Projects
2020
Biomarker discovery for novel targets in tumor stroma
Created analytical framework for integrating bulk RNA-seq and scRNA-seq data of tumor microenvi- ronment. Analyzed stroma subsets for biomarker identification; Performed tumor-specific association and survival analysis for prioritizing biomarkers.
2019
Consequences Profiling of CRISPR-Cas9 Mediated Genome Editing
Developed Illumina short read platform based assay (LongAmp-seq) to profile on-target CRISPR-Cas9 mutagenesis patterns, which revealed up to 31% large deletions that were previously missing from the gold standard amplicon short-range Next-Generation Sequencing(NGS).
Established pipeline for high-throughput profiling of editing consequences, including symmetric and asymmetric large deletions, insertions and chromosomal rearrangements.
Explored bioinformatics options to overcome the potential bias and errors from PCR and sequencing to achieve quantification.
2018
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2017
Off-Target Analysis for Personalized CRISPR-Cas9 gRNA Designs
Performed experimental genome-wide off-target screening in 5 individual lymphoblastoid cell lines, which proved that individual variants could alter CRISPR-Cas9 targeting profiles.
Developed bioinformatics tool for variant aware off-target screening and annotation-based ranking. Compared the performance of existing CRISPR-Cas9 off-target scoring algorithms and proposed a novel deep-learning algorithm for CRISPR/Cas9 off-target risk assessment.
2016
Genome Editing based Fine-Mapping within eQTL Credible Intervals
Combined multiplex CRISPR-Cas9 genome editing with single cell RNAseq to measure perturbation in transcript abundance for fine-mapping causal genomic variants with moderate throughput, which successfully identified two causal SNPs by screening 67 targets in parallel.
Performed genome editing and cell line preparation in low throughput (single-cell clone) and moderate throughput (lenti-virus library), with experimental and computational validation in editing efficiencies and transcript abundance variations.
Unbiased Genome-Wide Off-Target Site Detection Assay
Established assays for unbiased in-cellular genome-wide CRISPR off-target site detection, which had over 30-fold signal enrichment for on-target sites.
Explored the potential of using chromatin immunoprecipitation(ChIP) and click-chemistry for the la- beling of CIRSPR/Cas9 off-target sites and examined options for signal enrichment and background removal.
Prediction of Influenza B Vaccine Effectiveness from Sequence Data
Refined the antigenic determinant model of the influenza B virus based on its evolution from 1960 to 2014 for better annual flu vaccine design.
Established an estimate of flu B vaccine effectiveness against a range of viral strains based on antigenic distance, which outperformed the gold standard HI assay based on 1979-2014 epidemiology data.