Shangzhong Li

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My research focuses on CHO cell line optimization under the guidance of next and third generation sequencing.
Now I’m working on improving chinese hamster genome annotation by using proteogenomic technology and ribosome profiling. Traditional annotation pipelines use RNAseq, homology protein sequence alignment and prediction tools which would report more false protein coding genes and miss new genes. Proteogenomics sequencing utilizes RNAseq and proteomic data to annotate genome: RNAseq helps to define splice junctions and proteomics helps to verify the protein translation and coding frames. Ribosome profiling helps to reflect real time protein translation. These technologies combined together would provide a better annotation of the genome.
I also developed all kinds of pipelines for analyzing NGS and pacbio sequencing, including RNAseq quantification, structure variation detection, etc.

Contact information: shl198@eng.ucsd.edu