Statistics; Genomics; Systems Biology; Biostatistics
I am interested in Systems Biology and Statistical Analysis on Genomics Data. My goals are to develop mathematical and statistical methodologies to understand more on biological processes or networks through integrating various large scale genomics data. One of my current focus is to model the static and dynamic transcriptional regulatory networks for cell cycle and salt stress response in Yeast. This research involves statistical data analysis on genomics data, kinetic aspects of transcription, translation, protein-DNA and protein-protein interactions, graphic models in describing transcriptional regulatory network, and data mining for model inference in a high-dimensional space. The methodologies are developed using interdisciplinary approaches with more emphasis on statistics. This research is funded by the National Institutes of Health. Another research direction is to develop a pathway-based method to understand more on functional characteristics of human leukemogenic genes. The data from various laboratories or platforms will be integrated through an efficient statistical method. The prior pathway knowledge will be incorporated in the framework of pathway-based models. This research is funded by Yale Center for Clinical Investigation. I also collaborate with biologists to analyze high throughput data. My goal is to translate new methodologies in statistics into large-scale biological experimental designs and data analyses, where many new challenges are encountered.
Specialized Terms: Systems Biology; Statistical Analysis; Genomics
A Bayesian Error Analysis Model for reconstructing transcriptional regulatory networks.
Modeling for Transcriptional Regulatory Network N Sun, RJ Carroll, H Zhao. A Bayesian Error Analysis Model for reconstructing transcriptional regulatory networks. Proc. Natl. Acad. Sci. USA. 2006, 103(21): 7988-7993.
Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data.
Pathway-based Analysis N Sun, L Ma, D Pan, H Zhao and XW Deng. Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Molecular Biology, 2003, 53: 467–478.
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.
Y Jiao, SL Tausta, N Gandotra, N Sun, T Liu, NK Clay, T Ceserani, M Chen, L Ma, M Holford, H Zhang, H Zhao, X-W Deng & T Nelson. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nature Genetics Published online: 04 January 2009; | doi:10.1038/ng.282
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
L Ma, C Chen, X Liu, Y Jiao, N Su, L Li, X Wang, M Cao, N Sun, X Zhang, J Bao, J Li, S Pedersen, L Bolund, H Zhao, L Yuan, G K-S Wong, J Wang, XW Deng, J Wang. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research, 2005, 15: 1274-1283.
Full List of PubMed Publications
- Hou L, Sun N, Mane S, Sayward F, Rajeevan N, Cheung KH, Cho K, Pyarajan S, Aslan M, Miller P, Harvey PD, Gaziano JM, Concato J, Zhao H: Impact of genotyping errors on statistical power of association tests in genomic analyses: A case study. Genet Epidemiol. 2017 Feb; 2016 Dec 26. PMID: 28019059
- Sun N, Wang J, Gao Z, Dong J, He H, Terzaghi W, Wei N, Deng XW, Chen H: Arabidopsis SAURs are critical for differential light regulation of the development of various organs. Proc Natl Acad Sci U S A. 2016 May 24; 2016 Apr 26. PMID: 27118848
- Sun N, Zhao H: Putting things in order. Proc Natl Acad Sci U S A. 2014 Nov 18; 2014 Nov 7. PMID: 25380598
- Sun N, Zhao H: Reconstructing transcriptional regulatory networks through genomics data. Stat Methods Med Res. 2009 Dec. PMID: 20048387
- Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T: A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 2009 Feb; 2009 Jan 4. PMID: 19122662
- Sun N, Carroll RJ, Zhao H: Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc Natl Acad Sci U S A. 2006 May 23; 2006 May 15. PMID: 16702552
- Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW, Wang J: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 2005 Sep. PMID: 16140994
- Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW: Organ-specific expression of Arabidopsis genome during development. Plant Physiol. 2005 May. PMID: 15888681
- Sun N, Zhao H: Genomic approaches in dissecting complex biological pathways. Pharmacogenomics. 2004 Mar. PMID: 15016608
- Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW: A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 2003 Dec; 2003 Nov 6. PMID: 14605227
- Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H: PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics. 2003 Nov 7; 2003 Nov 7. PMID: 14604444
- Sun N, Ma L, Pan D, Zhao H, Deng XW: Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Mol Biol. 2003 Nov. PMID: 15010613
- Sun N, Walz JY: A Model for Calculating Electrostatic Interactions between Colloidal Particles of Arbitrary Surface Topology. J Colloid Interface Sci. 2001 Feb 1. PMID: 11161495