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： 网络计算实验室


研究兴趣
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工作经验
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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 CreditHours): Bio-Computing and Biological Intelligence, an undergraduate-levelcourse;
CS469 (3 CreditHours): Algorithms in Computational Biology, a graduate-level course;
CS410 (3 CreditHours): Artificial Intelligence, an undergraduate-level course;
EE359 (3 CreditHours): Data Mining Techniques, an undergraduate-level course;
English Writing(2 Credit Hours): Scientific Writing for Ph.D. students.


Part One: Selected Peer-Reviewed JournalArticles

LiuQ,WangYB;andYuanB.*;MatrixFactorizationfromaFewDominators,NeuralNetworksandLearningSystem,
IEEE/ACMTransactions onYear:2018,Nov;29(11):**.
WangY.;LiuQ;Yuan,B.*;TheLearningofaStructuralandFunctionalRepresentationforGeneExpressions:

ToRobustlyDissectComplexCancerPhenotypes,ComputationalBiologyandBioinformatics,IEEE/ACMTransactionson
Year:2018,15(1):1-14;

Cui FS; Yuan B.*;Fixation Probability of aBeneficial Mutation Conferring Decreased Generation Time in ChangingEnvironment, BMC Systems Biology, 2018,

Wang Y, Qian W, Yuan B. A graphical modelof smoking-induced global instability in lung cancer[J]. IEEE/ACM Transactionson Computational Biology and Bioinformatics, 2016,DOI10.1109/TCBB.2016.**.

Wang Y, Liu Q, Yuan B. Learning LatentVariable Gaussian Graphical Model for Biomolecular Network with Low SampleComplexity[J]. Computational and Mathematical Methods in Medicine, PMID:**, PMCID:PMC**,2016.

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

Cui F, Yuan B, Dynamics of morphologicalevolution in experimental Escherichia coli populations, Genetics and MolecularResearch, 2016, 15(3): gmr,**.

Wang Y, Qian W, Zhang S, et al. A LearningAlgorithm 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 ofmorphological stability in a long-term experiment with Escherichia coli[J]. IETsystems 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 ofBifurcation and Chaos. 24(02):**.

Tang KC, Ao P, Yuan B (2013). Robustreconstruction of the Fokker-Planck equations fromtime series atdifferent 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 stochasticapproach. Physical Review E, 87(6):062109.
Guan NY, Tao DC, Luo ZG, and Yuan B (2012). Online nonnegative matrixfactorization with robust stochastic approximation. IEEE Transactions on NeuralNetworks and LearningSystems, 23(7):1087-1099.

Shi JH, Chen TQ, Yuan RS, Yuan B, Ao P(2012). Relation of a new interpretation of stochasticdifferentialequations 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 factorizationand its variants. IEEE Transactions on SignalProcessing, 60(6):2882-2898.

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

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

Wan X, Zhang F, Chu Q, Zhang K, Sun F, YuanB, Liu ZY (2011). Three-dimensional reconstruction using an adaptivesimultaneous 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 fastgradient 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 schedulingscheme for a multi-objectiveoptimization on identical parallel machines. Studies inComputationalIntelligence,209:43-55.
Xu J et al. (2007) The genome of Malassezia globosa reveals specific lifestyleadaptations in a fungus associated with human skin diseases, Proc Natl Acad SciUSA, 104:18730-18735.
Chen J F, and Yuan B (2006) Detection of functional modules in the yeastprotein-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 annotationand 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 intothe human genome draft. Genome Research, 11:904-918.
Joensuu T, Hamalainen R, Yuan B, Johnson C, Tegelberg S, Gasparini P, ZelanteL, Pirvola U, Pakarinen L, Lehesjoki AE, de la Chapelle A, Sankila EM (2001)Mutations in a novel gene with transmembrane domains underlie Usher syndrometype 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 laChapelle A (2001). Mutations in the RNA component of RNase MRP cause apleiotropic human disease, cartilage-hair hypoplasia. Cell, 104:195-203.
Virtaneva K, Wright FA, Tanner SM, Yuan B, Lemon WJ, Caligiuri MA, BloomfieldCD, de La Chapelle A, Krahe R (2001). Expression profiling revealsfundamental biological differences in acute myeloid leukemia with isolatedtrisomy 8 and normal cytogenetics. Proc Natl Acad Sci USA, 98:1124-1129.
Chadwick RB, Jiang GL, Bennington GA, Yuan B, Johnson CK, Stevens MW, NiemannTH, Peltomaki P, Huang S, de la Chapelle A (2000). Candidate tumor suppressorRIZ is frequently involved in colorectal carcinogenesis. Proc Natl AcadSci USA, 97:2662-2667.
Majumder S, Ghoshal K, Li Z, Yuan B, Jacob ST (1999). Silencing ofmetallothionein-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-inducedoral cavity tumors. Oncogene, 15:1161-1170
Yuan B, Hu LH, Lentsch EM, Shum-Siu A, Hendler FJ (1997) Consistent allelicloss on mouse chromosome 7 distal to tyrosinase in 4NQO-induced oral cavitytumors 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 DNApolymorphisms 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 withoutadditional exposure. Cancer Research, 54:5310-5317.

Part II. Selected Peer-Reviewed ConferenceArticles



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

Tang KC, Yuan B (2013). Markovreconstruction of financial time series. The 4th InternationalConferenceon Intelligent Control and Information Processing, Beijing, China, 432-436.

Xu S, Jiao SY, Jiang PY, Cui FS, Yuan B, AoP (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 ofmorphological 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 onSystems
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 ControlConference, 6573-6580.

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

Zhang F, Xu L, Liu ZY, Yuan B (2007). UsingDomain-Based Structural Ensemble to Improve Structure Modeling. IEEE 7thInternational 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 ConservedStems for Accurate Structural Alignment of RNA Sequences. IEEE 7thInternational 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 ofpossible RNA secondary structures using multiple sequence alignments. The 22ndAnnual ACM Symposium on Applied Computing - Bioinformatics Track. Seoul, Korea.March 2007.
Zhang F, Xu L, Liu ZR, Yuan B (2007) Improve structural modeling based onconserved domain clusters and structure-anchored alignments. The 22nd AnnualACM Symposium on Applied Computing, Bioinformatics Track. Seoul, Korea. March2007.
Zhang F, Xu L, Chen JC, Liu ZY, Yuan B (2006) A method to integrate, assess,and characterize protein-protein interactions. 2006 IEEE Symposium onComputational 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 onconserved domain clusters. The 20th International Parallel & DistributedProcessing Symposium (IPDPS), workshop on High Performance ComputationalBiology. Rhodes Island, Greece. April 2006.
Zhang F, Feng SZ, Ozer H, Yuan B (2005) Clustering orthologs based on sequenceand domain similarities. The 8th International Conference onHigh-Performance Computing in Asia-Pacific Region, Beijing, China. November2005. p645-651.
Zhang F, Liu ZY, Chen J, Yuan B (2004) The construction of structural templatesfor the modeling of conserved protein domains. International Conference onBioinformatics and its Applications (ICBA’04), Fort Lauderdale, USA. December,2004.
Ozer, H., Chen, J., Zhang, F. and Yuan B (2004) Clustering of eukaryoticorthologs using the Markov graph-flow algorithm. International Conference onBioinformatics and its Applications (ICBA’04), Fort Lauderdale, USA. December,2004.
Lauria M, Bhalerao K, Pugalanthiran MM, and Yuan B (2004) Computationalmodeling of transcription machinery - The use of memory elements and bistableswitches as part of transcriptional logics. The 10th InternationalConference on DNA Computing. Milan, Italy. July 2004.
Lauria M, Bhalerao K, Pugalanthiran MM, Yuan B (2004) Building blocks of abiochemical CPU based on DNA transcription logic, 3rd Workshop on Non-SiliconComputation (NSC-3), Munich, Germany. June 2004.
Chen JF, Gibbs S, Sears R, Zhang F, and Yuan B (2004) Validation of conservedprotein-protein interactions by shape complementarity-based Houghtransformation. 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 iterativealgorithm for whole-genome assembly. Second Asia-Pacific BioinformaticsConference CRPIT, 29:145-153.










The Ministry of Education, China (985-2, 2008-2010);
The Natural Science Foundation of China (4 regulargrants, 2011-2014, 2012-2015, 2014-2018, 2015-2019);
The Ministry of Science and Technology (863,2014-2016)

2012.05 Research works in sparsitymodeling selected as one of the top 100 high impactpublications for theyear of 2011, Chinese Academia of Sciences, Beijing, China
2005.06 Joint Professor, NationalUniversity of Defense Technology, Changsha, China
2003.12 All time 10 most-viewed articlespublished by BioMed Central, UK
2002.10 Research work selected as one ofthe ten most significant achievements alltime at the OSUMedicalCenter, in “Historical Overview ofCancer ResearchAchievements at Ohio State” 2001-2002, and 2003-2003Annual Reports,Columbus, Ohio, USA
2002.09 Selected as one of the 30candidates (nationwide) for the AnnualDistinguishedYoungInvestigator Award of US(Keck Foundation), USA
2002.08 Research work featured in TheScience Coalition, an organization thatrepresents more than 100universities nationwide to strengthen thefederalgovernment’sinvestment in university-based scientificresearch, Washington DC, USA
2002.04 Guest Investigator, ChineseGenome Center, Beijing, China
2002.03 Guest Professor, HuazhongUniversity of Science and Technology, China
2002.03 Guest Professor, LanzhouUniversity, China
2001.10 Research workfeatured inThe Scientist (2001) October 15, “Human Genes:How Many? Consolidation oftranscript and protein databases suggests humansmay have more than 70,000genes”, USA
2001.09 President’s Letter forExcellence in Research, The Ohio State University, USA
2001.07 Research work featured in TheEconomist (2001) July 12, “Human Genome: thinkof a number, then doubleit”, London, UK
2001.07 Research work featured on many magazines,web sites, andnewspapers around the world, including NY Times, CanberraTimes, etc
2001.07 Research work featured in BBC(2001) July 8, “Disputes over number ofhuman genes”, London, UK
2001.06 Honorary Speaker, Solid Session,Nanyang Polytechnic University, Singapore
2001.05 Research work featured in TheNew Scientist (2001) May 5, Human GenomeAnalysis”, Washington DC, USA
2001.02 Featured in People in the News,Bioinform (2001) February 18, USA.
2001.02 Research work featured in GenomeBiology (2001) February 12,“Researchers to publish a third historic humangenome article this week”, London, UK
1994.04 Honorary Mention, The XXNational Medical Research Forum, Galveston, TX, USA
1994.03 Travel Award, American MedicalAssociation, Washington DC, USA
1994.03 Dean’s Letter for Excellence inResearch, University of Louisville School of Medicine, KY, USA
1994.03 First Place Award, The XXVMidwest Medical Research Forum, Omaha, USA
1993.11 Travel Award, Midwest MedicalResearch Forum, Omaha, USA
1993.10 The First Place Award, StudentResearch Day, University LouisvilleMedical School, USA
1990.06 Graduate Fellowship, Universityof Louisville Medical School, USA

2012.09 Member of Expert Committee,Chinese 973 Lead Project on “Synthetic Biology”,the Ministry of Scienceand Technology, Beijing, China
2012.09 Member of Expert Committee,Chinese 973 Lead Project on “The Basis ofIntelligence”, the Ministry ofScience and Technology, Beijing, China
2005.07 Chairman, Session of SystemsBiology and Bioinformatics, the 6th World MultiConference on Systemics,Cybernetics and Informatics, Orlando, Florida, USA
2004.12 Member, Steering Committee, the6th International Conference on Bioinformaticsand Its Applications, FortLauderdale, Florida, USA
2004.01 Member, Academia Sinica ReviewPanel, “National Research Program forGenomic Medicine”, Taipei
2003.04 External Board Member, KentuckyScience and Engineering Foundation, USA
2002.06 Member, Research AdvisoryCommittee, the OSU Medical Center, Columbus, USA
2001.06 Program Committee Member, andChairman of the Computational Biology andBioinformatics Session, The 2001International Symposium on InformationSystems and Engineering, Las Vegas,Nevada, USA
1999.09 Session Chair, Bioinformaticsand Microarray Technology,The Annual Stone Meeting, Put-In-Bay, Ohio, USA