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
Part One: Selected Peer-Reviewed Journal
Articles
Liu Q, Wang YB; and Yuan B.*; Matrix Factorization from a Few Dominators, Neural Networks and Learning System,
IEEE/ACM Transactions on Year: 2018, Nov; 29(11): 5749
5755.
Wang Y.; Liu Q; Yuan, B.*;The Learning of a Structural and Functional Representation for Gene Expressions:
To Robustly Dissect Complex Cancer Phenotypes, Computational Biology and Bioinformatics, IEEE/ACM Transactions on
Year: 2018, 15(1):1-14;
Cui FS; Yuan B.*;Fixation Probability of a
Beneficial Mutation Conferring Decreased Generation Time in Changing
Environment, BMC Systems Biology, 2018,
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.
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