Dan Cao

East Palo Alto, San Francisco Bay Area ad1kf5@r.postjobfree.com 650-***-****

https://www.linkedin.com/in/dancao/

SUMMARY

• Accomplished Molecular Cellular Biologist and Next Generation Sequencing (NGS) expert with over 20 years of research experience spanning both industry and academia.

• Proven expertise in developing NGS assays for a variety of applications, including cancer detection, microbiome study, infectious disease detection and CRISPR screens.

• Proficient in both wet lab techniques and bioinformatics data analysis.

• Enthusiastic about utilizing novel Molecular Cellular Biology and NGS approaches to drive assay development, enhance diagnosis, and develop new treatments for various diseases. EDUCATION

2002 Ph.D. in Molecular Cellular Biology, University of Arizona. 1998 B.S. in Cell Biology, Wuhan University, China. SELECTED SKILLS

• NGS assay development: whole genome sequencing, amplicon sequencing, other targeted sequencing, synthetic long read technologies, metagenomics application, bulk RNA-seq, single cell RNA-seq, assay development for cancer detection using FFPE and plasma (liquid biopsy) etc.

• Sample prep for NGS: FFPE, blood, stool, saliva, bacterial culture, cultured cell, etc.

• NGS data analysis: alignment, variant call, samtools, bedtools, picard, RNA-seq (bulk and single cell RNA-seq), de novo assembly, metaQUAST, other metagenomics analysis etc.

• Molecular and cellular techniques: DNA/RNA/protein isolation/extraction, mammalian cell culture, transfection, lentiviral packaging and titering, viral transduction, plasmid design, molecular cloning, single plex and multiplex PCR, RT-PCR, qPCR, primer design, northern blotting, western blotting, immunoprecipitation, fluorescence microscopy, RNAi screen, CRISPR screens, genotyping, and many other molecular, cellular, genomics and proteomics techniques. EXPERIENCE

June 2023 – Nov 2023: Principal Scientist, Atreca

• Optimized sample prep and NGS assay for lentiviral based genome-wide CRISPR screen platforms to enable target discovery.

• Developed qRT-PCR assays for CRISPRa and DNA genotyping assays for CRISPRko to validate the hits discovered from CRISPR screens.

• Managed, trained, and actively oversaw the work of a research associate involved in designing, conducting, and troubleshooting molecular biology and NGS workflows.

• Actively engaged in hands-on execution of experiments in the laboratory. July 2013 - June 2023: Scientist II Senior Scientist Staff Scientist, Illumina (SF Bay Area)

• Devised a rapid and simple multiplex PCR based amplicon sequencing method. Created a few amplicon panels such as 400plex cancer hotspot panel for both FFPE samples and circulating tumor DNA (ctDNA).

• Pioneered methods using Unique Molecular Identifier (UMI) for noise suppression and ultra-low frequency cancer mutation detection.

• Invented novel methods to simultaneously analyze cell free DNA and RNA in the blood.

• Developed methods for NGS library prep using raw lysate without the need of full DNA extraction. The method was published on Illumina website as part of application note for Nextera DNA library kit.

• Contributed to the development of novel sample prep and NGS assay for infectious disease samples ( Zika and SARS-CoV-2 etc) and clinical microbiome samples. Some of these turned into commercial product such as Covid-seq.

• Played a key role in technology development teams focusing on different novel approaches of synthetic long read technologies.

• Invented groundbreaking lentiviral based variant perturb-seq workflow by saturation mutagenesis and single cell RNA-seq to study the function of Variants of Unknown Significance.

• Led various projects, planned, coordinated, and actively oversaw the work of several research associates and junior scientists in the team, while also providing them mentorship and guidance.

• Independently conducted experiments in the lab, showcasing hands-on ability and contribution to the team's overall success.

• Analyzed various NGS data using established programs or internal pipelines.

• Collaborated with computational biologists to develop assay-specific data analysis pipelines and artificial intelligence-based genome interpretation tools.

• Fostered collaborations with external labs to explore novel applications of new NGS assays.

• Managed CROs on tasks such as vector and library construction, cell line development, lentiviral packaging etc.

July 2005 - June 2013: Postdoctoral fellow Research Associate, Laboratory of Dr. Mark Kay at Stanford University School of Medicine

• Investigated RNA-directed transcription in human cells using biosynthetic labeling by 4-thiouridine and next generation sequencing (RNA-seq).

• Studied the replication of Hepatitis Delta Virus in human cells using a proteomic-RNAi screen.

• Co-identified capped small RNA in Hepatitis Delta Virus replication. March 1999 – June 2003: Ph.D. student Postdoctoral fellow, Laboratory of Dr. Roy Parker at University of Arizona

• Built the world’s first computational model for mRNA degradation.

• Independently designed and conducted research on mRNA degradation in yeast using a combined approach of computational modeling and experimental analysis.

• Authored two original, peer-reviewed research articles, one of which appeared in the prestigious Cell journal.

• Assisted in the teaching of Biochemistry and Molecular Biology classes, led weekly discussion sessions. PUBLICATIONS

Cao, D. and Parker, R. 2001 Computational modeling of eukaryotic mRNA turnover. RNA. 7 (9): 1192-1212. Cao, D. and Parker, R. 2003. Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell. 113 (4): 533-545.

Haussecker, D., Cao, D., Huang, Y., Parameswaran, P., Fire, AZ. and Kay, MA. 2008. Capped small RNAs and Mov10 in human hepatitis delta virus replication. Nature Structure and Molecular Biology. Jul; 15(7): 714-21.

Cao, D., Haussecker, D., Huang, Y., and Kay, MA. Combined Proteomic-RNAi Screen for Host Factors Involved in Hepatitis Delta Virus Replication. RNA. 2009; 15 (11): 1971-9 Authors list TBD. Single cell sequencing as a general variant interpretation assay. In preparation for submission to Cell.

PATENTS

• Composition and methods for modulating activity of capped small RNAs.

• Preparation of nucleic acid libraries from DNA and RNA.

• Biotin-Streptavidin cleavage composition and library fragment cleavage.

• Analyzing expression of protein-coding variants in cells. FELLOWSHIPS

• Helen Hay Whitney Foundation Post-doctoral Fellowship (2005-2008).

• Damon Runyon Cancer Research Foundation Post-doctoral Fellowship (2004).

• Fellow award from Leukemia and Lymphoma Society (2004). REFERENCES

• Dr. Roy Parker, Professor at University of Colorado Boulder. Tel: 303-***-****. Email: ad1kf5@r.postjobfree.com

• Dr. Mark Kay, Professor at Stanford University. Tel: 650-***-****. Email: ad1kf5@r.postjobfree.com

• Dr. Paul Valdmanis, Associate Professor at University of Washington. Tel: 650-***-****. Email: ad1kf5@r.postjobfree.com

• Dr. Chenlu Hou, Senior Director, R&D at GRAIL. Tel: 510-***-****. Email: ad1kf5@r.postjobfree.com

• Dr. Hong Gao, Associate Principal Scientist, Illumina. Tel:650-***-****. Email: ad1kf5@r.postjobfree.com

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