NATHAN HEIBECK
Irvine,CA
Summary
I am an experienced bioinformatician with a strong background in next-generation sequencing and data analysis based from both academic study and industry experience. I am very team and people oriented and have natural leadership characteristics. I am eager to continue to expand my knowledge base of the field, and find new ways where my work can impact and help the lives of others!
Overview
5
5
years of professional experience
Work History
Health Science Bioinformatician
Los Angeles Department of Public Health
01.2024 - Current
- Oversee the processing of public health samples and submissions for Los Angeles County health department
- Utilize bioinformatic software to identify the phylogeny of various infectious disease agents including monkeypox, influenza, zika virus, and most notably, SARS CoV-2
- Transfer and analyze data results from the sequencers – both Illumina and Oxford Nanopore – to the Theiagen workspace and Google Cloud Server for genome assembly and strain typing
- Perform QA/QC of the assembly results from the various workflows using IGV and Nextclade, and manually adjust any assembly errors identified
- All passing samples are paired with public health information, before being prepped and submitted to three separate publicly accessibly databases – GISAID, NCBI, and GenBank
- Help to design and create a reporting dashboard for internal use to compare various metrics and trends emerging from the submitted data such as sample failure rates, submissions by region, and trending strains impacting public health
- Ensure compatibility with surveillance systems within and outside the agency
- Consult and advise epidemiologists on updated results and current trends in viral landscapes through LA county
- Work closely with public health scientist in the development of quality control system to ensure data integrity
Team lead and Bioinformatics Associate
Zymo Research
07.2021 - 01.2024
- Maintained and ran bioinformatics pipelines on both internal data for research and development purposes and public data to support health industry projects
- Designed workflows for streamlined processing and coordination of data on various projects including 16S amplicon, Shotgun WGS, metatranscriptomics, PacBio Full length 16S sequencing, metagenome assembly, and Covid strain typing
- Served as the team lead over the daily processing of next generation sequencing(NGS) data
- Coordinated the work of a small team of bioinformaticians and led analysis of NGS data through various pipelines for tens of thousands of samples annually
- Analyzed project results and implemented procedures for project improvement
- Applied new methods and approaches to troubleshoot issues and new situations
- Worked closely with Research and Development scientist, legal counsel, and marketing teams to develop quality products and quality controls
- Team lead on research project
- Developed and established a specialized modular workflow analyzing human gut microbiome health profiles utilizing NGS data (shotgun WGS data and/or 16S amplicon sequencing)
- Applied optimizations to bioinformatics softwares and pipelines using Linux, Python, R, HTML
- Served as department’s bioinformatics consultant for customer support and inquiry.
COVID-19 Testing Lab Technician
Contamination Source Identification (CSI) Laboratories
01.2020 - 01.2021
- Performed COVID-19 testing for Huntingdon, PA and surrounding areas
- Performed RNA extractions from patient swab samples for testing analysis according to regularly updated SOP’s according to CDC, CLIA and HIPPA recommendations
- Additionally, QA/QC sample prep and pipeline, document lab instrument functionality, mix reagent stock according to SOP guidelines, report lab results, and other lab housekeeping duties.
Research Assistant
Juniata College
01.2019 - 01.2021
- Conducted research focused on microbiome behavior responding to diet and co-expression patterns between a host and their incumbent gut microbiomes
- Research centered around model organisms used to replicate human microbiome networks in a variety of different mutant phenotypes
- Subjects undergo genetic analysis, assisted by several software such as RSEM, DESEQ2, and WGCNA, used for evaluating genetic co-expression between two different gene networks
- The goal being to find key gene interactions, known as node genes, that drive or mediate the co- expression between host and microbial networks
- Researched the dynamic relationship we share with our microbiomes, to determine and shape clinical therapeutic methods to address individual’s microbiome imbalances
- Prepared status briefing and presentations on project
- Presented research for peer review at conferences and led discussions with peer groups in similar fields of study.
Education
M.S. - Bioinformatics
Juniata College, College of Biology
Huntingdon, PA01.2021
B.S. - Biology
Juniata College
Huntingdon, PA01.2020
Skills
- Data Management, HIPPA, Public Health Information Security
- Leadership
- Interpersonal Communication
- Python, Linux, Rstudio, HTML
- Illumina, Oxford Nanopore Technogolies, PacificBio
- Amplicon Sequencing, Whole Genome Sequencing, Long read sequencing, Metatranscriptomics
- BWA, QIIME, Sourmash, IVG, Kraken, WGCNA, Biobakery
- Basespace, AWS, GCP
- Fastq, BAM, SAM, Fasta, VCF, BED
- NCBI, SRA, GenBank, GISAID, Greengene, Silva, Nextclade
- Strategic problem solving and planning
Presentations and Literature
ABASM 2020 -
A Lifetime Relationship: Co-expression of Host-Gut Microbial Genes Through WGCNA
M.S. Bioinformatics Thesis 2021 -
Analysis of Genetic Co-expression Within Host-Microbiome Gene Networks in Caenorhabditis Elegans Using Weighted
Correlation Network Analysis (WGCNA)
References
Dr. Regina Lamendella, Associate Professor of Biology, Head of Master’s in bioinformatics, and Co-Founder of Wrights Lab. 513-324-5252
Dr. Shuiquan Tang, Director of Bioinformatics, Microbiomics Services, Zymo Research. 1-949-394-5996
John Munteanu, Sr. Research Associate, Zymo Research. 1-562-469-9938
Timeline
Health Science Bioinformatician
Los Angeles Department of Public Health
01.2024 - Current
Team lead and Bioinformatics Associate
Zymo Research
07.2021 - 01.2024
COVID-19 Testing Lab Technician
Contamination Source Identification (CSI) Laboratories
01.2020 - 01.2021
Research Assistant
Juniata College
01.2019 - 01.2021
M.S. - Bioinformatics
Juniata College, College of Biology
B.S. - Biology
Juniata College
Similar Profiles
Louis PetersonLouis Peterson
Warehouse Worker I at County Of Los Angeles Department Of Public HealthWarehouse Worker I at County Of Los Angeles Department Of Public Health
Victor QuintanillaVictor Quintanilla
Intermediate Clerk at County Of Los Angeles Department Of Public HealthIntermediate Clerk at County Of Los Angeles Department Of Public Health
Yadira RamirezYadira Ramirez
Office Administrative Aid at Los Angeles Department of Public HealthOffice Administrative Aid at Los Angeles Department of Public Health