Jing Maria Zhang

Assistant Professor (07/2010 ~ present)
Department of Statistics

Faculty Affiliate:

Computational Biology and Bioinformatics
Yale University
24 Hillhouse Avenue Rm 206
New Haven, CT 06511

jing.zhang.jz349@yale.edu

Education:

Postdoctoral fellow, 06/2009 ~ 05/2010, Department of Statistics, Harvard University

Ph.D, 06/2009, Department of Statistics, Harvard University

MA, 03/2007, Department of Statistics, Harvard University

MA, 07/2005, Bioinformatics, Tsinghua University

BS, 07/2002, Automation, Tsinghua University

Teaching

Fall 2010, Data Analysis.
Spring 2011, Statistical methods in Genetics and Bioinformatics.
Fall 2011, Probability and Statistics
Spring 2012, Stochastic Process
Spring 2012, Statistical methods in Genetics and Bioinformatics
Fall 2012~Fall 2013, on leave

Research Interests

Bayesian inference on complicated interactions
Statistical genetics, Epigenetics
Genome-wise Association for human complex diseases
HIV drug resistance, viral and human genetic markers underlying the progression of persistent viral infection sustained by HIV, HBV, and HCV
Computational biology and Bioinformatics
Bayesian network, Graph Models
Biomedical image analysis, computational neuroscience, and biomedical informatics

Publications (students or postdoc coauthors are underlined)

1. Detecting hepatitis B viral amino acid sequence mutations in occult hepatitis B infections via Bayesian partition model. (2013) ZHICHAO LIAN, QI NING TIAN, YANG LIU, VALERIA CENTO, ROMINA SALPINI, CARLO FEDERICO PERNO, VALENTINA SVICHER, GANG CHEN, CONG LI, JING ZHANG (corresponding author). PLOS ONE, under review.

2. Inferring Functional Interaction and Transition Patterns via Dynamic Bayesian Variable Partition Model. (2013) Jing Zhang (first and corresponding author), Xiang Li, Cong Li, Xiu Huang, Guocheng Zhong, Dajiang Zhu, Kaiming Li, Xi Jiang, Changfeng Jin, Xintao Hu, Junwei Han, Lei Guo, Xiaoping Hu, Lingjiang Li, Tianming Liu. Under review. Human Brain Mapping.

3. Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. (2013) Mengjie Chen, Valentina Svicher, Anna Artese, Giosuè Costa, Claudia Alteri, Francesco Ortuso, Lucia Parrotta, Yang Liu, Chang Liu, Carlo Federico Perno, Stefano Alcaro, Jing Zhang (corresponding author). Bioinformatics 2013 Feb 15;29(4):451-60. doi: 10.1093/bioinformatics/btt002..

4. Dynamic Functional Connectomics Signatures for Characterization and Differentiation of PTSD Patients. Xiang Li, Dajiang Zhu, Xi Jiang, Changfeng Jin, Xin Zhang, Lei Guo, Jing Zhang, Xiaoping Hu, Jingjiang Li, Tianming Liu. (2013) Human Brain Mapping. Accepted.

5. Neighborhood Preserving Ordinal Regression. Yang Liu, Yan Liu, Keith C.C. Chan, Jing Zhang. (2012) ACM ICIMCS, the International Conference on Internet Multimedia Computing and Service. Indexed by EI.

6. Bayesian Exploration of Multilocus Interactions on the Genome-Wide Scale. Kozyryev I and Zhang J (corresponding author). Accetpted by American Journal of Bioinformatics. Vol 1, Page Numbers: 70-78 (2012) DOI: 10.3844/ajbsp.2012.70.78

7. High-Order Interactions in Rheumatoid Arthritis Detected by Bayesian Method using Genome-Wide Association Studies Data. (2012) Jing Zhang (first and corresponding author), Zheyang Wu, Chao Gao and Michael Q. Zhang. American Medical Journal, Volume 3, Issue 1, Pages 56-66, DOI: 10.3844/amjsp.2012.56.66 Supplementary Material can be downloaded from http://www.stat.yale.edu/~jz349/RA_paper/SupplementaryMaterials.zip

8. Inferring Consistent Functional Interaction Patterns from Natural Stimulus FMRI Data. (2012) Jiehuan Sun, Xintao Hu, Xiu Huang, Yang Liu, Kaiming Li, Xiang Li, Junwei Han, Lei Guo, Tianming Liu, Jing Zhang (corresponding author). Accepted by NeuroImage. http://dx.doi.org/10.1016/j.neuroimage.2012.01.142

9. Systematic Investigation on Interactions for HIV Drug Resistance and Cross-Resistance among Protease Inhibitors. (2012) Jing Zhang (first and corresponding author), Tingjun Hou, Yang Liu, Gang Chen, Xiao Yang, Jun S Liu and Wei Wang. Journal of Proteome Science & Computational Biology 2012 1: 2. DOI : http://dx.doi.org/10.7243/2050-2273-1-2

10. Kozyryev I and Zhang J (corresponding author). Bayesian Determination of Disease Associated Differences in Haplotype Blocks. American Journal of Bioinformatics, Volume 1, Issue 1, Pages 20-29 DOI: 10.3844/ajbsp.2012.20.29 (2012)

11. NOVEL HBSAG MARKERS TIGHTLY CORRELATE WITH OCCULT HBV INFECTION AND STRONGLY AFFECT HBSAG DETECTION. Valentina Svicher; Valeria Cento; Martina Bernassola; Maria Neumann-Fraune; Formijn Van Hemert; Mengjie Chen; Romina Salpini; Chang Liu; Roberta Longo; Michela Visca; Sara Romano; Valeria Micheli; Ada Bertoli; Caterina Gori; Francesca Ceccherini-Silberstein; Cesare Sarrecchia; Massimo Andreoni; Mario Angelico; Antonella Ursitti; Alberto Spanò; Jing Maria Zhang; Jens Verheyen; Giuseppina Cappiello; C.F. Perno. Antiviral Research 93(1):86-93. (2012)

12. Zhang, J. (first and corresponding author), Zhang, Q., Lewis, D., Zhang, M. (2012) A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction. American Journal of Biostatistics. Volume 2, Issue 1 Pages 1-10. DOI: 10.3844/amjbsp.2011.1.10

13. Zhang, Y., Zhang, J., Liu, S.J (2011) Block-based Bayesian Epistasis Association Mapping With Application to WTCCC Type 1 Diabetes. Annals of Applied Statistics Vol. 5, No. 3, 2052–2077. Software BEAM2 can be downloaded from Yu Zhang’s webpage: http://www.stat.psu.edu/~yuzhang/

14. Identification and structural characterization of novel genetic elements in the HIV-1 V3 loop regulating coreceptor usage. Valentina Svicher, Claudia Alteri, Anna Artese, Fabio Mercurio, Jing Zhang, Giosuè Costa, R D’Arrigo, Stefano Alcaro, Giorgio Palù, Massimo Clementi, Maurizio Zazzi, Massimo Andreoni, Andrea Antinori, Adriano Lazzarin, Francesca Ceccherini-Silberstein, Carlo Federico Perno on behalf of the OSCAR study group. Antiviral Therapy 16(7):1035-45 (2011)

15. Key-genetic Elements in HIV-1 gp120 V1, V2, and C4 Domains Tightly and Differentially Modulate gp120 Interaction with the CCR5 and CXCR4 N-terminus and HIV-1 Antigenic Potential. V Svicher*, M Chen*, C Alteri, G Costa, S Dimonte, Chang Liu, L Parrotta, C Dimaio, S Carta, M Surdo, P Saccomandi, S Alcaro, F Ceccherini-Silberstein, A Artese, JM Zhang** (joint corresponding author), CF Perno** The 2nd International HIV & Hepatitis Virus Drug Resistance Workshop. (2011) ANTIVIRAL THERAPY Volume: 16 Issue: 4 Pages: A14-A14

16. Specific HBsAg genetic-determinants are associated with occult HBV-infection in vivo and HBsAg-detection. V Svicher, V Cento, M Bernassola, M Neumann-Fraune, M Chen, R Salpini, Chang Liu, R Longo, M Visca, S Romano, V Micheli, A Bertoli, G Gubertini, N Marino, F Mazzotta, C Sarrecchia, M Andreoni, M Angelico, A Ursitti, A Spanò, F Ceccherini, JM Zhang, J Verhejen, G Cappiello, CF Perno. The 2nd International HIV & Hepatitis Virus Drug Resistance Workshop. (2011) ANTIVIRAL THERAPY Volume: 16 Issue: 4 Pages: A85-A85

17. Zhang, J., Hou, T., Wei, W., Liu, S.J. (2010) Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. PNAS 107, 1321.

Highlight of this paper from PNAS Media Selections:

http://www.pnas.org/site/misc/selections_1_11_10.shtml

http://www.pnas.org/content/107/4/1255.full

Science Daily news on this paper:

http://www.sciencedaily.com/releases/2010/01/100111154918.htm

Harvard Crimson’s article on this paper:

http://www.thecrimson.com/article/2010/1/14/hiv-drug-resistance-mutations/

UCSD news release on this paper:

http://physicalsciences.ucsd.edu/news/releases/release_detail.php?release_id=281

18. Zhang, J., Li, F., Li, J., Zhang, M. Q., Zhang, X. (2004) Evidence and Characteristics of putative human alpha recombination hotspots. Hum. Mol. Genet. 13, 2823

Ding K., Zhang J. (joint first author), Zhou K., Shen Y., Zhang X. (2005) htSNPer 1.0: software for haplotype block partition and htSNPs selection, BMC Bioinformatics 6, 38.

Software is available at here or http://www.chgb.org.cn/htSNPer/htSNPer.html

20. Ding K., Zhou K., Zhang J., Knight J., Zhang X., Shen Y. (2005) The effect of haplotype definitions on inference of haplotype block structure and htSNPs selection, Molecular Biology and Evolution, 22, 148-159

Books and Book chapters

21. Ivan Kozyryev and Jing Zhang (corresponding author). (2013) Bayesian Analysis of Complex Interacting Mutations in HIV Drug Resistance and Cross-Resistance. Invited Chapter for book “Structural Bioinformatics”, Springer book series "Advances in Experimental Medicine and Biology". Accepted

22. Jing Zhang and Jun S. Liu. Statistical Methods and Models in Human Diseases and Genetics Studies. Contract with Springer. In preparation.

Awards

· 2012 Seessel Award to Junior Faculty, Yale University

· 2011 Seessel Award to Junior Faculty, Yale University

· 2010 Seessel Award to Junior Faculty, Yale University

· 2008 Spring Excellence in Teaching Award Harvard University

· 2003~2004 Top One Graduate Student Award–Intel Scholarship

· 2002~2003 Tsinghua University Excellent Graduate student Award

· 2002 Beijing Excellent Graduate Award

· 2002 Tsinghua University Outstanding Graduate with Honors

· 2000~2001 Tsinghua University Excellent Student Award Scholarship–

China Weal

· 1999~2000 Tsinghua University Excellent Student Award Scholarship–

Schneider Electric

· 1998~1999 Tsinghua University Excellent Student Award Scholarship–

Schneider Electric

Students and Postdocs mentored

Undergraduate:

1. Ivan Kozyryev, Major: Applied Math. 2011, Thesis: Determining Disease associated differences in Linkage Disequilibrium Boundaries using a Bayesian model and MCMC. With distinction.

2. Diana Shen, Major: Statistics. 2011, Thesis: Statistical Analysis of HIV drug resistance data.

3. Varoon Kumar Bashyakarla, Major: Statistics, 2012, Thesis: A Genome-wide Association Study of Single Nucleotide Polymorphisms Associated with Hypertension.

4. Kevin Zhang, Major: Statistics, 2012, Thesis: Bayesian Epistasis Association Mapping Analysis

of Type 2 Diabetes.

5. Gang Chen, Major: Economics, 2012, research Project: HCV Drug Resistance Analysis.

6. Cameron Musco, Major: Computer Science. Research Project: Bayesian method for detecting rare mutations.

Graduate students:

Tingting Jiang, Wenjing Ge, Steve Ho, Haben Michael, Chao Gao, Chang Liu, Zhixiang Lin, Yao Fu, Seung Hun Lee, Guocheng Zhong, Joseph Kim,

On the Ph.D qualifying committee:

Mengjie Chen, Lucus Lochovsky,

On the Ph.D thesis committee: Rao Fu

Rotation:

Gadareth Higgs, Tingting Jiang

Postdoctoral Associates:

Yang Liu, Zhichao Lian.

Visiting professor:

Prof. Jianchuang Xing

Invited Talks

April 12, 2013 Department of Computer Science, University of Georgia
March 7, 2013 Department of Statistics, University of Missourri, Columbia,
Feb. 28, 2013 Department of Computer Science, University of Missourri, Columbia.
Dec. 4, 2012 "LONI Presents" talk. Laboratory of Neuro Image, UCLA, USA
Oct. 12-14, Invited Plenary Speaker,

The 4th Annual International Conference on Computational and Systems Biology (ICCSB2012), Shanghai Jiao Tong University, China

Sept. 27, 2012 Department of Probability and Statistics, Boston University, USA
July 24, 2012 Department of Computer Science, Jilin University, China.
May 7, 2012 Bioinformatics program, UCLA, USA
March 16, 2012 Department of Mathematics and Statistics, Georgia State University, USA
March 5-7, 2012 International Conference and Exhibition on Biometrics and Biostatistics, Omaha, USA
June 30, 2011 The 20th Applied Statistics Symposium, New York City.
March 11, 2011 Department of Computer Science, Institute of Bioinformatics

University of Georgia

“Bayesian Inference of Complicated interactions with application of HIV drug resistance”

Mar 26, 2010 Department of Statistics,

Chinese University of Hong Kong.

“Bayesian Inference of Interactions in

Biological Problems”.

Mar 25, 2010 Li Ka Shing Institute of Health Sciences,

Chinese University of Hong Kong.

Mar 23, 2010 Department of Psychiatry,

The University of Hong Kong

Mar 04, 2010 Department of Mathematics and Statistics,

University of Massachusetts, Amherst

Feb 24, 2010 Department of Biostatistics,

University of Minnesota,

Feb 19, 2010 Department of Mathematical Sciences,

Worcester Polytechnic Institute,

Feb 09, 2010 Department of Statistics

University of Kentucky,

Feb 04, 2010 Department of Statistics

Ohio State University,

Feb 02, 2010 The Division of Biostatistics

New York University School of Medicine

Jan 18, 2010 Department of Statistics,

Yale University

“Bayesian Inference of Interactions in

Biological Problems”.

Dec 21, 2009 Division of Pharmacoepidemiology and

Pharmacoeconomics,

Brigham and women’s hospital,

Harvard Medical school

“Bayesian Models and Methods for Selecting

Covariates and Interactions”.

Dec 09, 2009 Department of Mathematics & Statistics,

Mount Holyoke College

· Sep 17, 2009 Department of Biostatistics and Bioinformatics

Emory University

Professional Activities

Editorial member: American Journal of Biostatistics

Editorial member: Journal of Proteome Science and Computational Biology

Ø Review papers for Journal of the American Statistical Association (JASA)

Ø The American Journal of Human Genetics, the plant Cell,

Annals of Applied Statistics, Biostatistics, PNAS, PLoS One

Statistical Applications in Genetics and Molecular Biology

Cell Research, BMC Genetics, Journal of Probability and Statistics,

Asia Pacific Bioinformatics Conference,

Computational Statistics and Data Analysis

IEEE Transaction, Journal of Agricultural, Biological, and Environmental Statistics