EDUCATION

Ph.D.,  Statistical Genetics & Bioinformatics, Zhejiang University, Hangzhou, China, 2003 to present

Expected Graduation Data: June, 2008

B.S. Biological Science, Zhejiang University, Hangzhou, China, 1999-2003

Thesis: Predicting Superior Genotypes based on QTL Effects in Multiple Environments

RESEARCH INTEREST

Mapping genetic architecture of complex trait for experimental populations: Most phenotypic variations result from segregation of multiple genes which are sensitive to genetic, sexual, external environments. A comprehensive understanding of genetic architecture underlying complex trait is a great challenge in the post-genomic era. During my Ph.D. study, I mainly focused on developing statistical models and methods to map the genetic architecture of complex trait including QTLs, epistasis, QTL-environment interaction and epistasis-environment interaction for experimental populations (e.g. DH, RIL, F2, RIX and so on), and to map the interspecific genetic interaction in host-parasite interaction system.

Microarray Data Analysis: Microarray has become an increasingly popular biotechnique in biological and medical researches, and has been widely applied in classification of treatment subtypes using expression patterns of biomarkers. I was also interested in developing statistical methods to identify differential expression genes (DEGs), with the aim of identifying expression biomarkers for treatment subtypes, such as tumor types or other human diseases.

Expression quantitative trait loci (eQTL) analysis: Currently, I am interested in developing methods to map QTL and genetic interaction (epistasis) of gene expression traits. In some model organisms, phenotype data, genotype data and expression data of a mapping population are available. My further interest is to integrate the information of these three data resources for more deep and systematic understanding the genetic basis of complex traits.

ACADEMIC EXPERIENCE

Software Development: QTLNetwork

QTLNetwork is a software package for mapping the genetic architecture of complex traits in experimental population, which could handle data from multiple-environment trials (METs). It could not only map single-locus effect QTL, but also detect epistasis, QTL-environment interaction and epistasis-environment interaction. More information could be found: http://ibi.zju.edu.cn/software/qtlnetwork.

My contributions to this project:

1)      Design the architectural system of the whole software.

2)      Develop the models and methods of QTL mapping.

3)      Design and develop the whole QTL mapping computation system.

4)      Debugging and testing.

Software Development: QTModel

QTModel software is designed for experimental data analysis. It currently have three modules including mixed (Mixed linear model analysis), array (Microarray data analysis), and diallele (Quantitative trait analysis based on diallele cross). More information could be found: http://ibi.zju.edu.cn/software/qtmodel.

My contributions to this project:

1)      Design the architectural system of the whole software.

2)      Design and develop the module mixed.

3)      Develop the models and methods of the array module and involved in its programming.

4)      Debugging and testing.

Conference organization

1)      Organized the China-UK Systems Biology Workshop chaired by Prof. Jun Zhu and Prof. John Findlay in 2005, Zhejiang University, Hangzhou, China.

2)      Involved in organizing the Annual Workshop of Quantitative Trait Analysis from 2003 to 2006.

3)      Involved in organizing the 3rd International Conference of Quantitative Genetics chaired by Prof. William Hill, Prof. Bruce Weir, Prof. Junyi Gai and Prof. Changxin Wu in 2007, Zhejiang University, Hangzhou, China.

Teaching Assistant:

1)      Department of Biological Science, Zhejiang University from 2003 to 2006.

2)      College of Agriculture and Biotechnology, Zhejiang University from 2003 to 2006.

PUBLICATION

First-author Papers

1)      Yang J and Zhu J (2005) Methods for predicting superior genotypes under multiple environments based on QTL effects. Theor  Appl Genet, 110: 1268-1274.

2)      Yang J, Zhu J and Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics, 23: 1527-1536.

3)      Yang J, Hu CC, Hu H., Yu RD, Xia Z, Ye XZ and Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24: 721-723.

4)      Yang J, Wu WR and Zhu J (2008) Mapping interspecific genetic architecture in host-parasite interaction system. Genetics (in press).

5)      Yang J, Li CD, Xue G, Gupta S, Lance R, Zhang GP, Loughman R and Zhu J (2008) A strategy for high throughput mapping of quantitative trait loci based on diversity arrays technology (DArT). BMC Genomics (submitted)

6)      Yang J, Zou YY and Zhu J (2008) Identification of differentially expressed genes by two-treatment microarray experiment. (in preparation)

7)      Yang J, Hayat Y and Zhu J (2008) Mapping Genetic Architecture of Complex Traits by Recombinant Inbred Intercross Design in Multiple Environments. (in preparation)

Co-author Papers

1)      Zou YY, Yang J and Zhu J (2006) A robust statistical procedure to discover expression biomarkers using   microarray genomic expression data. J Zhejiang Univ Sci B, 7(8): 603-607.

2)      Liu GF, Yang J and Zhu J (2006) Mapping epistatic QTL for biomass yield and its components in rice (Oryza sativa L.). Yi Chuan Xue Bao, 33(7): 607-616.

3)      Liu GF, Yang J, Xu HM and Zhu J (2007) Influence of epistasis and QTL × environment interaction on heading date of rice (Oryza sativa L.). J Genetics and Genomics, 34: 608-615.

4)      Han LD, Yang J and Zhu J (2007) Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants. J Genetics and Genomics, 34: 562-568.

5)      Hu CC, Ye XZ, Zhang Y, Yu RD, Yang J and Zhu J (2007) 3D graphical visualization of the genetic architectures underlying complex traits in multiple environments. J Zhejiang Univ Sci A, 8(4): 563-567.

6)      Liu GF, Zhou HK, Hu H, Zhu ZH, Hayat Y, Xu HM and Yang J (2007) Genetic analysis for brix weight per stool and its component traits in sugarcane (Saccharum officinarum). J Zhejiang Univ Sci B, 8(12): 860-6.

7)      Liu GF, Yang J, Xu HM, Hayat Y and Zhu J (2008) Genetic analysis of grain yield conditioned on its component traits in rice (Oryza sativa L.). Australian Journal of Agricultural Research, 59: 189-195.

Book Chapters

1)      Yang J and Zhu J (2007) Mixed Linear Model Approaches for Complex Trait Analysis. In Lai TL, Qian LF and Shao QM (Eds.), Asymptotic Theory in Probability and Statistics with Applications. China Higher Education Press.

PROJECT INVOLVEMENT

1)      Molecular Virtual Breeding for Major Crops, National High Technology Program (863 Program), 2003.

2)      Statistical models and methods for cDNA array expression profile analysis, National Science Foundation, 2005.

3)      Functional genomics research and molecular improved of cotton fibber quality. National Basic Research Program (973 Program), 2006.

HONORS & AWARDS

1)        Academic Scholarship for Excellent Undergraduate of Zhejiang University, 1999-2002

2)        Excellent Graduate Student for Undergraduate of Zhejiang University, 2003

3)        Academic Scholarship for Excellent Graduate of Zhejiang University, 2004-2007