Justin Chou Email & Phone Number

San Diego, Ca, Us

Chicago, Illinois, United States

El Cajon, California, United States

• Developed a pipeline for generating gene expression TPM data from fastq files, utilizing existing Nextflow workflows and writing novel python and R scripts• Built a Docker-ized Solr server to store TPM data and other relevant gene and sample information for easy querying• Took on the role of Head of Bioinformatics after the departure of the senior bioinformatics scientist, adopting managerial duties of working more closely with the interns to delegate tasks and check on workload, progress, and satisfaction• Established a step-by-step guide for primer probe design, covering all the caveats and nuances of the procedure, that was well-received and applied by lab scientists• Collaborated with lab scientists to procure, filter, and analyze gene expression data for in-house and/or desired cell lines• Tested, updated, and wrote Nextflow workflows, using Azure for both input and output

• Contracted through Insight Global as a software test engineer to write tests for DRAGEN services, including Illumina Connected Analytics (ICA) and EdgeOS, utilizing Pytest and Jama Connect• Utilized Illumina’s EdgeOS UI and Postman to simulate analysis pipelines from sequencing start to analysis end to identify bugs and ensure coverage of edge cases• Collaborated with professionals from several teams in order to onboard and work on numerous projects and tasks simultaneously, with minimal guidance

San Diego, California, United States

• Made updates to proprietary API relevant to the company’s tools and services and assisted in the transition of legacy tools to more sleek and innovative designs, utilizing Django REST Framework in Docker containers in development and implementing changes according to requests and needs of both external customers and internal scientists• Built a NGS Variant Calling pipeline that utilized Trimmomatic, Bowtie2, SAMtools, and BCFtools to confirm accuracy of synthetic products provided by the field scientists• Independently wrote scripts requested by scientists to visualize data utilizing Biopython and classify customer orders leveraging ElasticBLAST with AWS• Assisted in ML algorithm training by running simulations on data to improve the calling accuracy of one of the company’s primary services, the findings of which helped train the machine learning model lead by my supervisor• Collaborated closely with many different experts, including scientists to make efficient improvements and updates to our API, UX engineers to ensure requested changes to API functioned properly end to end, developers to gain better understanding, through paired programming, of innovative tools that could be leveraged, and project managers to organize, prioritize, and streamline projects and workflows

Rockville, Maryland, United States

• Performed demultiplexing and bioinformatics quality control, analysis, and data deliveryof Whole Exome Sequencing and, primarily, Whole Genome Sequencing data, usingsoftware and tools such as Isaac, XMAS, GATK, FastQC, AWS, and Globus• Managed techniques and key performance metrics to filter and clean data, and reviewedperformance indicators to locate and correct code and data source problems• Defined problems, reconciled data, and validated against source information• Coordinated with Lab, Sales, and IT departments, as well as clients, on data issues,communicating and explaining data analysis conclusions directly to management teamsand clients in understandable language tailored for specific audience needs• Provided insight on the statistics or results of data in response to clients' questions• Wrote or updated internal department SOP for various techniques and analyses• Promoted twice within 12-months to handle complex and advanced tasks for keycustomers

Baltimore, Maryland Area

MS in Bioinformatics (NGS focus)

Rockville, Md

• Maintained and developed a graph database representation of a bacterial pan-genome using Neo4j and Cypher scripts. Utilized a graph database to provide visualization of the pan-genome as well as access a multitude of analytic tools for manipulating data• Implemented ReactomeDB’s graph database representation of the reactome. Combined both databases to allow for simultaneous querying of both genome data and reactome data, increasing the functionality of the graph database

La Jolla, Ca

• Worked in a bioinformatics lab under the supervision of Dr. Paul Insel and supervisor Dr. Krishna Sriram. Explored association of copy number variation and differential gene expression in cancers• Utilized a principal variance component analysis script in edgeR to determine principal components that largely attribute to variance in cancer differential gene expression data

La Jolla, Ca

BS in Bioengineering: BioinformaticsMinor in Mathematics with a focus in Statistics

La Jolla, Ca

• Worked in a bioinformatics wet lab under the supervision of Dr. Julian Schroeder and supervisor Aaron Stephan. Explored the genome of mutant Arabidopsis to analyze the mechanisms and pathways that mediate resistance to environmental stresses in plants• Programmed and revised python scripts utilizing API such as Bowtie2 and SAMtools for DNA sequencing of the genomes of these mutant variants to locate single nucleotide polymorphisms

Mountain View, Ca

• Performed an independent research project, exploring how innovative informatics technologies can improve efficiency and effectiveness of airline operations center staff, such as dispatchers, by improved integration and search of the diverse data sets used during the origination, execution, and termination of flights.• Benchmarked natural language parsing technology and keyword extraction API, as well as assessed AOC data sets for automation support.

San Jose

• Worked with a team to create software to store information in documents in MongoDB. Learned REST and JSON to better understand databases. Project included implementing numerous API and facets of java, including Quartz scheduling, JavaMail, JSoup HTML Templates, HTML CSS Formatting, and JMS. • Used Git with Eclipse to share programming with other members of the team. Used Google Chrome’s Advanced Rest Client to test programs. Explored Tibco and Weblogic JMS servers.

Master'S Degree, Bioinformatics, 3.760

Activities and Societies: Eclectics

Bachelor'S Degree, Bioinformatics, 3.475

Activities and Societies: Alpha Phi OmegaMinor in Mathematics with a focus in Statistics

High School Degree

Activities and Societies: Marching Band, Science Club, Gardening Team