Chen Sun

Department of Bioinformatics and Biostatistics
Shanghai Jiao Tong University

Room 221, Building 4, Biology Complex
800 Dongchuan Road, Minhang District
Shanghai, China, 200240

E-mail: verne91 AT sjtu DOT edu DOT cn

I have graduated from SJTU.

Now I am a PhD student at University of Michigan.

Here is my current personal website.

Education

2014.9 - 2017.3	M.S. in Bioinformatics (with honors)	Shanghai Jiao Tong University, Shanghai, China
2010.9 - 2014.7	B.S. in Bioinformatics	Shanghai Jiao Tong University, Shanghai, China
2012.2 - 2014.7	B.A. in History	Shanghai Jiao Tong University, Shanghai, China

In progress.
We sequenced more than 400 whole genomes of gastric cancer patients with very high sequencing depth in order to find the disease related variations.

Constructed Pan-genome analysis pipeline, including
- - sequence quality control
- - whole genome de novo assembly for 3,010 rice genomes
- - genomic mapping
- - pan-genome sequences construction
- - gene annotation of pan-genome sequences
- - gene clustering based on sequence homology
- - gene and gene family presence/absence determination
- - functional(GO) analysis
- - novel gene validation using RNA-seq data
- - phylogenetic analysis based on presence/absence variation (PAV) of gene and gene family
Implemented job submitting with LSF and SLRUM system on π supercomputer of SJTU (total computing time > 1.3 million CPU core hours).

Constructed database and visualization tools for 3,000 rice pan-genome analysis results.
Developed webpages with HTML, CSS and JavaScript.
Implemented serveral search functions and table browsers with PHP and MySQL.
Built visualization page with a dynamic tree browser and JBrowse framework.
Integrated pan-genome reference, gene annotation, gene PAV information and RNA-seq data into genome browser.

Presented a ”map-to-pan” strategy for high-resolution pan-genome studies.
Integrated available tools and in-house programs at different steps for eukaryotic pan-genome analysis.
Developed project website and performed regular maintenance.

Called SNP from genomic mapping results.
Designed pipeline for Shigella pan-genome analysis (including gene family presence/absence analysis, functional enrichment, evolution history of Shigella spp., etc.)
Constructed phylogenetic relationship of more than 700 strains.

Designed a logistic regression model for classification of human activities based on sensor data.
Implemented the model with Python and obtained high precision and recall (both 0.89).

Designed a method to detect signal shapes of histone modifications around transcription factor biding sites (TFBS).
Predicted TFBS with epigenetic signal characters.

Designed a kth-order Hidden Markov Model (HMM) to classify a set of short genomic sequences from different species.
Implemented the model with Python to predict the source of new sequences.

Located human genomic regions with higher similarities to amphibians than to mammals from multiple sequence alignment of 46 manmal genomes.
Fuctional analysis with GO database.

Surveyed and analyzed epigenetic data and distribution of repeat sequences on UCSC Genome Browser.
Summarized DNA methylation loci in different repeat regions.

Sun, C. et al. "RPAN: Rice Pan-genome Browser for ~3000 Rice Genomes", Nucleic Acids Res., 2017; 45 (2): 597-605. doi: 10.1093/nar/gkw958. [Full Text]

Hu, Z., Sun, C. et al. "EUPAN enables pan-genome studies of a large number of eukaryotic genomes", Bioinformatics 2017 btx170. doi: 10.1093/bioinformatics/btx170 (joint first author). [Full Text]

Huang, W. et al. "Widespread of Horizontal Gene Transfer in the Human Genome", BMC Genomics 2017 18:274 doi: 10.1186/s12864-017-3649-y. [Full Text]

Wang, W. et al. "Harnessing natural variation in Asian Cultivated Rice (Oryza sativa L.): SNPs, structual variationis and pan-genomes", in revision for Nature.