Provide computational biology and cancer genomics consulting to biotech and pharmaceutical companies

Lead the computational biology and data science efforts at an early stage biotech startup company. Target identification; genomic data analysis; clinicogenomic study design; drug resistance.

• Helped to shape and execute a strategic vision for the analysis and interpretation of genomic characterization data for the Cancer Dependency Map (DepMap) project.• Lead the computational biology team in the Cancer Cell Line Encyclopedia (CCLE) project --a public collection of cancer cell line data consisting of over 1000 human cancer cell lines. Contributed to the experimental design, data generation and analysis of DNA methylation, microRNA expression, Proteomics, Metabolomics, Chromatin profiling, and DNA and RNA sequencing datasets, collaborated closely with biologists and engineers from academia and industry.• Integrated genomic characterization data with perturbation data (RNAi, CRISPR/Cas9, small molecules) and cancer genome data (TCGA/ICGC) to identify and prioritize new drug targets and biomarkers and study mechanisms of drug resistance

• Developed state-of-the-art computational methods for integrative analysis of large-scale biological data including next generation sequencing (WES, WGS, RNAseq), proteomics (RPPA, TK-Luminex, Mass Spec), Metabolomics and Epigenetic data. Applying these methods to predict sensitivities to drug treatment and shRNA and CRISPR gene knockdown/ knockout, find novel cancer vulnerabilities, and investigate the mechanisms of drug resistance

Developed novel computational analysis and experimental validation:To normalize high-throughput genomic assays and statistically remove sequence specific biasesTo predict genome-scale nucleosome binding profiles using a context-based sequence modelDeveloped experimental system to validate predictions of mutation impact on gene regulation

Developed a novel method to process RNA-Seq short reads and reconstruct CHO cDNA sequencesAnalyzed Microarray data, designed and performed quantitative PCR and Western blot experiments to identify gene expression changes in dexamethasone treated CHO cells

Developed advanced context-based document processing and indexing tools for the online life science search engine (www.NextBio.com) using JAVA.

Developed a real-time method to detect micro emboli in transcranial Doppler ultrasound signals using autoregressive modeling and wavelet transforms. Developed accelerated adaptive methods for reconstruction of signals from non-uniform samples.