Education

Ph.D. in Bioinformatics, Chinese Academy of Sciences, 2011

B.S. in Biology, Shandong University, 2004

 

Experience

2011-2013: Postdoctoral fellow at the Wang Genomics Lab

 

Current Position

Postdoc at CHOP

 

Research Area

development of wANNOVAR server, systems biology modeling of biological networks

 

Research

wANNOVAR web server

wANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software, to facilitate biologists without bioinformatics skills taking full advantage of the sequencing data.

Given a list of single nucleotide variants (SNVs) and insertions/deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a "variants reduction" protocol to identify a subset of potentially deleterious variants.

 

Dynamic modular architecture of protein-protein interaction networks

The protein-protein interaction (PPI) networks are dynamically organized as modules, and are typically described by hub dichotomy: ‘party’ hubs act as intramodule hubs and are coexpressed with their partners, yet ‘date’ hubs act as coordinators among modules and are incoherently expressed with their partners. However, there remains skepticism about the existence of hub dichotomy. Since different algorithms and data sets were used in previous studies to test the model of hub classification, the conclusions may be largely influenced by the potential inherent biases. In this study, we evaluated two data sets of yeast interactome, and systematically investigated the behavior of hubs from multiple perspectives including co-expression patterns, topological roles and functional classifications. Our results revealed consistency between the two data sets, confirming the presence of hub dichotomy. Furthermore, we analyzed a human interactome data set, and demonstrated that the modular architecture of the PPI networks was more complicated than hub dichotomy.

 

 

Publications

  1. Chang X, Shi L, Gao F, Russin J, Zeng L, He S, Chen TC, Giannotta SL, Weisenberger DJ, Zada G, Wang K*, Mack WJ*. Genomic and transcriptomic analysis reveals an oncogenic functional module in meningiomas. Neurosurgical Focus, 35:e3, 2013
  2. Chang X, Xu T, Li Y, Wang K. Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs. Scientific Reports, 3:1691, 2013 
  3. Chen G, Chang X, Curtis C, Wang K. Precise inference of copy number alterations in tumor samples from SNP arrays. Bioinformatics, 29:2964-2970, 2013
  4. Shi L, Chang X, Zhang P, Coba M, Lu W, Wang K. The functional genetic link of NLGN4X knockdown and neurodevelopment in neural stem cells. Human Molecular Genetics, 22:3749:3760, 2013
  5. Gao F, Shi L, Russin J, Zeng L, Chang X, He S, Chen TC, Giannotta SL, Weisenberger DJ, Zada G, Mack WJ, Wang K. DNA methylation in the malignant transformation of meningiomas. PLoS ONE, 8:e54114, 2013 
  6. Chang X, Wang K. wANNOVAR: annotating genetic variants for personal genomes via the web. Journal of Medical Genetics. 49:433-436, 2012