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.
SP081 (2 Credit Hours): Bio-computing and Biological Intelligence, a undergraduate-level course;
CS469 (3 Credit Hours): Algorithms in Computational Biology, a graduate-level course;
CS424 (3 Credit Hours): Artifical Intelligence - A Machine Learning Approach, a undergraduate-level course;
Englishing Writing for PhD Students (2 Hours)
Part One: Selected Peer-Reviewed Journal Articles
YA MA, QJ Tan, RS Yuan, B Yuan, P Ao (2013), Potential Function in a Continuous Dissipative Chaotic System: Decomposition Scheme and Role of Strange Attractor. International Journal of Bifurcation and Chaos (in press);
KC Tang, P Ao, B Yuan (2013), Robust reconstruction of the Fokker-Planck equations from time series at different sampling rates. Europhysics Letters, 102(4):40003;
RS Yuan, XA Wang, YA MA, B Yuan, P Ao (2013), Exploring a noisy van der Pol type oscillator with a stochastic approach. Physical Review E, 87(6):062109.5;
Y Tang,RS Yuan, YA Ma (2012), Dynamical Behaviors Determined by the Lyapunov Function in Competitive Lotka-Volterra Systems, Physical Review E , 2013, 87 (1), 012708；
NY Guan, DC Tao, ZG Luo and B Yuan (2012): NeNMF: An optimal gradient method for solving non-negative matrix factorization and its variants, IEEE Transactions on Signal Processing 60(6):2882-2898;
JH Shi, TQ Chen, R Yuan, B Yuan, P Ao (2012): Relation of a New Interpretation of Stochastic Differential Equations to Ito Process, J. Statistical Phys 148:579-590;
NY Guan, DC Tao, ZG Luo and B Yuan (2012): Online Nonnegative Matrix Factorization with Robust Stochastic Approximation, IEEE Transactions on Neural Networks and Learning Systems 23(7):1087-1099;
Wan et al (2011) Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography, J. Structural Biology 175(3):277-287;
NY Guan,DC Tao,ZG Luo,B Yuan (2011): Non-Negative Patch Alignment Framework. IEEE Transactions on Neural Networks 22(8): 1218-1230;
T Sun, R Yuan et al (2011): Exploring a minimal two-component p53 model, Physical Biology 7(3):1478-1489;
NY Guan, DC Tao, ZG Luo, B Yuan (2011): Manifold Regularized Discriminative Nonnegative Matrix Factorization with Fast Gradient Decent. IEEE Transactions on Image Processing 20(7): 2030-2048;
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 JF, 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, H?m?l?inen 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 U S A, 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 U S A, 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
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.