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农业生物技术国家重点实验室学术报告

题目：应用于生物大数据时代的云平台

主讲： Dr. Changhui Yan

Associate Professor (Tenured), North Dakota State University

时间：2015年7月21日 周二上午10:30-11:30am

地点：生命科学中心2018会议室

 

NGS（Next Generation Sequencing) 技术的迅猛发展和应用为我们带来了海量的基因序列信息，并把生物科学带入了大数据时代。 如何高效的从这些大数据中挖掘出有用的东西是生物信息学和基因组学共同面临的挑战。大数据在储存，传输，和分析等各个环节都对计算方法和硬件平台提出了新的要求。要对一个大型的基因组进行组装，或者对转录组进行比较分析，往往需要比较强大的计算设备。购买和管理这些设备对大多数中小型的生物实验室来说是一个沉重的负担。即使假设每个实验室都能负担得起，一个学校拥有多套独立的计算设备也不是一种经济合理的方案。因为一个实验室可能花多数的时间来准备生物样品和进行相关实验，需要计算分析的时间相对还是少数。这样就造成了昂贵的计算设备在大多数的时间里处于闲置状态。云计算运用虚拟化技术，可以让多用户有效的分享同一套设备。 这样可以极大的提高设备利用率，从总体上减少开支。我们在北达科达州立大学搭建一个基于 OpenStack 的云平台供本校老师和美国农业部的合作者用于 NGS 分析。为了让没有生物信息和计算机背景的合作者也能很好的应用NGS到他们的研究中去，我们根据合作者各种任务的不同特点设计和优化了一系列的简单易用的分析流程。运用我们的云平台，合作者可以快速的从原始的基因序列数据中挖掘出有用的知识。

 

Education

Ph.D. Computer Science, Bioinformatics & Computational Biology, 2005, Iowa State University, Ames, USA.

M.S. Cellular & Molecular Biology, 2000, Peking University, Beijing, China.

B.S.  Genetics and Cell Biology, 1997, Peking University, Beijing, China.

Employment

Aug, 2014-Present     Associate Professor, Department of Computer Science, North Dakota State University, Fargo, ND, USA

Jan, 2010-Aug, 2014  Assistant Professor, Department of Computer Science, North Dakota State                    University, Fargo, ND, USA

Aug, 2005-Dec, 2009       Assistant Professor, Department of Computer Science, Utah State                                  University, Logan, UT, USA

Selected Publications from Total 35 peer-reviewed articles and book chapters:

1.      Horvath, D.P., Hansen, S.A., Moriles-Miller, J.P., Pierik, R., Yan, C., Clay, D.E., Scheffler, B., Clay, S.A. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. New Phytologist. 2015 Feb 25. doi: 10.1111/nph.13351. [Epub ahead of print].

2.      Singh, R.K., Cho, K., Padi, S.K., Yu. J., Haldar, M., Mandal. T., Yan, C., Cook, G., Guo, B., Mallik, S., Srivastava, D.K. Mechanism of N-acylthiourea Mediated Activation of Human Histone Deacetylase 8 (HDAC8) at Molecular and Cellular levels. J Biol Chem. 2015 290(10):6607-6619.

3.      LeBoldus, J.M., Kinzer, K., Zhu, Y., Yan, C., Friesen, T. and Brueggeman, R. Genotype-by-sequencing of the plant pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology. Molecular Plant Pathology 2014 Oct 24. doi: 10.1111/mpp.12214. [Epub ahead of print].

4.      Yan, C., Y. Wang. A Graph Kernel Method for DNA-Binding Site Prediction. BMC Systems Biology 2014, 8(Suppl 4): S10.

5.      Shjerve, R.A., Faris, JD, Brueggeman, R.S., Yan, C., Zhu Y., Koladia, V., Friesen T.L. Evaluation of a Pyrenophora teres f. teres mapping population  reveals multiple independent interactions with the barley 6H chromosome region. Fungal Genetics and Biology 2014, 70:104-112.

6.      Cheng, W. and Yan, C. Detecting Periodicity Associated with the Alpha-Helix Structure Using Fourier Transform. Computational Molecular Bioscience 2012, 2(4):109-114.

7.      Alvarez, M. and Yan, C. A new protein graph model for function prediction. J Comp. Bio. Chem. 2012, 37：6-10.

8.      Alvarez, M. and Yan, C. A graph-based semantic similarity measure for the gene ontology. J Bioinform Comput Biol. 2011, 9(6): 1–15.

9.      Alvarez, M., Qi, X. and Yan, C. A shortest-path graph kernel for estimating gene product semantic similarity. J Biomed Semantics, 2011, 2:3.

10.  Yan, C. and Luo, J. An Analysis of Reentrant Loops. Protein J. 2010, 29(5):350-4.

11.  Hu, J. and Yan, C. A comparative analysis of protein interfaces.  Protein Pept Lett. 2010, 17(11):1450-1458.

12.  Hu, J. and Yan, C., A tool for calculating binding-site residues on proteins from PDB structures. BMC Struct Biol. 2009, 9:52.

13.  Ju, W., Shan, J., Yan, C., and Cheng, H. Discrimination of disease-related non-synonymous single nucleotide polymorphisms using multi-scale RBF kernel fuzzy support vector machine. Pattern Recognition Letters 2009, 30:391-396.

14.  Hu, J. and Yan, C. Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information BMC Bioinformatics 2008, 9:297.

15.  Yan, C., Hu, J. and Wang, Y. Discrimination of outer membrane proteins with improved performance. BMC Bioinformatics 2008, 9:47.

16.  Hu, J. and Yan, C. A Method for discovering transmembrane beta-barrel proteins in gram-negative bacterial proteomes. Computational Biology and Chemistry 2008 32:298-301.

17.  Yan, C., Hu, J. and Wang, Y. Discrimination of outer membrane proteins using a K-nearest neighbor method. Amino Acids 2008 35(1):65-73.

18.  Hu, J., and Yan, C. An improved method for alpha-helical transmembrane protein topology prediction. Bioinformatics and Biology Insights 2008 2: 67-74.

19.  Yan, C., Wu, F., Jernigan, R.L., Dobbs, D., and Honavar V. Characterization of protein-protein interfaces. The Protein Journal 2008 27(1):59-70.