教师名录

苑 波 教授

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办公室电话:+86-21-3420-6341

办公地点:SEIEE-3-424

电子邮件:yuanbo@cs.sjtu.edu.cn

实验室:

  • 研究兴趣
  • 教育背景
  • 工作经验
  • 教授课程
  • 论文发表
  • 项目资助
  • 获奖信息
  • 学术服务
Understanding the biological circuits that perform computations within the cell is a central problem in computational and systems biology. From the point of view of informatics and systemics, biology offer the challenge of understanding the complex behaviors of interacting molecules evolved to operate with both remarkable precision and robustness in the context of genes, environments and their complex interactions. The theme of our research is stochasticity, central to properly capture both the stability and the multiple sources of uncertainties needed for modeling biosystems in a realistic way. We are developing analytical and computational frameworks to model such complex and stochastic behaviors using a combined discrete (Markov Chain) and continuous (Stochastic Differentials) approach, starting from bi-stable switches, limited cycles to feed-forward loops as well as their coupling. Our goal is to adequately describe observed stochasticity, variations and heterogeneity in biological systems for multiple scales of biological organizations.
1990-1995 Ph.D., Molecular Genetics, University of Louisville School of Medicine, USA 
1987-1989 M.S.,  Biochemistry, University of Louisville, USA  
1978-1983 B.S.,  Beijing Medical College (Currently Peking University Medical School), Beijing, China
2006-present Professor, Dept. of Computer Science and Engineering, Shanghai Jiaotong University, China
2002-2006    Co-Director, Pharmacogenomics Program, The Ohio State University, USA
2002-2006    Assistant Professor (Tenure-Track), Departments of Biomedical Informatics and Pharmacology, the Ohio State University, USA
1997-2002    Research Scientist, Human Cancer Genetics Program, The Ohio State University, USA
1995-1997    Postdoctoral Fellow, Brown Cancer Center, University of Louisville, USA  

SP081 (2 Credit Hours): Bio-Computing and Biological Intelligence, an undergraduate-level course;

CS469 (3 Credit Hours): Algorithms in Computational Biology, a graduate-level course;

CS410 (3 Credit Hours): Artificial Intelligence, an undergraduate-level course;

EE359 (3 Credit Hours): Data Mining Techniques, an undergraduate-level course;

English Writing (2 Credit Hours): Scientific Writing for Ph.D. students. 


Part One: Selected Peer-Reviewed Journal Articles

Wang Y, Liu Q, Huang S, Yuan B. Learning a structural and functional representation for
gene expressions: To robustly dissect complex cancer phenotypes[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016,DOI 10.1109/TCBB.2017.2702161.


Wang Y, Qian W, Yuan B. A graphical model of smoking-induced global instability in lung cancer[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016,DOI 10.1109/TCBB.2016.2599867.


Wang Y, Liu Q, Yuan B. Learning Latent Variable Gaussian Graphical Model for Biomolecular Network with Low Sample Complexity[J]. Computational and Mathematical Methods in Medicine, PMID: 27843485, PMCID:PMC5097857,2016.


Wang J, and Yuan B. Curl flux induced drift in stochastic differential equations in the zeromass limit[J]. Physica A: Statistical Mechanics and its Applications, 2016, 462:898-911.


Cui F, Yuan B, Dynamics of morphological evolution in experimental Escherichia coli populations, Genetics and Molecular Research, 2016, 15(3): gmr,15038991.


Wang Y, Qian W, Zhang S, et al. A Learning Algorithm for Bayesian Networks and Its Efficient Implementation on GPU[J]. Parallel & Distributed Systems IEEE Transactions on, 2016, 27(1):17-30.


Cui F, Yuan B. Evolutionary dynamics of morphological stability in a long-term experiment with Escherichia coli[J]. IET systems biology, 2014, 9(1): 25-30.


Ma YA, Tan QJ, Yuan RS, Yuan B, Ao P (2014). Potential function in a continuous dissipative chaotic System: decomposition scheme and role of strange attractor. International Journal of Bifurcation and Chaos. 24(02):1450015.

 

Tang KC, Ao P, Yuan B (2013). Robust reconstruction of the Fokker-Planck equations from time series at different sampling rates. Europhysics Letters, 102(4):40003.

 

Yuan RS, Wang XA, Ma YA, Yuan B, Ao P (2013). Exploring a noisy van der Pol type oscillator with a stochastic approach. Physical Review E, 87(6):062109.

Guan NY, Tao DC, Luo ZG, and Yuan B (2012). Online nonnegative matrix factorization with robust stochastic approximation. IEEE Transactions on Neural Networks and Learning Systems, 23(7):1087-1099.

Shi JH, Chen TQ, Yuan RS, Yuan B, Ao P (2012). Relation of a new interpretation of stochastic differential equations to Ito process. Journal of Statistical Physics, 148(3):579-590.

 

Guan NY, Tao DC, Luo ZG and Yuan B (2012). NeNMF, An optimal gradient method for solving non-negative matrix factorization and its variants. IEEE Transactions on Signal Processing, 60(6):2882-2898.

Xu W, Yuan B, Ao P (2011). Construction of Lyapunov function for dissipative gyroscopic system. Chinese Physics Letters, 28:050201.

Guan NY, Tao DC, Luo ZG, Yuan B (2011). Non-negative patch alignment framework. IEEE ransactions on Neural Networks, 22(8):1218-1230.


Wan X, Zhang F, Chu Q, Zhang K, Sun F, Yuan B, Liu ZY (2011). Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron
tomography. J. Structural Biology, 175(3):277-287.

Guan NY, Tao DC, Luo ZG, Yuan B (2011). Manifold regularized discriminative nonnegative matrix factorization with fast gradient decent. IEEE Transactions on Image Processing, 20(7):2030-2048.

Fan LY, Zhang F, Wang GM, Yuan B, Liu ZY (2009). A self-adaptive greedy scheduling scheme for a multi-objective optimization on identical parallel machines. Studies in Computational Intelligence, 209:43-55.


Xu J et al. (2007) The genome of Malassezia globosa reveals specific lifestyle adaptations in a fungus associated with human skin diseases, Proc Natl Acad Sci USA, 104:18730-18735.  

Chen J F, and Yuan B (2006) Detection of functional modules in the yeast protein-protein interaction network, Bioinformatics, 22(18): 2283-2290. 

Wright FA, Lemon WJ, Zhao WD, Sears R, Zhuo D, Wang JP, Yang HY, Baer T, Stredney D, Spitzner J, Stutz A, Krahe R, and Yuan B (2001) A draft annotation and overview of the human genome.  Genome Biology, 2(25):1-18. 

Zhuo D, Zhao DW, Yang HY, Wang JP, Sears R, Kwon DH, Gordon D, Gibbs S, Dai D, Yang Q, Baer T, Spitzner J, Stredney D, Stutz A, Krahe R, Wright FA, and Yuan B (2001) Assembly, functional annotation and integration of UNIGENE clusters into the human genome draft.  Genome Research, 11:904-918. 

Joensuu T, Hamalainen R, Yuan B, Johnson C, Tegelberg S, Gasparini P, Zelante L, Pirvola U, Pakarinen L, Lehesjoki AE, de la Chapelle A, Sankila EM (2001) Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3.  Am. J. Hum. Genetics, 69:673-684.  

Ridanpaa M, van Eenennaam H, Pelin K, Chadwick R, Johnson C, Yuan B, vanVenrooij W, Pruijn G, Salmela R, Rockas S, Makitie O, Kaitila I, de la Chapelle A (2001).  Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia.  Cell, 104:195-203.  

Virtaneva K, Wright FA, Tanner SM, Yuan B, Lemon WJ, Caligiuri MA, Bloomfield CD, de La Chapelle A, Krahe R (2001).  Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics.  Proc Natl Acad Sci USA, 98:1124-1129.  

Chadwick RB, Jiang GL, Bennington GA, Yuan B, Johnson CK, Stevens MW, Niemann TH, Peltomaki P, Huang S, de la Chapelle A (2000). Candidate tumor suppressor RIZ is frequently involved in colorectal carcinogenesis.  Proc Natl Acad Sci USA, 97:2662-2667.  

Majumder S, Ghoshal K, Li Z, Yuan B, Jacob ST (1999). Silencing of metallothionein-I gene in mouse lymphosarcoma cells by DNA methylation.  Oncogene, 18:6287-6295. 

Yuan B, Oechsli MN, Hendler FJ (1997). A region within murine chromosome 7F4, syntenic to the human 11q13 amplicon, is frequently amplified in 4NQO-induced oral cavity tumors.  Oncogene, 15:1161-1170 

Yuan B, Hu LH, Lentsch EM, Shum-Siu A, Hendler FJ (1997) Consistent allelic loss on mouse chromosome 7 distal to tyrosinase in 4NQO-induced oral cavity tumors with loss of heterozygosity at Ha-ras-1.  Molecular Carcinogenesis, 19:8-16. 

Yuan B, Shum-Siu A, Lentsch EM, Hu LH, Hendler FJ (1996). Frequent DNA polymorphisms exist in inbred CBA/J and C3H/HeN mice.  Genomics, 38:58-71. 

Yuan B, Heniford BW, Ackermann DM, Hawkins BL, Hendler FJ (1994) Harvey ras (H-ras) point mutations are induced by 4NQO in murine oral squamous epithelia, while squamous cell carcinomas and loss of heterozygosity occur without additional exposure.  Cancer Research, 54:5310-5317. 


Part II. Selected Peer-Reviewed Conference Articles


Wang Y, Liu Q, Huang S, Yuan B. Learning a structural and functional representation for
gene expressions: To robustly dissect complex cancer phenotypes [C]//2016 IEEE International Conference on Systems Biology (ISB). IEEE, 2016.


Tang KC, Yuan B (2013). Markov reconstruction of financial time series. The 4th International Conference on Intelligent Control and Information Processing, Beijing, China, 432-436.

 

Xu S, Jiao SY, Jiang PY, Cui FS, Yuan B, Ao P (2012). Escape from Infinite Adaptive
Peak. Proceedings of 2012 IEEE Conference on Systems Biology, X’ian, China, 268-273.

 

Cui FS, Yuan B (2012). Analysis of morphological evolution in a long-term experiment with
Escherichia Coli. Proceedings of 2012 IEEE Conference on Systems Biology, X’ian, China, 211-215.

 

Jiao SY, Wang YB, Yuan B, Ao P (2012). Dynamics of Coexistence of Asexual and Sexual
Reproduction in Adaptive Landscape. Proceedings of 2012 IEEE Conference on Systems
Biology, X’ian, China, 192-196.

 

Jiao, SY, Wang YB, Yuan B, Ao P (2011). Kinetics of Muller’s Ratchet from Adaptive
Landscape Viewpoint. Proceedings of 2011 IEEE Conference on Systems Biology, 27-32.

 

Yuan RS, Ma YA, Yuan B, Ao P (2011). Potential Function in Dynamical Systems and the
Relation with Lyapunov Function. Proceedings of the 30th Chinese Control Conference, 6573-6580.

 

Liu GL, Luo ZG, Yuan B, Ma XT (2009). A fast binary image segmentation algorithm and its
application to in situ hybridization data. Proceeding s of the 2nd International Conference on
Biomedical Engineering and Informatics (BMEI’09).

 

Zhang F, Xu L, Liu ZY, Yuan B (2007). Using Domain-Based Structural Ensemble to Improve Structure Modeling.  IEEE 7th International Symposium on Bioinformatics and Biomedical Engineering (BIBE), Boston, USA. Oct. 14-17, 2007.  


Fang XY, Luo ZG, Yuan B, and Wang ZH (2007) Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences.  IEEE 7th International Symposium on Bioinformatics and Biomedical Engineering (BIBE), Boston, USA. Oct. 14-17, 2007.  

Fang XY, Wang ZH, Luo ZG, Yuan B, Ding F (2007) The detection and assessment of possible RNA secondary structures using multiple sequence alignments. The 22nd Annual ACM Symposium on Applied Computing - Bioinformatics Track. Seoul, Korea. March 2007. 

Zhang F, Xu L, Liu ZR, Yuan B (2007) Improve structural modeling based on conserved domain clusters and structure-anchored alignments. The 22nd Annual ACM Symposium on Applied Computing, Bioinformatics Track. Seoul, Korea. March 2007. 

Zhang F, Xu L, Chen JC, Liu ZY, Yuan B (2006) A method to integrate, assess, and characterize protein-protein interactions.  2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computation Biology (CIBCB), Toronto, Canada. September 2006. P16-22.  

Zhang F, Xu L, Yuan B (2006) A method to improve structural modeling based on conserved domain clusters. The 20th International Parallel & Distributed Processing Symposium (IPDPS), workshop on High Performance Computational Biology.  Rhodes Island, Greece. April 2006. 

Zhang F, Feng SZ, Ozer H, Yuan B (2005) Clustering orthologs based on sequence and domain similarities.  The 8th International Conference on High-Performance Computing in Asia-Pacific Region, Beijing, China. November 2005. p645-651. 

Zhang F, Liu ZY, Chen J, Yuan B (2004) The construction of structural templates for the modeling of conserved protein domains. International Conference on Bioinformatics and its Applications (ICBA’04), Fort Lauderdale, USA. December, 2004. 

Ozer, H., Chen, J., Zhang, F. and Yuan B (2004) Clustering of eukaryotic orthologs using the Markov graph-flow algorithm. International Conference on Bioinformatics and its Applications (ICBA’04), Fort Lauderdale, USA. December, 2004. 

Lauria M, Bhalerao K, Pugalanthiran MM, and Yuan B (2004) Computational modeling of transcription machinery - The use of memory elements and bistable switches as part of transcriptional logics.  The 10th International Conference on DNA Computing. Milan, Italy. July 2004. 

Lauria M, Bhalerao K, Pugalanthiran MM, Yuan B (2004) Building blocks of a biochemical CPU based on DNA transcription logic, 3rd Workshop on Non-Silicon Computation (NSC-3), Munich, Germany. June 2004. 

Chen JF, Gibbs S, Sears R, Zhang F, and Yuan B (2004) Validation of conserved protein-protein interactions by shape complementarity-based Hough transformation. Fifth International Conference on Software Engineering, Artificial Intelligence, and Parallel/Distributed Computing. Beijing, China. May 2004. 

Wang DL, Lauria M, Wright F, and Yuan B (2004) Megaweaver: an iterative algorithm for whole-genome assembly.  Second Asia-Pacific Bioinformatics Conference CRPIT, 29:145-153.


The Ministry of Education, China (985-2, 2008-2010);

The Natural Science Foundation of China (4 regular grants, 2011-2014, 2012-2015, 2014-2018, 2015-2019);

The Ministry of Science and Technology (863, 2014-2016)

 

2012.05 Research works in sparsity modeling selected as one of the top 100 high impact publications for the year of 2011, Chinese Academia of Sciences, Beijing, China

 

2005.06 Joint Professor, National University of Defense Technology, Changsha, China

 

2003.12 All time 10 most-viewed articles published by BioMed Central, UK

 

2002.10 Research work selected as one of the ten most significant achievements all time at the OSU Medical Center, in “Historical Overview of Cancer Research Achievements at Ohio State” 2001-2002, and 2003-2003 Annual Reports, Columbus, Ohio, USA

 

2002.09 Selected as one of the 30 candidates (nationwide) for the Annual Distinguished Young Investigator Award of US (Keck Foundation), USA

 

2002.08 Research work featured in The Science Coalition, an organization that represents more than 100 universities nationwide to strengthen the federal government’s investment in university-based scientific research, Washington DC, USA

 

2002.04 Guest Investigator, Chinese Genome Center, Beijing, China

 

2002.03 Guest Professor, Huazhong University of Science and Technology, China

 

2002.03 Guest Professor, Lanzhou University, China

 

2001.10 Research work featured in The Scientist (2001) October 15, “Human Genes: How Many? Consolidation of transcript and protein databases suggests humans may have more than 70,000 genes”, USA

 

2001.09 President’s Letter for Excellence in Research, The Ohio State University, USA

 

2001.07 Research work featured in The Economist (2001) July 12, “Human Genome: think of a number, then double it”, London, UK

 

2001.07 Research work featured on many magazines, web sites, and newspapers around the world, including NY Times, Canberra Times, etc

 

2001.07 Research work featured in BBC (2001) July 8, “Disputes over number of human genes”, London, UK

 

2001.06 Honorary Speaker, Solid Session, Nanyang Polytechnic University, Singapore

 

2001.05 Research work featured in The New Scientist (2001) May 5, Human Genome Analysis”, Washington DC, USA

 

2001.02 Featured in People in the News, Bioinform (2001) February 18, USA.

 

2001.02 Research work featured in Genome Biology (2001) February 12, “Researchers to publish a third historic human genome article this week”, London, UK

 

1994.04 Honorary Mention, The XX National Medical Research Forum, Galveston, TX, USA

 

1994.03 Travel Award, American Medical Association, Washington DC, USA

 

1994.03 Dean’s Letter for Excellence in Research, University of Louisville School of Medicine, KY, USA

 

1994.03 First Place Award, The XXV Midwest Medical Research Forum, Omaha, USA

 

1993.11 Travel Award, Midwest Medical Research Forum, Omaha, USA

 

1993.10 The First Place Award, Student Research Day, University Louisville Medical School, USA

 

1990.06 Graduate Fellowship, University of Louisville Medical School, USA

2012.09 Member of Expert Committee, Chinese 973 Lead Project on “Synthetic Biology”, the Ministry of Science and Technology, Beijing, China

 

2012.09 Member of Expert Committee, Chinese 973 Lead Project on “The Basis of Intelligence”, the Ministry of Science and Technology, Beijing, China

 

2005.07 Chairman, Session of Systems Biology and Bioinformatics, the 6th World Multi Conference on Systemics, Cybernetics and Informatics, Orlando, Florida, USA

 

2004.12 Member, Steering Committee, the 6th International Conference on Bioinformatics and Its Applications, Fort Lauderdale, Florida, USA

 

2004.01 Member, Academia Sinica Review Panel, “National Research Program for Genomic Medicine”, Taipei

 

2003.04 External Board Member, Kentucky Science and Engineering Foundation, USA

 

2002.06 Member, Research Advisory Committee, the OSU Medical Center, Columbus, USA

 

2001.06 Program Committee Member, and Chairman of the Computational Biology and Bioinformatics Session, The 2001 International Symposium on Information Systems and Engineering, Las Vegas, Nevada, USA

 

1999.09 Session Chair, Bioinformatics and Microarray Technology, The Annual Stone Meeting, Put-In-Bay, Ohio, USA

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