Computational Biologst

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Hairi Li

USA 858-***-**** *******@*****.***

Professional Summary

Experienced Computational Biologist with expertise in analyzing large-scale biological datasets, including Next-Generation Sequencing (NGS) and single-cell omics. Skilled in developing bioinformatics pipelines, applying machine learning models, and integrating multi-omics data for biomarker discovery and drug development. Highly collaborative team player with a strong publication record (60+ peer-reviewed papers and patents). Adept at communicating findings to multidisciplinary teams and contributing to cutting-edge research in genomics and precision medicine. Key Skills

• NGS Data Analysis: RNA-seq, ATAC-seq, ChIP-seq,

WGS/WES, panel-seq, scRNA-seq, scATAC-seq, scTCR-

seq, scBCR-seq, spatial transcriptomics (10x Genomics, Visium, Giotto)

• Multi-Omics Data Integration: scRNA-seq & scATAC-seq

• Computational & Statistical Methods: Machine Learning, Data Mining, Sequence Analysis

• Programming & Tools: Python, R/Bioconductor, Bash, C++, SQL, GitHub, Nextflow, Docker

• Bioinformatics Pipelines: GATK, Bowtie, BLAST, STAR, TRUST4, Cell Ranger, Seurat, Scanpy, DESeq2, edgeR, limma, XGBoost, TensorFlow

• Data Visualization: ggplot2, Seaborn

• High-Performance Computing: HPC clusters, Cloud

Computing (AWS, Google Cloud)

• Open-Source Data Utilization: TCGA, IMGT, NCBI,

GenBank, PDB, SABDAB, GTEx

• Collaboration & Communication: Cross-Functional

Teamwork, Experimental Design, Scientific Writing

Professional Experience

PRINCIPLE SCIENTIST/DATA ANALYST 04/2022 - Current Single Cell Genomics, Zafrens - San Diego, CA (Biotech)

• Developed bioinformatics pipelines for high-throughput NGS data analysis (RNA-seq, TCR-seq, BCR-seq, ICD-seq).

• Led the development of workflows for scRNA-seq, scTCR-seq, scBCR-seq, and scICD-seq.

• Applied machine learning techniques for single-cell transcriptomic data analysis and biomarker discovery. RESEARCH SCIENTIST 11/2021 - 03/2022

Single Cell Genomics, Biospyder Technologies - San Diego, CA (Biotech)

• Designed and implemented computational pipelines for single-cell RNA-seq and RASL-seq analysis.

• Performed differential expression, pathway, and network analysis on scRNA-seq datasets.

• Worked closely with R&D teams to integrate computational insights into drug discovery programs. POSTDOCTORAL RESEARCHER/PROJECT SCIENTIST/DATA ANALYST 01/2002 - 10/2021 University of California - San Diego, CA

• Developed bioinformatics workflows for genomics projects involving RNA-seq, ATAC-seq, WGS, and single-cell sequencing.

• Applied machine learning for network and pathway analysis, integrating multi-omics datasets.

• Identified cancer biomarkers through transcriptomic and splicing analysis.

• Developed high-throughput NGS technologies, including RNA-seq and RASL-seq.

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• Operated and optimized sequencing platforms, including Illumina-based workflows.

• Published 60+ peer-reviewed papers and contributed to patents in the field of genomics and computational biology. Education

Jiamusi Medical College - P.R.China M.D.

Medicine

China Medical University - P. R. China M.S.(Fellow) Endocrinology

Activities and Honors (selected)

• Li HR, Wang-Rodriguez J, Nair TM, Yeakley JM, Kwon YS, Bibikova M, Zheng C, Zhou L, Zhang K, Downs T, Fu XD, Fan JB. Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res. 2006;66(8):4079-88

• Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD, Yeo GW. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A. 2008;105(51):20179-84

• Li H, Zhou H, Wang D, Qiu J, Zhou Y, Li X, Rosenfeld MG, Ding S, Fu XD. Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery. Proc Natl Acad Sci U S A. 2012;109(12):4609-14

• Li H, Qiu J, Fu XD. RASL-seq for Massively Parallel and Quantitative Analysis of Gene Expression. Curr Protoc Mol Biol. 2012 Apr;Chapter 4:Unit4.13.1-9

Patent

• Hai-Ri Li, Hyun Chul Lee, Mankil Jung, Sudhir V Shah. Treatment of diabetic nephropathy and microalbuminuria. US patent No. 6267992; World International patent No. WO 01/22981 A1vv

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