Post-Doctoral Research Scientist – Probes Enrichment and DNA Methylation

Zymo Research Corporation • Irvine, CA

8d • $85,000 - $100,000 • Onsite

About The Position

Zymo Research is seeking a postdoctoral research scientist to join its Epigenetics Technology group and develop next-generation sequencing (NGS) methods for targeted DNA methylation analysis and cancer research. The scientist will advance probe enrichment and library preparation programs from experimental concepts through feasibility testing, optimization, validation, and product development. This hands-on role combines molecular biology, enzymology, probe design, nucleic acid biochemistry, and sequencing library construction to improve target recovery, molecular complexity, and quantitative accuracy in low-input samples, including cell-free DNA (cfDNA) and formalin-fixed paraffin-embedded (FFPE) tissue DNA.

The position involves independently planning and conducting research across probe enrichment, DNA methylation, and cancer assay development, including variant and SNP analysis. The scientist will develop and validate novel NGS workflows, optimize probes and assays, characterize enzymes and reaction conditions, evaluate performance using reference materials and specimens, and interpret sequencing quality data in collaboration with bioinformatics scientists. The role also includes documenting results, preparing SOPs and technical transfer packages, contributing to publications and invention disclosures, and providing scientific guidance and training to Research Associates and Interns.

The position is onsite at Zymo Research headquarters in Irvine, California. The estimated annual base compensation range is $85,000–$100,000. Zymo Research describes itself as a provider of research tools and products serving the scientific community since 1994, and a workplace recognized by the Orange County Register and as a Top Workplace USA.

Requirements

• Ph.D. in molecular biology, biochemistry, epigenetics, genetics, genomics, or a related field.
• First-authored publications demonstrating original scientific contributions.
• Hands-on NGS methods development experience, including design, optimization, troubleshooting, and quantitative evaluation of sequencing library preparation workflows.
• Proficiency designing, optimizing, and troubleshooting probe-based target enrichment assays for NGS applications, including methylation and variants/SNPs.
• Strong molecular biology background, including nucleic acid manipulation, primer and probe design, PCR and qPCR/ddPCR, adapter ligation, enzymatic reactions, and DNA and library quality control.
• Strong enzymology background, including practical experience designing controlled biochemical assays, interpreting enzyme activity and substrate dependence, and optimizing reaction conditions and multi-enzyme workflows.
• Experience with DNA methylation profiling or assay development and probe-based target enrichment; understanding of how conversion chemistry and hybridization affect specificity, recovery, and downstream sequencing.
• Ability to design rigorous experiments, analyze quantitative results, distinguish technical artifacts from biological signals, and maintain clear, traceable records.
• Strong scientific writing, communication, and collaboration skills.
• Scientific objectivity, creativity, independent execution, sound judgment, strong organization, and a collaborative approach to practical product development problems.

Nice To Haves

• Experience with cancer epigenetics, liquid biopsy, cfDNA or FFPE samples, and targeted cancer methylation panels.
• Experience with exome capture assays.
• Experience with RNA-DNA hybrid biochemistry, selective digestion, protected-copy synthesis, modified nucleotides, or custom adapter architectures.
• Experience with UMI-based sequencing, linked genetic and epigenetic measurements, digital PCR, enzyme characterization or engineering, or automation and product transfer.
• Working knowledge of sequencing data analysis and statistics.
• Familiarity with R or Python and experience collaborating with bioinformatics scientists.

Responsibilities

• Independently design and execute research plans for probe enrichment, DNA methylation, and cancer assay development projects, including variant and SNP analyses.
• Define experimental controls, milestones, feasibility criteria, and technical risks; communicate progress, resource needs, and decisions to the team leader.
• Develop NGS workflows integrating target enrichment, methylation analysis, and library construction; assess compatibility among enzymatic reactions, conversion chemistry, adapter incorporation, amplification, and sequencing while minimizing sample loss and bias.
• Design and optimize DNA and RNA hybridization probes and capture panels for cancer-associated methylation regions and complementary genomic targets.
• Evaluate hybridization specificity, enrichment efficiency, target recovery, coverage uniformity, and performance across GC content and input levels.
• Develop and optimize target enrichment workflows for DNA methylation analysis, assessing specificity, recovery, reproducibility, and compatibility with downstream sequencing.
• Develop NGS methods for cancer research in collaboration with bioinformatics scientists.
• Characterize and optimize polymerases, exonucleases, ligases, and other nucleic-acid-modifying enzymes; use time-course and substrate studies to assess activity, specificity, fidelity, processivity, and reaction compatibility, and collaborate with the protein team on enzyme selection and improvement.
• Design and optimize primers and probes for qPCR, digital PCR, and targeted sequencing assays.
• Develop quantitative readouts for target enrichment, depletion, conversion, and molecule recovery, using orthogonal measurements to distinguish true recovery from amplification-related effects.
• Develop low-input workflows for cfDNA, FFPE DNA, and defined reference materials; evaluate fragment-length effects, DNA damage, conversion-related loss, amplification bias, and adapter artifacts.
• Validate assays using methylation and variant/SNP standards, defined mixtures, synthetic controls, and appropriate cancer and non-cancer specimens.
• Assess methylation accuracy, enrichment, unique molecule recovery, reproducibility, analytical sensitivity and specificity, and variant errors where applicable.
• Interpret NGS quality and performance data with bioinformatics colleagues, including on-target fraction, usable coverage, duplicates, UMI recovery, conversion metrics, and background error.
• Document results, prepare SOPs and technical transfer packages, and contribute to publications and invention disclosures.
• Provide scientific guidance and training to Research Associates and Interns assigned to the work.
• Contribute to other projects that leverage relevant skills.

Benefits

• Medical, dental, vision, and life insurance coverages
• EAP sessions
• Vacation time plus company holidays
• Paid sick leave
• Generous 401(k) with matching
• Employee referral bonus
• Complimentary fruit, snacks, and beverages
• Complimentary catered lunches on Thursdays
• Complimentary EV charging
• Cell phone stipend

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree