陈伯林


的个人主页 http://teacher.nwpu.edu.cn/blchen

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基本信息 The basic information

陈伯林

计算机学院

博士研究生毕业

哲学博士

副教授

计算机科学与技术-计算机软件与理论

教育教学 Education And Teaching

硕士课程编号:105065       硕士留学生课程编号:108629

课程名称:计算生物学

英文译名:Computational Biology

先修要求:数据结构

内容简介:计算生物学是由计算机科学、数学与生物学等多学科交叉形成的一门新兴学科,属于当前自然科学与信息科学领域的前沿研究领域之一。本课程旨在介绍与计算生物学相关的基础知识、研究方法及其应用等方面的内容。在课程内容的安排上,本课程不是简单的将计算机科学、数学以及生物学的知识罗列、组合起来,而是以最基本的生物学知识为基础,以数学知识为工具,介绍计算机科学在生命科学领域的应用。通过本课程的学习,希望帮助学生了解当前生命科学研究领域的热点问题及其研究方法。并通过实例分析的手段训练学生分析问题、解决问题的能力,以提高学生独立的科研能力。本课程的授课对象为计算机相关专业的硕士生和博士生

主要参考书:

[1] Neil C. Jones and Pavel A. Pevzner. An introduction to bioinformatics algorithms. The MIT press, 2004.

[2] Mourad Elloumi and Albert Y. Zomaya Algorithms in computational molecular biology, Wiley, 2011.

招生信息 Admission Information

Positions for master students in Computational Biology are now available. I am interested in recruiting high-caliber undergraduate students who have expertise in the areas of computer science, or applied mathematics. The students who are self-motivated and have publications in relevant scientific journals are encourages to apply.

科学研究 Scientific Research

Research areas

Research areas include but not limit to computational and systems biology, genomic and proteomic data analysis, disease gene identification, protein complex identification, dynamic network analysis, gene methylation data analysis etc.


Grant Information

[3] Feature self-learning method for complex disease gene identification

supported by the National Natural Science Foundation of China (NSFC), No. 61602386, CNY 190K, 2017-2019

[2] Identifying disease related genes by using multiple data integration and logistic regression

supported by the Northwestern Polytechnical University (NPU) under the name of the fundamental research funds for the central Universities (as the additional support for the startup fund for young professionals), No. 3102015JSJ0011, CNY 100K, 2015-2016

[1] Identifying disease related genes by using multiple data integration and logistic regression

supported by the Northwestern Polytechnical University (NPU) under the name the startup fund for young professionals, No. 3102015QD029, CNY 80K, 2015-2016

学术成果 Academic Achievements

Refereed Journal  Papers


[15] C Aouiche(#), B Chen(#,*), XQ Shang.Predicting stage-stepcific cancer related genes and their dynamic modules by integrating multiple datasets. BMC Bioinformatics 2019, accepted (Impact factor: 2.213)

[14] C Aouiche(#), XQ Shang*, B Chen(#,*). Copy number variation related disease genes. Quantitative Biology 2018, 6(2): 99-112.

[13] B Chen, XQ Shang, M Li, JX Wang, FX Wu*. Identifying individual-cancer-related genes by rebalancing the training samples. IEEE Transactions on Nanobioscience2016, 15(4), 309-315. (Impact factor: 1.969) 

[12] XQ Shang, Y Wang, B Chen*. Identifying essential proteins based on dynamic PPI networks and RNA-Seq datasets. SCIENCE CHINA Information Science 2016, 070106. (Impact factor: 0.885)

[11] T Jiang, ZH Li, XQ Shang, B Chen, WB Li, ZL Yin. Constrained query of order-preserving submatrix in gene expression data. Frontiers of Computer Science in China. 2016. Accepted.

[10] B Chen, M Li, JX Wang, XQ Shang and FX Wu. A fast and high performance multiple data integration algorithm for identifying human disease genes. BMC Medical Genomics 2015,8(Suppl 3): S2. (Impact factor: 2.873) 

[9] B Chen, M Li, JX Wang, FX Wu. Disease gene identification by using graph kernels and Markov random fields. SCIENCE CHINA Life Sciences 2014, 57(11), 1054-1063. (Impact factor: 1.512)

[8] W Fan, B Chen, G Selvaraj and FX Wu. Discovering biological patterns from short time-series gene expression profiles with integrating PPI data. Neurocomputing 2014, 145, 3-13. (Impact factor: 2.005, EI Compendex)

[7] B Chen, JX Wang, M Li and FX Wu. Identifying disease genes by integrating multiple data sources. BMC Medical Genomics 2014, 7(Suppl 2): S2. (Impact factor: 3.914)

[6] J Sun, B Chen and FX Wu. An improved peptide-spectral matching algorithm through distributed search over multiple cores and multiple CPUs. Proteome Science 2014 12:18. (Impact factor: 1.878, equally contribution as the first author)

[5] B Chen, W Fan, J Liu and FX Wu. Identifying protein complexes and functional modules – from static PPI networks to dynamic PPI networks. Briefings in Bioinformatics2014, 15(2), 177-194. (Impact factor: 5.919)

[4] B Chen and FX Wu. Identifying protein complexes based on multiple topological structures in PPI networks. IEEE Transactions on Nanobioscience 2013,12(3), 165-172. (Impact factor: 1.768, EI Compendex)

[3] J Shi, B Chen and FX Wu. Unifying protein inference and peptide identification with feedback to updated consistency between peptides. Proteomics 2013, 13(2), 237-247. (Impact factor: 3.973)

[2] B Chen, J Shi, S Zhang and FX Wu. Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy. Proteomics2013, 13(2), 269-277. (Impact factor: 3.973)

[1] Z Yuan, J Shi, W Lin, B Chen and FX Wu. Features-based deisotoping method for tandem mass spectra. Advances in Bioinformatics 2011, Article ID 210805, 12 pages.

P.S. All the impact factors are based on the state of the publication year.


 Refereed Conference Papers:

[12] B Chen(#,*), C Aouiche(#), and X Shang. Integrating multiple datasets to discover stage-specific cancer related genes and stage-specific pathways. Bioinformatics and Biomedical Engineering (IWBBIO 2019), International Conference on (accepted)

[11] P Luo, L Tian,  B Chen, Q Xiao, and FX Wu*. Predicting disease genes from clinical single sample-based PPI networks. Bioinformatics and Biomedical Engineering (IWBBIO 2018), International Conference on, 247-258. (EI Compendex)

[10] P Luo, L Tian, B Chen, Q Xiao, and FX Wu*. Predicting gene-disease associations with manifold learning. Bioinformatics Research and Applications (ISBRA 2018), International Symposium on, 265-271. (EI Compendex)

[9] B Chen, Y Jin, and X Shang*. Net2Image: A network representation method for identifying cancer-related genes Bioinformatics Research and Applications (ISBRA 2017), International Symposium on, 337-343. (EI Compendex)

[8] B Chen, XQ Shang, M Li, J Wang and FX Wu. A two-step logistic regression based algorithm for identifying individual-cancer-related genes. Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, 195-200. (EI Compendex)

[7] B Chen, M Li, J Wang and FX Wu. A logistic regression based algorithm for identifying human disease genes.Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on, 197-200. (EI Compendex)

[6] B Chen, J Wang and FX Wu. Prioritizing human disease genes by multiple data integration. Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on, 621. (EI Compendex)

[5] B Chen, J Shi and FX Wu. Not all protein complexes exhibit dense structures in S. cerevisiae PPI network. Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on, 470-473. (EI Compendex)

[4] B Chen, Y Yan, J Shi, S Zhang and FX Wu. An improved graph entropy-based method for identifying protein complexes. Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on, 123-126. (EI Compendex)

[3] J Shi, B Chen and FX Wu. Improving accuracy of peptide identification with consistency between peptides. Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on, 191-196. (EI Compendex)

[2] B Chen, L Liu and FX Wu. Inferring gene regulatory networks from multiple time course gene expression datasets. Systems Biology (ISB), 2011 IEEE International Conference on, 12-17. (EI Compendex)

[1] B Chen. Topological patterns identification for sneak circuit analysis. Reliability, Maintainability and Safety, 2009, ICRMS 2009. 8th International Conference on, 133-137. (EI Compendex)

 

学术活动 Professional Activities

2018.10.12-14        CBC 2018 - Bioinformatics conference, Xi'an, China

2018.08.18-21        ISB 2018 - International Conference on Computational Systems Biology, Guiyuang, China

2018.03.04-08        Keystone Symposia 2018 - Manipulation fo the gut microbiota for metabolic health, Canmore, Canada