Post-Doctoral Research Scientist – Probes Enrichment and DNA Methylation

Zymo Research; Irvine (CA); On-site; USD 85,000 - 100,000; Full time

Benefits offered by this job

Medical, Dental, Vision, and Life

401(K) with matching

Employee Referral Bonus

Fruit, snacks, and beverages

Catered lunches on Thursdays

EV charging

Cell phone stipend

Job summary

Zymo Research Corporation is seeking a postdoctoral research scientist to advance NGS methods for targeted DNA methylation analysis and cancer research within the Epigenetics Technology group. The role covers probe enrichment, library preparation, and quantitative accuracy in low-input samples, including cfDNA and FFPE DNA.

The ideal candidate brings a strong molecular biology and enzymology background and hands-on NGS development experience, with opportunities to contribute to publications and

Qualifications

• PhD with first-authored publications demonstrating original contributions.
• Hands-on NGS methods development including library prep workflows.
• Experience with probe-based target enrichment for methylation & variants.

Responsibilities

• Design and execute research plans across probe enrichment, methylation, and cancer assay development.
• Develop NGS workflows integrating target enrichment, methylation analysis, and library construction.
• Design primers/probes for qPCR/ddPCR and targeted sequencing assays; provide quantitative readouts.
• Collaborate with bioinformatics to interpret data and prepare transfer packages.

Skills

Molecular biology

Enzymology

NGS methods development

Probe design

qPCR/ddPCR

Data analysis

Education

PhD in molecular biology

Epigenetics

Biochemistry

Genomics

Tools

R

Python

Exome capture

UMI-based sequencing

Job description

Zymo Research is seeking a postdoctoral research scientist to join the Epigenetics Technology group and develop next-generation sequencing (NGS) methods for targeted DNA methylation analysis and cancer research. The scientist will advance multiple probe enrichment and library preparation programs, from experimental concepts through feasibility testing, optimization, validation, and product development.

This hands-on role requires a strong background in molecular biology and enzymology and demonstrated NGS methods development experience. The scientist will integrate 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.

Join us in making a meaningful impact!

Essential Duties and Responsibilities

• Independently design and execute research plans across probe enrichment, DNA methylation, and cancer assay (variants/SNPs) development projects. Define controls, milestones, feasibility criteria, and technical risks; communicate progress, resource needs, and decisions to the team leader.
• Develop novel NGS workflows that integrate target enrichment, methylation analysis, and library construction. Analyze compatibility of 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 (variants/SNPs analyses). Evaluate hybridization specificity, enrichment efficiency, target recovery, coverage uniformity, and performance across GC content and input levels.
• Be willing to contribute to other projects leveraging relevant skills.

Experimental Development and Validation

• Develop and optimize novel target enrichment workflows for DNA methylation analysis, evaluating specificity, recovery, reproducibility, and compatibility with downstream sequencing.
• Develop innovative NGS methods for cancer research, integrating molecular biology and enzymology to improve assay performance in collaboration with bioinformatics scientists.
• Apply enzymology to characterize and optimize polymerases, exonucleases, ligases, etc and other nucleic acid-modifying enzymes. Use time-course and substrate studies to assess activity, specificity, fidelity, processivity, and reaction compatibility; 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 & variant/SNP standards, defined mixtures, synthetic controls, and appropriate cancer and non-cancer specimens. Assess methylation accuracy, enrichment, unique molecule recovery, reproducibility, and analytical sensitivity and specificity; characterize 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.

Supervisory Responsibilities and Core Competencies

• Provide scientific guidance and training to potential Research Associates and Interns assigned to the work. Demonstrate scientific objectivity, creativity, independent execution, sound judgment, strong organization, and a collaborative approach to solving practical product development problems.

Education and Experience

• Ph.D. in molecular biology, biochemistry, epigenetics, genetics, genomics, or a related field, with first-authored publications demonstrating original scientific contributions.
• Demonstrated hands-on NGS methods development experience, including design, optimization, troubleshooting, and quantitative evaluation of sequencing library preparation workflows.
• Proficiency in designing, optimizing, and troubleshooting probe-based target enrichment assays for NGS applications (methylation & variants/SNPs).

Required Scientific and Technical Skills

• 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 with 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, with an 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.

Preferred Qualifications

• 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.

About Us:

Since its inception in 1994, Zymo Research has been proudly serving the scientific community by providing innovative, reliable, and high-quality research tools and products. Whether it's DNA, RNA, epigenetics, microbiomics, protein, or yeast-based research, our philosophy remains the same: To provide the highest quality products in the industry while ensuring they are both simple to use and reliable in their performance.

Recognized as a Top Workplace by the Orange County Register in 2021, 2022, and named a Top Workplace USA in 2023, Zymo Research continues to be a vibrant community where employees thrive, feel connected, and are inspired by their work. If you are passionate about contributing to scientific advancement and want to be part of an exceptional team in a dynamic, growing company, we'd love to hear from you!

Compensation, Benefits, and Perks:

The estimated base compensation range for this position is $85,000-100,000 annually at the time of posting. Actual compensation details will be provided in writing at the time of offer, if applicable, and is based on several factors we believe fairly and accurately impact compensation, including geographic location, experience, knowledge, skills, abilities, and other job permitted factors.

Zymo Research also offers competitive benefits and perks including:

• Medical, Dental, Vision, and Life Insurance Coverages
• EAP Sessions
• Generous 401(K) with matching
• Employee Referral Bonus
• Complimentary fruit, snacks, and beverages
• Complimentary catered lunches on Thursdays
• Complimentary EV Charging
• Cell phone stipend

Equal Employment Opportunity Employer:

Zymo Research welcomes candidates of all backgrounds. These include sex, age, color, race, religion, marital status, national origin, ancestry, sexual orientation, gender, gender identity, gender expression, physical & mental disability, medical condition, genetic information, military and veteran status, or any other protected status as defined by federal, state, or local law.

Location:

Onsite – Zymo Research HQ - 17062 Murphy Ave, Irvine, CA 92614