About

I am a Bioinformatics and System Biology PhD student at UC San Diego under the supervision of Dr. Abraham Palmer to study computational genetics based on long reads sequencing. Before my PhD program, I worked with Dr. Abraham Palmer on genotyping pipeline development and optimization for 2.5 years.

On the side, I also do micriobiome meta-analysis with Dr. Shi Huang, where I mainly focus on microbiome SNVs calling pipeline development and machine learning application on metagenomics.

Before joining Dr. Abraham Palmer's Lab, I recieved my B.S. in Computer Engineering from UC San Diego. BTW to make everyone's life easier, I go by Den.

Publications

Jiang, S.*, Chen, D.*, Ma, C., Liu, H., Huang, S., Zhang J. Establishing a novel inflammatory bowel disease predictive model based on gene markers identified from single nucleotide mutation of intestinal microbiota. iMeta. 1, e40 (2022).
*These authors contributed equally

Ma, C.*, Zhang, C.*, Chen, D.*, Jiang, S., Shen, S., Huo, D., Huang, S., Zhai, Q., Zhang J. Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota. Commun Biol 4, 1198 (2021)
*These authors contributed equally

Presentations

Chen, D., Nguyen, K., Cohen, K., Polesskaya, O., Sebat, J., Palmer, A.A. Calling Structural Variants in Extended Rat Pedigree Using PacBio HiFi Sequencing. ASHG 2022, Los Angeles, CA, November 25-29, 2022, poster.

Chen, D., Chitre, A.S., Nguyen, K., Cohen, K., Cheng, R., Polesskaya, O., Palmer, A.A. Hybrid Genotyping Pipeline on Lc-WGS and ddGBS Sequences for Heterogeneous Stock Rats. The 19th Annual Meeting of the Complex Trait Community in Collaboration with the Rat Genomics Community, University of Colorado, September 29-30, 2022, oral presentation.

Chen, D., Cheng, R., Chitre, A.S., Polesskaya, O., Palmer, A.A. Low-Coverage Whole Genome Sequence Genotyping Pipeline on Heterogeneous Stock Rats. ASHG 2021, October 18-22, 2021, poster.

Chen, D., Chitre, A.S., Li, J., Settles, M.L., Glasper, E.R., Fisher, H.S., Luo, P.X., Trainor, B.C., Palmer, A.A., Polesskaya, O. Low-Coverage Whole Genome Sequence Genotyping Pipeline for Peromyscus Californicus. The 18th Annual Meeting of the Complex Trait Community in Collaboration with the Rat Genomics Community, September 1-3, 2021, oral presentation.

Chen, D., Huang, S., Song, S.J., Swafford, A.D., Knight, R. Leverage the Power of Massive Public Datasets Through Qiita. IBM AI Research Week, MIT, September 16-20, 2019, poster.