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

2003.12 All time 10 most-viewed articles published by BioMed Central, UK.
2002.10 Research work was selected as one of the ten most significant achievements all time at the OSU Comprehensive Cancer Center, in “Historical Overview of Cancer Research Achievements at Ohio State” 2001-2002, and 2003-2003 Annual Reports.
2002.09 Selected as one of the 30 candidates (nationwide) for the Distinguished Young Investigator Award (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.
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”.
2001.09 President’s Letter for Excellence in Research, The Ohio State University.
2001.07 Research work featured in The Economist (2001) July 12, “Human Genome: think of a number, then double it”.
2001.07 Research work featured in BBC (2001) July 8, “Disputes over number of human genes”.
2001.05 Research work was featured in The New Scientist (2001) May 5, Human Genome Analysis”.
2001.02 Featured in People in the News, Bioinform (2001) February 18.
2001.02 Research work featured in Genome Biology (2001) February 12, “Researchers to publish a third historic human genome article this week”.
1994.04 Honorary Mention, The XX National Medical Research Forum, Galveston.
1994.03 Travel Award, American Medical Association.
1994.03 Dean’s Letter for Excellence in Research, University of Louisville School of Medicine.
1994.03 First Place Award, The XXV Midwest Medical Research Forum, Omaha.
1993.11 Travel Award, Midwest Medical Research Forum.
1993.10 The First Place Award, Student Research Day, University Louisville Medical School.
1987.01 Graduate Fellowship, University of Louisville.

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;

Part One: Selected Peer-Reviewed Journal Articles

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)