Chen Sun

Ann Arbor Algorithms

E-mail: cnsun AT umich DOT edu
Google Scholar

Education

2017.7 - 2023.5	PhD in Bioinformatics	University of Michigan, Ann Arbor, MI, USA
2019.9 - 2023.5	M.A. in Statistics	University of Michigan, Ann Arbor, MI, USA
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

2023.5 - Present	Scientist	Ann Arbor Algorithms, Ann Arbor, MI, USA
2017.7 - 2023.5	Research Assistant	University of Michigan, Ann Arbor, MI, USA
2022.6 - 2022.9	Applied Scientist Intern	Amazon, Palo Alto, CA, USA
2012.7 - 2017.3	Research Assistant	Shanghai Jiao Tong University, Shanghai, China
2014.3 - 2017.3	Intern	Shanghai Center for Bioinformation Technology, Shanghai, China

Development of Deep Learning Models for Digital Biomarker Discovery (2023-Present)
Deep learning-based single cell CNV caller development (2022 - 2023)
Single cell CNV simulator (2021 - 2023)
Identification of Somatic CNV in Human Neurons with Single-cell sequencing (2019 - 2023)
Predicting Multiple Myeloma Prognosis (Winter rotation, 2018)
Simulation of Cancer Progression (Fall rotation, 2017)
Validation of L1-Hs Insertions using 10X Genomics (Summer rotation, 2017)
3000 Rice Genomes Project (Nov. 2013 - Mar. 2017)
Rice Pan-genome Browser for 3000 Rice Genomes Project (RPAN, Mar. 2015 - Apr. 2016)
Toolbox for Eukaryotic Pan-genome Analysis (EUPAN, Sept. 2015 - June 2016)
Shigella Pan-genome Project (Dec. 2015 - June 2016)
Sensor Based Human Activity Recognition (Apr. 2015 - June 2015)
Epigenetic Signal Character around TFBS (Oct. 2013 - June 2014)
Taxonomic Classification of Short Genomic Sequences (Nov. 2013 - Dec. 2013)
Horizontal Gene Transfer in Human Genome (Summer Intern, 2013)
Epigenetics within Repeat Region in Mammal Genomes (Summer Intern, 2012)
Enzymatic Activity of Microorganisms Associated with Sponge (Oct. 2010 - Apr. 2012)

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; 33(15) :2408-2409. doi: 10.1093/bioinformatics/btx170. [Full Text]

Sun, C. et al. "Prognostic model for multiple myeloma progression integrating gene expression and clinical features", GigaScience, 2019. doi: 10.1093/gigascience/giz153. [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. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice", Nature, 2018. doi: 10.1038/s41586-018-0063-9. [Full Text]

Hu, Z. et al., "Novel sequences, structural variations and gene presence variations of Asian cultivated rice", Scientific Data, 2018. doi:10.1038/sdata.2018.79. [Full Text]

Qiao, Y. et al. "MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms", Biology Direct, 2018. doi:10.1186/s13062-018-0220-y. [Full Text]

Yan, F. et al. "Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes", BMC Genomics, 2019. doi:10.1186/s12864-019-5951-3. [Full Text]

Duan, Z. et al. "HUPAN: a pan-genome analysis pipeline for human genomes", Genome Biology, 2018. doi:10.1186/s13059-019-1751-y. [Full Text]

Sun, C. et al. "Mapping Mosaic Copy Number Variation in Human Neurons", Nature Communications, 2024; Accepted. [Full Text on Biorxiv]