苑 波 Bo Yuan
333 W. 10th Ave, Suite 5072
The Ohio State University
Columbus, OH 43210
Phone: (614) 292-0656
E-mail: yuan.33@osu.edu
苑波教授出生于 1960 年。1976 年高中毕业后赴大西北插队锻炼。1978 至 1983 年在北京
大学医学院（原北京医学院）学习，1987 年赴美留学。1989 年获美国路易维尔大学生物
化学硕士学位，1995 年获该校分子遗传学博士学位。先后在麻省理工学院等院校做过博
士后研究员。现任美国俄亥俄州立大学生物信息学系终身制助理教授，博士生导师, 并兼
任该校药物基因组学研究所所长。2001 年，苑波教授领导的实验室是人类基因组国际计
划和 Celera 公司之后，全世界第三家完成人类和小鼠基因组破译和全功能分析的单位。
2002 年获全美杰出青年科学家奖提名。
苑波教授的研究方向包括复杂系统的结构和演化，基因相互作用网络的功能多样性和稳定
性，蛋白质三维结构和相互作用的预测，生物信息学算法，全基因组功能分析，以及机器
学习、并行计算等方法的应用。
CURRENT POSITION
2002.4 -
Assistant Professor (Tenure-Track)
Departments of Biomedical Informatics, and Pharmacology
College of Medicine and Public Health, The Ohio State University
EDUCATION
1990-1995
Ph.D., Molecular Genetics, University of Louisville School of Medicine
1987-1989
M.S., Biochemistry, University of Louisville
1978-1983
B.S., Beijing Medical University, China
PROFESSIONAL EXPERIENCES
2002.10-
Co-Director, Program in Pharmacogenomics, College of Medicine and Public
Health, The Ohio State University
1997.9-02.2
Member, Comprehensive Cancer Center
College of Medicine and Public Health, The Ohio State University
1997.9-02.2
Director/Research Scientist, Laboratory of Bioinformatics and Computational
Biology James Cancer Hospital and Solove Research Institute, The Ohio State
University
HONORS AND RECOGNITIONS
2005.07
Chairman, Session of Systems Biology and Bioinformatics, the 6th World Multi-
1
2005.06
Conference on Systemics, Cybernetics and Informatics, Orlando, Florida
Joint Professor, National University of Defense Technology, Changsha, China
2004.12
Member, Steering Committee, the 6th International Conference on Bioinformatics
and Its Applications, Fort Lauderdale, Florida
2004.01
Member, Academia Sinica Review Panel on “National Research Program for
Genomic Medicine”, Taipei
2003.12
All time 10 most-viewed articles published by BioMed Central, UK
2003.04
External Board Member, Kentucky Science and Engineering Foundation
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 was 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.
2002.06
Member, Research Advisory Committee, The Ohio State University
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 was 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 was featured in Economist (2001) July 12, “Human Genome: think
of a number, then double it”
2001.07
Research work was featured worldwide on many magazines, web sites, and
newspapers, including NY Times, Canberra Times…
2001.07
Research work was featured in BBC (2001) July 8, “Disputes over number of
2
2001.06
human genes”
Honorary Speaker, Solid Session, Nanyang Polytechnic University, Singapore
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
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 was featured in Genome Biology (2001) February 12,
“Researchers to publish a third historic human genome article this week”
1999.09
Session Chair, Bioinformatics and Microarray Technology
The Annual Stone Lab Biology Meeting, Put-In-Bay, Ohio, USA
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
1990.06
Graduate Fellowship, University of Louisville Medical School
SELECTED PUBLICATIONS (*Corresponding Author)
Chen JF, Yuan B*(2006), Detecting functional modules in the yeast protein-protein
interaction network. Bioinformatics 22(18): 2283-2290
Chen JF, Zhang F, Gokhale Z, Wang DL, Ma JS, and Yuan B* (2005) Inferring complex
genotype-phenotype interaction through protein-protein interaction networks (submitted,
Genome Research)
Chen JF, Zhang CQ, and Yuan B* (2005) Detection of functional modules within gene
interaction networks by a weighted graph and the shortest-path algorithm (submitted,
Genome Research)
3
Zhang J, Borth H, Zhang F, Chen JF, Luo ZG, and Yuan B* (2005) Genome-wide search
for functional non-coding RNAs and their potential targets (submitted, Genome
Research)
Ozer H, Zhang F, Mayhew M, Zhang YF, Bai SM, Chen JF, and Yuan B* (2005)
Clustering of eukaryotic orthologs and their associated paralogs using the Markov graphflow algorithm (in press)
Zhang F, Chen JF, Liu ZY, and Yuan B* (2005) The construction of structural templates
for the computational modeling of conserved protein domains (in press)
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, June 2004 (held in conjunction with ISCA 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
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 (40 papers accepted from 320 submissions).
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 (35 papers accepted from 118 submissions)
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, Hämäläinen 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, 69:673684.
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
4
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.
Wang JL*, Yuan B, Zhang P, Tamburro CH (1994) Molecular epidemiology of acrylonitrile and
regiospecific modification of Ha-ras Oncogene. Advanced Chemistry, 241:153-173.
Joseph G, Barker RL, Yuan B, Martin A, Medeiros J, Peiper SC* (1994) Post transplantation
plasma cell dysplasia. Cancer, 74:1959-1964.
Yuan B, Wong JL* (1991) Inactivity of acrylonitrile epoxide to modify a Ha-ras DNA in a nonfocus transfection-transformation assay. Carcinogenesis 1991, 12:787-791.
SELECTED ABSTRACTS
D Zhuo, WD. Zhao, HY Yang, JP Wang, R Sears, DH Kwon, D Gordon, S Gibbs, D Dai, T
Baer, D Stredney, A Stutz, R Krahe, FA Wright, B Yuan. Physical mapping and functional
annotation of 60,000 human genes. Oncogenomics-dissecting cancer through genome research.
Tucson, AZ, January 25-27, 2001.
KI Virtaneva, FA Wright, SM Tanner, B Yuan, WJ Lemon, MA Caligiuri, CD Bloomfield, A de
la Chapelle, R Krahe. Gene expression profiling reveals fundamental biological differences in
AML with trisomy 8 and normal cytogenetics. Oncogenomics-dissecting cancer through
genome research. Tucson, AZ, January 25-27, 2001.
Chadwick RB, Yuan B, Bennington GA, Johnson CK, Stevens MW, Aaltonen LA, Peltomaki
PT, de la Chapelle A. High resolution mapping of chromosome 1p deletions in hereditary and
sporadic CRC cancers by combined high density single nucleotide polymorphism and
microsatellite analysis. Cytogenetics and Cell Genetics 1999, 87:166.
5
Sears R, McDonald S, Gibbs S, Karanko S, Daly M, Goodheart D, Wang JP, Johnson C, Gao X,
Hendrickson B, Huang JQ, Wang DL, Krahe R, Wright FA, Chadwick R, Yuan B. Toward
Fully Automated Genotyping, Loss of Heterozygosity and Linkage Analysis - Combination of
PE 3700 Automated Sequencer, Software Systems in UNIX, Relational Database, CORBA,
Annotated Human Genome Database, and Web Interface. Annual Stone Lab Meeting, Put-inBay, Ohio, September 17-19, 1999.
Gibbs S, Sears R, Yang HY, Wang JP, Gao G, Lemon W, Krahe K, Wright FA, and Yuan B.
Automation, Quality Control, And Data Mining in A High-Throughput Microarray Environment.
Annual Stone Lab Meeting, Put-in-Bay, Ohio, September 17-19, 1999.
Wang JP, Sears R, Yang Q, Dai D, Kwon DH, Krahe K, Wright FA, Yuan B. in silico mining
for candidate genes from the human genome - integration of function, position, expression,
sequence, and taxonomy information in a relational database. Annual Stone Lab Meeting, Putin-Bay, Ohio, September 17-19, 1999.
Hendler FJ, Yuan B, Shum-Siu A. Hras1 methylation affects tumorigenesis and loss of
heterozygosity (LOH) in 4NQO-induced oral cavity tumors. DNA Methylation, imprinting, and
the Epigenetics of Cancer, Las Croabas, Pierto Rico, 1997.
Yuan B, Shum-Siu A, Hendler FJ. The 5’ H19 imprinted region is maintained while
downstream CpG sites are randomly demethylated in 4NQO transformed murine oral
keratinocytes and induced oral cavity tumors. DNA Methylation, Imprinting, and the Epigenetics
of Cancer, Las Croabas, Pierto Rico, 1997.
Gaugler MG, Yuan B, Shum-Siu A, Achim Gossler, Hendler FJ. Murine Hras1 methylation
sites can be allele specific, tissue specific, and random in embryo, adult and transformed tissues.
DNA Methylation, Imprinting, and the Epigenetics of Cancer, Las Croabas, Pierto Rico, 1997.
Yuan B, Shum-Siu A, Letsch EJ, Hu LH, Hendler FJ. Frequent polymorphism exist in inbred
CBA/J and C3H/HeH mice. Molecular Mouse Genetics, Cold Spring Harbor, NY, 1996.
Yuan B, Hendler FJ. Quantitation of EGF receptor mRNA by competitive polymerase chain
reaction. The 7th Annual Meeting on Oncogenes, Frederick, MD, June 1991.
Yuan B, Hendler, F, Ha-ras point mutations in 4-nitroquinoline-i-oxide (4-NQO) induced
murine oral squamous cell carcinogenesis. 9th Annual Meeting on Oncogenes, Frederick, MD,
June 1993.
Hendler FJ, Yuan B, Heniford BW, Ackermann DM. Homozygous Ha-ras mutations occur in
4NQO induced murine oral squamous carcinogenesis. J Cell Biochem 18C:N403,1994.
Yuan B, Heniford B, Hendler FJ. Chromosomal degeneration in carcinogen induced murine oral
squamous cell carcinogenesis. Amer Ass Cancer Res 35:904, 1994.
Hendler FJ, Yuan B, Heniford BW, Leonberger M, Shum-Siu A, Hawkins B. 4NQO induced
murine oral cavity tumors mimic human head and neck cancer. 4th Research Workshop on the
Biology, Prevention, Treatment of Head and Neck Cancer, Sept 1994.
Hendler FJ, Yuan B, Oechsli MN, Hu L, Lentsch EM, Shum-Siu A. 4-nitroquinoline-loxide
(4NQO) induced Ha-ras mutations in squamous epithelium are associated with a cascade of
molecular events which eventuate in loss of heterozygosity (LOH), gene amplification, and
6
genomic instability during neoplastic transformation in murine and human models. Molecular
Biology of Cancer: Implications for Prevention and Therapy, Amer Ass Cancer Res Symposia,
Maui, Hl, 1995.
Oechsli M, Yuan B, Lentsch E, Worth C, Peiper S, Hendler FJ. Human keratinocytes exposed
to short term 4-nitroquinoline-l -oxide (4NQO) develop Ha-ras point mutations and loss of
heterozygosity (LOH). Amer Ass Cancer Res 36: 1090, 1995.
Hu L, Yuan B, Hendler F. 4-nitroquinoline-l -oxide (4NQO) induced oral cavity Ha-ras
mutations lead to loss of heterozygosity (LOH), gene amplification, and genomic instability
during neoplastic transformation. Amer Ass Cancer Res 36: 3229, 1995.
Lentsch E, Yuan B, Hendler FJ. Genomic instability at chromosome 11 in a murine oral cavity
cancer model. American Society for Head and Neck Surgery. Palm Desert, CA, 1995.
Hendler FJ, Yuan B, Oechsli MN, Hu L, Lentsch EM, Shum-Siu A. 4-Nitroquinoline-loxide
(4NQO) induced H. ras mutations in squamous epithelium eventuate in loss of heterozygosity
(LOH), gene amplification, and genomic instability during neoplastic transformation in murine
and human models. Cancer Genetics and Tumor Suppressor Genes, Frederick MD, 1995.
Oechsli M, Hu L, Lentsch E, Yuan B, Worth C, Peiper S, Hendler FJ. Human and murine
keratinocytes after a short exposure to 4-nitroquinoline-l -oxide (4NQO) develop Ha-ras point
mutations, loss of heterozygosity (LOH) and are immortalized. Neoplastic Transformation in
Human Cell Systems in Culture: Mechanisms of Carcinogenesis, Chicago IL, 1995.
Huber JL, Yuan B, Hendler FJ. Hras1 mutations frequently occur in head and neck carcinoma
developing in American tobacco chewers. International Symposia on Advances in Head and
Neck Cancer, Kiel, Germany, 1996.
Huber JL, Alagar RK, Yuan B, Hendler FJ. Hras1 mutations frequently occur in head and neck
carcinoma developing in American users of oral tobacco products. Cancer Susceptibility Genes
and Molecular Carcinogenesis, Amer Assoc for Cancer Research Symposia, Keystone, CO,
1996.
Yuan B, Shum-Siu A, Lentsch EM, Hu L, Hendler FJ. Frequent DNA polymorphisms in inbred
CBA/J and C3H/HeH mice suggests that these strains have a mutator phenotype. Cancer
Susceptibility Genes and Molecular Carcinogenesis, Amer Assoc for Cancer Research Symposia,
Keystone CO, 1996
Menes JC, Heniford BW, Ackermann DM, Leonberger M, Yuan B, Hendler FJ. 4Nitroquinoline-1-oxide (4NQO) induced murine head and neck squamous cell carcinoma which
develop during exposure to 13-cis retinoic acid are much larger and have Hras mutations and
loss of heterozygosity. Cancer Susceptibility Genes and Molecular Carcinogenesis, Amer Assoc
for Cancer Research Symposia, Keystone CO, 1996.
Hendler FJ, Yuan B, Lentsch EM, Hu L, Shurn-Siu A, Oechsli MN, Menes JC, Alagar RK.
4-Nitroquinoline-1-oxide (4NQO) induced murine oral cavity carcinogenesis results in Hras1
mutations, gene amplification and genomic instability. Cancer Susceptibility Genes and
Molecular Carcinogenesis, Amer Assoc for Cancer Research Symposia, Keystone CO, 1996.
Alagar R, Yuan B, Heniford BW, Menes J, Hendler FJ. Exposure of mice to 4NOO results in
Hras1 and not Ki-ras2 mutations in foregut tumors. Amer Ass Cancer Res 37, 1996.
7
Yuan B, Shum-Siu A, Lentsch EM, Hu LH, Hendler FJ. Frequent DNA polymorphisms in
inbred CBA and C3H mice. Amer Ass Cancer Res 37: 3749, 1996.
Huber JL, Alagar R, Yuan B, Bumpous J, Hendler FJ. High incidence of Ha-ras point mutations
in head and neck squamous cell carcinomas (HNSCC) developing in tobacco chewers. Amer Ass
Cancer Res 37- 3934, 1996.
PUBLISHED BOOK CHEPATERS
Hendler FJ, Yuan B, Oechsli MN, Lentsch EM, Menes JC, Shum-Siu A, Hu LH, Hawkins B,
Heniford BW: 4NQO oral carcinogenesis, a murine model of human head and neck cancer.
Advances in Head and Neck Cancer, Elsevier Science B.V., 89-95, 1996.
Huber JL, Yuan B, Alagar R, Bumpous JM, Ackermann DM, Martin AW, Korfhage LG and
Hendler FJ- Hrasl mutations frequently occur in head and neck carcinoma among American
tobacco chewers. Advances in Head and Neck Cancer, Elsevier Science B.V., 79-87, 1996.
SOFTWARE AND DATABASES DEVELOPED (* Senior Corresponding Author)
Wang JP, Sears R, Yang Q, Dai D, Kwon DH, Krahe K, Wright FA, *Yuan B. in silico mining
for candidate genes from the human genome - integration of function, position, expression,
sequence, and taxonomy information in a relational database
Gibbs S, Sears R, Yang HY, Wang JP, Gao G, Lemon W, Krahe K, Wright FA, and *Yuan B.
Automation, Quality Control, And Data Mining in A High-Throughput Microarray Environment
(http://pandora.med.ohio-state.edu/abstracts/microarray.html)
Sears R, McDonald S, Gibbs S, Karanko S, Daly M, Goodheart D, Wang JP, Johnson C, Gao X,
Hendrickson B, Huang JQ, Wang DL, Krahe R, Wright FA, Chadwick R, *Yuan B. Toward
Fully Automated Genotyping and Linkage Analysis - Combination of PE 3700 Automated
Sequencer, Software Systems in UNIX, RDBMS, CORBA, Annotated Human Genome
Database, and Web Interface (http://pandora.med.ohio-state.edu/abstracts/genotyping.html)
Dai D, Yang HY, Wang JP, *Yuan B. Identification of splicing variants in human and rodent
transcripts (http://pandora.med.ohio-state.edu/cgi-bin/dean/variant.cgi)
Li ZR, Sun H, Wright FA, *Yuan B. Identification of tissue, pathology, or development specific
genes using a relational database system
(http://genome.med.ohio-state.edu/genome/jsp/gmvs/datamining/expression_profile.jsp) and
(http://genome.med.ohio-state.edu/genome/jsp/gmvs/geneindexing/consensus.jsp)
Zhao D, Sears R, Wang JP, *Yuan B. Functional annotation and browsing of human
chromosome 22 (http://megatron.med.ohio-state.edu/cgi-bin/biocomputing/chromosome22.cgi)
Yang HY, Gibbs S, Wright FA, *Yuan B. Web-based Genechip Informatics System.
(http://pandora.med.ohio-state.edu/cgi-bin/biocomputing/Ron/Demo.cgi)
Zhuo D, Zhao D, Sears R, Wang JP, *Yuan B. Functional annotation and browsing of human
chromosome 21 (http://megatron.med.ohio-state.edu/cgi-bin/Chr21/Chr21.cgi)
Sun H, Li ZR, Wright FA, *Yuan B. OSU Human and Mouse Genome Browser using JDBC,
XML and Java Serverlet (http://genome.med.ohio-state.edu/genome/index.jsp)
8
Dai Dean, Sears R, Yang HY, Wang JP, Quo JP, *Yuan B. HCG search engine using RDBMS
and Perl-DBI (http://http://pandora.med.ohio-state.edu/cgi-bin/datamining/search.cgi)
Gordon D, Sears R, Sun H, *Yuan B. Web Based Sequence Annotation - Developing a MultiPlatform Discovery Suite (http://pandora.med.ohio-state.edu/abstracts/annotation.html)
McDonald S, Sears R, *Yuan B. OSUMAT, a C program to decode and convert ABI 3700 binary
format to automatically parse trace information (compiled in Digital UNIX system).
Sears R, *Yuan B. OSU_typer, an applet based chromatogram viewer to edit and visualize 3700
genotyping trace files via JDBC to the underlying RDBMS.
Sears R, *Yuan B. WEB-LOH, a perl CGI and perl DBI based web interface for a large-scale
LOH analysis and integration with genome database
Sears R, Goodheart D, *Yuan B. PediWeb, a perl CGI, perl DBI and perl GD based web
interface for the presentation of pedigree information.
Sears R, *Yuan B. WEB-GHGUI, a perl CGI, DBI, and GD based web interface for the
automation and integration of large-scale linkage analysis.
McDonald S, Sears R, *Yuan B. NEWMAT3700, a C program to automatically call allele sizes
of 3700 trace files in a large-scale microsatellite-based genotyping projects, based on MIT’s
newmat, which was originally programmed for ABI slab gel systems.
Sun H, Wang DL, *Yuan B. SNP_finder, a C program to parse and identify potential SNPs
along with ORF and translation, quality information.
Li ZR, Sun H, Wang DL, Wright FA, *Yuan B. cDNA-mapper, a perl based system to parse and
clean up blast alignments and specifically map cDNA into genomic backbone.
DL Wang, *Yuan B, *Wright FA. getlist, clustering software to glamorize pairwise
relationships.
DL Wang, *Wright FA, *Yuan B. OSU_Assembler. A C program to verify and clean up
sequence clusters in whole genome assembly projects.
Sears R, Wright FA, *Yuan B. OSU_Scaffolder, a RDBMS and perl based system to assemble
genomic scaffolds using mate-pair, BAC ends and other mapping information
FELLOWS AND STUDENTS TRAINED
Current Members:
Names (Highest Degree)
Jingchun Chen (M.S.)
Fa Zhang (M.S.)
Hassan Borth (M.S.)
Jun Li (Ph.D.)
Muthu Pugalanthiran (M.S.)
Period
09/02 - present
09/02 - present
10/03 - present
01/04 - present
01/04 - present
Field of Study
Systems Biology
Systems Biology
Bioinformatics
Bioinformatics
Systems Biology
Member of Thesis Committee:
Solomon Gibbs
06/02 - present
Yuheng Li
05/03 - present
Current Position
Ph.D. Student
Ph.D. Student
Ph.D. Student
Visiting Scientist
Ph.D. Student
Electrical Engineering
Computer Science and Engineering
9
Shihong Mao
01/05 - present
Computer Science and Engineering
Former Fellows and Students Supervised:
Names (Highest Degree)
Period
David D. Zhao (Ph.D.)
08/99 - 10/00
Degen Zhuo (Ph.D.)
05/00 - 10/00
Jianping Wang (M.S.)
06/98 - 05/00
Shannon McDonald (B.S.) 03/98 - 09/00
Heeyung Yang (B.S.)
01/00 - 10/00
Dean Dai (B.S.)
04/00 - 09/00
Moye Ji (Ph.D.)
04/01 - 12/01
Dohun Kwon (B.S.)
01/00 - 07/00
David Gordon (B.S.)
05/98 - 12/00
Jianping Guo (M.S.)
09/99 - 04/01
Qing Yang (M.S.)
05/98 - 12/98
Chad Meek (B.S.)
08/99 - 06/00
Yan Wang (B.S.)
01/99 - 05/99
Joel Stevens (M.S.)
04/21 – 05/21
Bill Ge (Ph.D.)
01/98 - 08/99
Steve Orem (M.S.)
06/99 - 12/99
Niddy Bagga (B.S.)
02/01 - 09/01
Hao Sun (Ph.D.)
06/01 - 02/02
Xiao-Ping Shen (M.D.)
02/01 - 12/02
Zhiru Li (M.S.)
05/01 - 12/02
Russell Sears (B.S.)
05/98 - 07/03
Solomon Gibbs (B.S.)
10/99 - 09/03
Dara Goodheart (B.S.)
09/00 - 12/01
Xiaokui Mu (Ph.D.)
05/00 - 12/01
Jing Fang (B.S.)
01/01 - 02/02
Brian Lan
06/03 - 05/04
Aryan Lan
06/03 - 05/04
Rotation Students Trained
Weihong Qiu
Xianhua Cao
Marianne Lee
Ling Ding
Irene Joseph
Andrew Johnson
Tanping Li
Joel Schultz
Hassan Borth
Gary Drwal
Hatice Ozer
Zoee Gokhale
Sarah Javiad
Field of Work
Genome Annotation
Genome Annotation
Data mining
Genotyping LIMS
Web based RDBMS
Web based RDBMS
Database Integration
CGI-DBI/Sybase
Genome Annotation
Web-based RDBMS
Data mining
JDBC and RDBMS
Microarray LIMS
Data mining
Genome Analysis
Microarray LIMS
Genome Assembly
Genome Analysis
Genome Annotation
Expression Profiling
Protein Modeling
Protein Recognition
Genotyping LIMS
Promoter Profiling
Genome Analysis
Molecular Docking
Molecular Docking
(Fall, 2002), Biophysics
(Fall, 2002), Biophysics
(Winter, 2002), Biophysics
(Summer, 2003), IBGP
(Summer, 2003), Biophysics
(Summer, 2003), IBGP
(Fall, 2003), Biophysics
(Fall, 2003), Biophysics
(Fall and Winter, 2003), Biophysics
(Winter, 2003), IBGP
(Winter and Spring, 2003), Biophysics
(Summer, 2004), Biophysics
(Winter, 2004), Biophysics
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Current Employer
Johnson & Johnson
Duke University
Nationwide
Harvard University
LabBook Inc
LabBook Inc
CSHL, Postdoc
Cornel University
LabBook Inc
LabBook Inc
Quest
Huntington Bank
OSU
NIH
Celera
Industry
Lucent
OSU
China Academics
Industry
UC Berkley
US Air force
UC Berkley
OSU
OSU
Northwestern U.
Northwestern U.
INVITED KEYNOTE OR PLENARY PRESENTATION
Functional annotation of the human genome draft. China-EU Workshop on Bioinformatics and
Functional Genomics. Shanghai, China, June 14th 2001.
To decipher the human book of life. The 2001 International Symposium on Information Systems
and Engineering (ISE'2001). Las Vegas, Nevada, June 26th 2001 (Keynote).
Whole Genome Shotgun Assembly. Summer Institute on Advanced Computation SIAC2001Bioinformatics and Data Mining. Wright State Information Technology Research Institute &
Ohio Supercomputer Center. Dayton, Ohio, August 28th, 2001 (Keynote).
Assembly and annotation of the human genome using large linux clusters. Cambridge
Healthtech Institute’s Inaugural High Performance Computing – Strategic Applications for
Genomics and Proteomics. La Jolla, California, January 14, 2002
The initial assembly, analysis, and comparison of the mouse genome to the human genome.
Sixth International Lake Tahoe Symposium on Integrating Genomics, Epigenomics, Proteomics,
and Phenomics in Drug Discovery and Diagnosis. Lake Tahoe, Nevada, January 28th 2002.
Comparative analysis of the human and mouse genome drafts. Cambridge Healthtech Institute’s
Eleventh Annual Bioinformatics and Genome Research. San Diego, California, June 5th 2002
To dissect complex-trait disease using a genomics approach. Environmental Diseases’ 2003
Symposium on Experimental Models of Human Disease. Austin, Texas, May 4th 2003.
Modularity of biological functions at the systems level – inferring complex genotype-phenotype
relationship through protein-protein interaction networks. Pharmaceutical Sciences World
Congress (PSWC2004), Kyoto, Japan, May 31th 2004.
Computational prediction and characterization of mammalian noncoding RNAs and their
targets. The 6th International Conference on Bioinformatics and Its Applications, Fort
Lauderdale, Florida, December 15th 2004.
INVITED PRESENTATIONS
Carcinogenesis Occurs as a Cascade of Genetics Events. Department of Research and
Development, Sandoz Co, East Hanover, NJ, Nov 14th 1994.
Genomic Instability Occurs as a Late Event in Murine Squamous Cell Carcinogenesis. Cancer
Center, University of Pennsylvania, Philadelphia, PA, April 2nd 1995.
Ha-ras point mutation, Loss of Heterozygosity and Gene Amplifications Are Required in Murine
Squamous Cell Carcinogenesis. Division of Molecular Genetics, NIEHS, Research Triangle
Park, NC, June 5th 1995.
Molecular Cascade in Tumorigenesis. Division of Medical Oncology, University of Virginia,
Charlottesville, VA, June 20th 1996.
DNA Methylation Directs Allele-Specific Mutageneisis. The Johns Hopkins Oncology Center.
Baltimore, MA, June 29th 1996.
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Allele-Specific Methylation Affects the Specificity and Selectivity of Carcinogen-Induced
Neoplastic Transformation. Whitehead Institute, Cambridge, MA, September 5th 1996.
Loss of Genomic Imprinting in Neoplastic Transformations. Division of Molecular
Immunology, Scripts Institute, La Jolla, CA, April 15th 1997.
Genome-Wide Mapping of Methylated CpG Sites. Division of Human Cancer Genetics, Ohio
State University, Columbus, OH, August 25th 1997.
Regional Loss of Imprinting in Tumorigenesis. Department of Immunology and Virology, Ohio
State University, Columbus, OH December 15th 1997.
Automated Assembly and Analysis Shotgun Sequences. Children Hospital, Ohio State
University, Columbus, OH, April 12th 1998.
The Development of a Comprehensive Biocomputing System at the OSU. Comprehensive Cancer
Center, Ohio State University, Columbus, OH, Dec 7th 1998.
Transcript Assembly and the Creation of a Gene-Oriented Human cDNA Index. Comprehensive
Cancer Center, Ohio State University, Columbus, OH, Nov 4th 1999.
In Silico Mining for Candidate Genes. Heart and Lung Institute, Ohio State University,
Columbus, OH, January 12th 2000.
Comprehensive Annotation of Human Chromosomes 21 and 22. LabBook Co, Columbus, OH,
June 25th 2000.
To Decipher the Human Book of Life. Ohio Supercomputing Center, Columbus, OH, April 12th
2001.
Parallel Computing in a Large Linux Cluster Environment. Ohio Supercomputing Center,
Columbus, Ohio, May 18th 2001.
Draft Annotation and Overview of the Human Genome. Department of Medical Biochemistry,
Ohio State University, April 15th 2001.
Mining for Gene Expression Profiles from Existing EST and SAGE Databases. LeedScope
Bioinformatics Inc., Columbus, Ohio, May 24th 2001.
Initial Analysis of the Human Genome Draft. Genome Center, Las Amos National Laboratory,
Las Amos, NM, June 6th 2001.
Functional Annotation and Physical Mapping of 60,000 Human Genes. Shanghai Institute of
Biotechnology, Shanghai, June 14th 2001.
Genome-Scale Identifications for Paralogous Genes. National Bioinformation Center, Shanghai,
China, June 15th 2001.
To Develop National Strength in Functional Genomics and Bioinformatics. Biotechnology
Center, China, Shengzhen, June 16th 2001.
To Decipher the Book of Life. National Cancer Center, Singapore, June 19th 2001
Physical Mapping and Functional Annotation of 60,000 Human Genes. Division of Medical
Research, National Cancer Center, Singapore, June 19th 2001.
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To Decipher the Book of Life. School of Information Technology, National Singapore Nanyang
Polytechnic, Singapore, June 20th 2001.
Data Warehousing and Integration of Large Heterogeneous Data. Ohio Supercomputer Center,
Columbus, Ohio, June 29th 2001.
Assembly, Functional Annotation, and Integration of UNIGENE Clusters into the Human
Genome Draft. Department of Computer and Information Sciences, Wright State University,
August 29th 2001.
Analysis of Human Genome and Its Applications in Human Genetics. Nanjing University,
Nanjing, China, October 5th 2001.
Human Genome, How Many Genes? Zhejiang University, Hangzhou, China, October 8th 2001.
Human Genome, its Structure and Functional Content. Shandong University, Jinan, China,
October 13th 2001.
The Use of Large Linux Clusters to Assemble and Annotate Human and Mouse Genomes.
Ohio Supercomputer Center, Columbus, OH, November 5th 2001.
Complete Assembly, Annotation, and Comparison of the Mouse Genome Draft to the Human
Genome. James Cancer Hospital and Solove Research Institute, Columbus, OH, November 7th
2001.
Complete Assembly of the Human and Mouse Genomes. NIDCD, NIH, Bethesda, MA,
December 7th 2001.
Functional and Structural Organization of the Human Genome. Integrated Biomedical Science
Program, Ohio State University, Columbus, January 25, 2003
Structural Diversity, Evolution, and Functional Organization of the Human Proteome.
Department of Biochemistry, Ohio State University, Columbus, November 12, 2004
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TEACHING
2002 Fall
Course Director, IBGP730
Computational Algorithms in Biological Sequence, Structure, and
Function Analysis, 3 credit hours (25 Students)
The Ohio State University
2002 Fall
Course faculty member, CHE694
Chemoinformatics, 1 credit hour (32 students)
The Ohio State University
2002 Winter
Course Director, IBGP705
Introduction of Bioinformatics, 1 credit hour (35 students)
The Ohio State University
2002 Winter
Course Faculty Member, IBGP731
Biomedical Image Analysis, 3 credit hours (6 students)
The Ohio State University
2003 Fall
Course Director, IBGP730
Algorithms in Biological Sequence, Structure, and
Function Analysis, 3 Credit Hours (27 students)
(with 9 student projects and papers)
The Ohio State University
2003 Fall
Course faculty member, CHE694
Chemoinformatics, 1 credit hour (24 students)
The Ohio State University
2003 Winter
Course faculty member, IBGP725
Pharmacogenomics, 1 credit hour (12 students and fellows)
The Ohio State University
2004 Fall
Course Director, IBGP730
Algorithms in Biological Sequence, Structure, and
Function Analysis, 3 Credit Hours (12 students)
The Ohio State University
SERVICES
02-Present
Guest Professors, Huazhong University of Science and Technology, and
Lanzhou University
02-Present
Director, Committee for the OSU Distinguished Series in Computational
Biology and Bioinformatics
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02-Present
Director, Seminar and Journal Club Committee
Department of Biomedical Informatics, OSU
02-03
Member, Faculty Recruitment Committee
Department of Pharmacology, OSU
02-Present
Member, Research Committee
The College of Medicine and Public Health, OSU
REVIEWERS
Journals:
BMC Bioinformatics, Bioinformatics, and Drug Discovery and Development,
Journal of Bioinformatics and Computational Biology
Grants:
Two R01 grants (Taiwan Genome and Bioinformatics Program), and one P01
grant (Taiwan Genome and Bioinformatics Program)
GRANTS AND CONTRACTS (YUAN, PI)
Ohio Genome Alliance
(05/00-06/01, $350,000)
LabBook Fellowship
(03/20-02/22, $275,000)
P&G Genome Initiative Fund
(06/02-05/05, $500,000)
NIH R01 GM072747-01
(09/05-08/10, $1,200,000), resubmitted on the 1st of
November, 2004 and pending
RESEARCH WORK COMMERCIALIZED
OSU Human Genome DatabaseTM Powered by LabBook
(http://www.labbook.com/products/query.asp)
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