li, Z., Yang, G.H., Yang, S., Bolund, L., Kristiansen, K., Zheng, H.C., Li, S.C., Zhang, X.Q., Yang, H.M., Wang, J., Sun, R.F., Zhang, B.X., Jiang, S.Z., Wang, J., Du, Y.C. and Li, S.G. (2009) The genome of the cucumber, Cucumis sativus L.
Nature Genetics, 41:1275-1281.
[Online PDF]
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2009-10-10 Publication
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Wu, X.M., Guo, J., Zhang, D.Y. and Lin, K.* (2009) The properties of hub proteins in a yeast-aggregated cell cycle network and its phase sub-networks.
Proteomics, 9:4812-4824.
[Online PDF]
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2009-09-20 News
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同济大学生物信息系招收免试研究生启事
同济大学生物信息学系成立于2009年，作为同济大学重点建设的新兴学科之一，拥有以哈佛大学刘小乐教授为首的具有国际一流水平的科研团队，雄厚的师资力量和充足的经费支持。现面向全国招收2010级免试研究生，所招收的研究生的培养将在中美联合研究团队的共同指导下进行。……点击详细信息
相关资料：果蝇的核小体定位与基因调控
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2009-07-02 Seminar
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Title: Computationally reconstructing the evolutionary history of mammalian genomes
Speaker: Dr. Ma Jian, Department of Bioengineering, University of Illinois at Urbana-Champaign
Venue:The Bioinformatics Training Center, College of Life Science
Time:16:00-17:30, Friday, 2009-07-10
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2009-06-27 Graduation & Admission
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祝贺我实验室八位同学毕业！
毕业生：吴晓梅，郭洁，张珊珊，周玮，赵磊，张冰君，黄一飞，吕杰
欢迎五位同学加入我实验室！
新同学：黄伟奇，张彦，李明，江丽，李俊娥
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2009-06-01 Publication
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Fu, C. and Lin, K.* (2009) Computational Analysis of miRNA and Target mRNA Interactions: Combined Effects of The Quantity and Quality of Their Binding Sites.
Progress in Biochemistry and Biophysics, 36(5):608-615.
68:248-255.
[Online PDF]
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2009-05-28 Publication
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Li, N., Lv, J. and Niu, D.K.* (2009) Low contents of carbon and nitrogen in highly abundant proteins: Evidence of selection for the economy of atomic composition.
Journal of Molecular Evolution, 68:248-255.
[Online PDF]
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2009-05-20 Seminar
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Title: How to become genomes？
Speaker: Dr. Zhu Huaiqiu, Department of BME, Peking University
Venue: Room 503, College of Art & Communication
Time: 10:00，Wednesday, May 20 2009
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2009-02-28 Publication
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Lin, K., Zhang D.Y.* and He F. (2009) Demographic trade-offs in a neutral model explains death rate-abundance rank relationship.
Ecology, 90(1):31-38.
[Online PDF]
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2009-02-25 News
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热烈祝贺我实验室生物信息学二级学科博士点成立!
[查看详情]
欢迎有志于生物信息学研究的同学报考我实验室！
[报考指南]
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2009-02-12 Awards
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祝贺我实验室同学在2008年度研究生奖学金评选中获奖！
综合奖学金: 黄一飞(学术优秀型)，吕杰(学术优秀型)，张蕾颖(社会工作型)
求是奖学金：郭洁
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2008-11-13 Publication
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Niu, D.K. (2008) Exon definition as a potential negative force against intron losses in evolution.
Biology Direct, 3:46.
[Online PDF]
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2008-08-20 Publication
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Lv, J., Li, N. and Niu, D.K.* (2008) Association between the availability of environm
ental resources and the atomic composition of organismal proteomes: Evidence from Prochlorococcus st
rains living at different depths.
Biochemical and Biophysical Research Communications, 375:241-246.
[Online PDF]
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2008-06-27 Graduation & Admission
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祝贺我实验室六位同学毕业！
毕业生：雒应琴，周红军，朱蕾，周晓婷，赵森，刘晓
欢迎五位同学加入我实验室！
新同学：李臻，李伟，杨宇飞，闫鹏程，曹建立
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2008-06-12 Publication
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Huang, Y.F. and Niu, D.K.* (2008) Evidence against the energetic cost hypothesis for the short introns in highly expressed genes.
BMC Evolutionary Biology, 8:154.
[Online PDF]
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2008-03-02 Publication
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Zhou, H.J. and Lin, K.* (2008) Excess of microRNAs in large and very 5′ biased introns.
Biochemical and Biophysical Research Communications, 368:709-715.
[Online PDF]
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2008-02-20 Publication |
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Guo, J., Wu, X.M., Zhang, D.Y. and Lin, K.* (2008) Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset.
Nucleic Acids Research, 36(6):2002-2011.
[Online PDF] |
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2007-09-25 Awards |
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祝贺我实验室牛登科副教授入选教育部2007年度“新世纪优秀人才支持计划”（自然科学类）！ |
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2007-07-25 Publication |
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Luo, Y.Q., Fu, C., Zhang, D.Y. and Lin, K.* (2007) BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
BMC Bioinformatics, 8:266.
[Online PDF] |
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2007-06-26 Publication |
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Li, S.W., Feng, L. and Niu, D.K.* (2007) Selection for the miniaturization of highly expressed genes.
Biochemical and Biophysical Research Communications, 360:586-592.
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2006-12-28 Awards |
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祝贺我实验室同学在2006年度研究生奖学金评选中获奖！
综合奖学金: 朱蕾(学术优秀型), 冯靓(学术优秀型)
励耘奖学金: 雒应琴(一等奖), 吴晓梅(二等奖) |
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2006-12-18 Publication |
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Wu, X.M., Zhu, L., Guo, J., Fu, C., Zhou, H.J., Dong, D., Li, Z.B., Zhang, D.Y. and Lin, K.* (2006) SPIDer: Saccharomyces protein-protein interaction database.
BMC Bioinformatics, 7:S16.
[Online PDF] |
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2006-12-18 Seminar |
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Title: Novelties in Genomes
Speaker: Dr. Wen Wang (王文), Kunming Institute of Zoology, Chinese Academy of Sciences
Venue: The Bioinformatics Training Center, College of Life Sciences
Time: 10:30-11:30, Friday, Dec 22 2006 |
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2006-12-18 Seminar |
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Title: Evolution of spliceosomal introns and alternative splicing
Speaker: Dr. Scott Roy, Allan Wilson Centre for Molecular Ecology and Evolution, Massey University
Venue: The Bioinformatics Training Center, College of Life Sciences
Time: 13:00-16:00, Wednesday, Dec 20 2006 |
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2006-12-18 Seminar |
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Title: New Genes Behind Males: Results from Computational Genomics and Gene Replacement Experiments
Speaker: Prof. Dr. Manyuan Long (龙漫远),
Department of Ecology and Evolution, Committee on Genetics, The University of Chicago
Venue: The Bioinformatics Training Center, College of Life Sciences
Time: 10:30-11:30, Tuesday, Dec 19 2006 |
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2006-07-15 Publication |
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Luo, Y.Q., Fu, C., Zhang, D.Y. and Lin, K.* (2006) Overlapping genes as rare genomic markers: the γ-Proteobacteria phylogeny as a case study.
Trends in Genetics, 22(11):593-596.
[Online PDF] |
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2006-07-14 Publication |
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Lin, K.*, Zhu, L. and Zhang, D.Y. (2006) An initial strategy for comparing proteins at the domain architecture level. Bioinformatics, 22(17), 2081-2086.
[Online PDF] |
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2006-05-17
Seminar |
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Title: Assigning Orthologous Duplicated Genes through Duplication Models
Speaker: Zhang Luoxin (Associate Professor), Department of Mathematics, National University of Singapore
Venue: Room 504, College of Life Sciences
Time: 16:00, Wednesday, May 17 2006 |
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2005-04-20 Seminar |
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新加坡基因组研究院刘建华博士来我实验室进行学术交流及合作洽谈！ |
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2005-03-23 Seminar |
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美国哥伦比亚大学机器学习中心Phil Long博士到我实验室进行学术指导与交流，
报告及讨论内容将主要涉及：机器学习如何应用于蛋白-蛋白相互作用分析等。 |
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2004-11-23 Seminar |
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应林魁副教授邀请新加坡国立大学计算机学院、新加坡信息与通讯研究院Lim
Soon Wong教授和新加坡基因组研究院Prasanna R Kolatkar教授来我院进行学术交流和学术报告。 |
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报告时间：2004.11.23 8:30 - 11:30
报告人： Lim Soon Wong
报告题目： Gene finding and gene feature recognition
报告地点：生物信息学培训中心
报告时间：2004.11.23 14:30 - 17:00
报告人： Prasanna R Kolatkar
报告题目： Experimantal on the X-ray structures of
2 protein with domain swapping
报告地点：生物信息学培训中心 |
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2004-07-31 News |
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热烈祝贺第一届“国家生命科学与技术人才培养基地生物信息学教师暑期研讨班”圆满结束！诚挚的感谢创腾科技有限公司、SGI公司和教育部高等教育出版社的大力支持！ |
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