Jing 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.maria.zhang@gmail.com
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
Fall 2013, Topics in Bayesian Inference and Data Analysis
Spring 2014, Statistical methods in Genetics and Bioinformatics

Research Interests

Bayesian inference on complicated interactions, Big data analysis
NeuroImage analysis, Brain mapping
Statistical genetics, Epigenetics
Genome-wise Association for human complex diseases
Computational Virology, 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. Involvement of Key Genetic Elements in the C-terminus domain of HBV Surface Antigen in Mechanisms Underlying Levels of Serum HBV-DNA in Vivo. (2014) Carmen Mirabelli; Matteo Surdo; Formijn Van Hemert; Zhichao Lian; et al. Jing Maria Zhang; Massimo Andreoni; Mario Angelico; Jens Verheyen; Francesca Ceccherini-Silberstein; Carlo Federico Perno; Valentina Svicher. Submitted to PLOS One.

2. Atomic Dynamic Functional Interaction Patterns for Characterization of ADHD (2014) Jinli Ou, Zhichao Lian, Li Xie, Xiang Li, Peng Wang, Yun Hao, Dajiang Zhu, Rongxin Jiang, Yufeng Wang, Yaowu Chen, Jing Zhang (joint corresponding author), Tianming Liu. Human Brain Mapping, Accepted.

3. Inferring Functional Interaction and Transition Patterns via Dynamic Bayesian Variable Partition Model. (2014) 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. Accepted. Human Brain Mapping. Software can be found here.

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. Identifying Functional Networks via Sparse Representation of Whole-brain FMRI Signals. Jinglei Lv, Xi Jiang, Xiang Li, Dajiang Zhu, Hanbo Chen, Tuo Zhang, Shu Zhang, Xintao Hu, Junwei Han, Heng Huang, Jing Zhang, Lei Guo, Tianming Liu. Under review. Brain Structure and Function.

6. Detecting cell assembly interaction patterns via Bayesian based change-point DETECTION and GRAPH Inference model. (2014) Zhichao Lian, Xiang Li, Hongmiao Zhang, Hui Kuang, Kun Xie, Jianchuan Xing, Dajiang Zhu, Joe Z. Tsien, Tianming Liu, Jing Zhang (corresponding author). ISBI 2014 - IEEE International Symposium on Biomedical Imaging.

7. Characterizing Brain State Dynamics via Hidden Markov Models. (2014) Jinli Ou, Li Xie, Changfeng Jin, Xiang Li, Dajiang Zhu, Rongxin Jiang, Yaowu Chen, Wei Hao, Jing Zhang (joint corresponding author), Lingjiang Li, Tianming Liu. Under review. IEEE Transactions on Biomedical Engineering.

8. Generalized FMRI Activation Detection via Bayesian Magnitude Change Point Model. (2014) Zhichao Lian, Jinglei Lv, Jianchuan Xing, Xiang Li, Xi Jiang, Dajiang Zhu, Jiansong Xu, Marc N. Potenza, Tianming Liu, Jing Zhang (corresponding author). ISBI 2014 - IEEE International Symposium on Biomedical Imaging.

9. Exploring functional brain dynamics via a Bayesian connectivity change point model. (2014) Zhichao Lian, Xiang Li, Jianchuan Xing, Jinglei Lv, Xi Jiang, Dajiang Zhu, Jiansong Xu, Marc N. Potenza, Tianming Liu, Jing Zhang (corresponding author). ISBI 2014 - IEEE International Symposium on Biomedical Imaging.

10. Dynamic Network Partition Via Bayesian Connectivity Bi-Partition Change Point Model (2014) Zhichao Lian, Xiang Li, Thomas Young, Yun Hao, Jianchuan Xing, Jinglei Lv, Xi Jiang, Dajiang Zhu, Tianming Liu, Jing Zhang (corresponding author). ISBI 2014 - IEEE International Symposium on Biomedical Imaging.

11. Modeling Brain Functional Dynamics via Hidden Markov Models. (2013) Jinli Ou, Li Xie, Peng Wang, Xiang LI, Dajiang Zhu, Rongxin Jiang, Yufeng Wang, Yaowu Chen, Jing Zhang* (joint corresponding author), Tianming Liu. The 6th International IEEE EMBS Conference on Neural Engineering. NER 2013.

12. 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). Journal of Proteomics & Bioinformatics. Accepted

13. Identifying Functional Networks via Sparse Coding of Whole Brain FMRI signals. (2013) Jinglei Lv*, Xi Jiang, Xiang LI, Dajiang Zhu, Hanbo Chen, Tuo Zhang, Shu Zhang, Xintao Hu, Junwei Han, Heng Huang, Jing Zhang, Lei Guo, Tianming Liu. The 6th International IEEE EMBS Conference on Neural Engineering. NER 2013.

14. Group-wise Change Point Detection in Task FMRI Data by Bayesian Methods. (2013) Jianchuan Xing, Jinglei Lv, Zhichao Lian, Xiang LI, Dajiang Zhu, Tianming Liu, Jing Zhang (corresponding author). The 6th International IEEE EMBS Conference on Neural Engineering. NER 2013

15.    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..

16.  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.

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

18.   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 SupplementaryMaterials.zip

19.  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). NeuroImage Volume 61, issue 4, page 987-999.

20.   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

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

22.   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)

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

24. Block-based Bayesian Epistasis Association Mapping With Application to WTCCC Type 1 Diabetes.(2011) Zhang, Y., Zhang, J., Liu, S.J 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/

25.      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)

26.    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

27.    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

28.    Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. Zhang, J., Hou, T., Wei, W., Liu, S.J. (2010)  Proceedings of the National Academy of Sciences of the United States of America  (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

29. htSNPer 1.0: software for haplotype block partition and htSNPs selection, Ding K., Zhang J. (joint first author), Zhou K., Shen Y., Zhang X. (2005) BMC Bioinformatics 6, 38. Software is available at here or http://www.chgb.org.cn/htSNPer/htSNPer.html

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

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

Books and Book chapters

32. 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

33. 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

Professional Activities

n Editorial member: American Journal of Biostatistics

n Editorial member: Journal of Proteome Science and Computational Biology

l Invited reviewer for NSF/NIH grant review panel.

l Review papers for

Journal of the American Statistical Association (JASA), Statistica Sinica, the plant Cell, Annals of Applied Statistics, Biostatistics, Bioinformatics, BMC Bioinformatics, NeuroImage, PLoS One, Statistical Applications in Genetics and Molecular Biology, Cell Research, BMC Genetics, BMC Research Note, Journal of Probability and Statistics, Asia Pacific Bioinformatics Conference, Computational Statistics and Data Analysis, IEEE Transactions on Computational Biology and Bioinformatics, Journal of Agricultural, Biological, and Environmental Statistics

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, Steven Wei 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, Yang Liu

Rotation:

Gadareth Higgs, Tingting Jiang

Postdoctoral Associates:

Yang Liu, Zhichao Lian.

Visiting professor:

Prof. Jianchuang Xing

Invited Talks

· Aug 5-6, 2013, Integrative Biology-2013, Las Vegas, USA

· Aug 1, 2013, EITA-YIC 2013, the 3rd EITA Young Investigator Conference, MIT, Boston, USA

June 8-14, 2013 Invited Chair to lead the discussion group, SAMSI, NeuroImaging Data Analysis, 2013
April 19, 2013 Department of Bioinformatics and Biostatistics, Emory University
April 12, 2013 Department of Computer Science, University of Georgia
March 7, 2013 Department of Statistics, University of Missouri, Columbia,
Feb. 28, 2013 Department of Computer Science, University of Missouri, 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