STEM OPT Bioinformatics Jobs
Bioinformatics roles in genomics, computational biology, and data analysis are strong matches for STEM OPT work authorization. Your STEM degree qualifies you for the 24-month extension beyond initial OPT, giving you up to 36 months total, as long as your employer is enrolled in E-Verify.
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Zymo Research is seeking a Bioinformatics Scientist to join the Epigenetics Technology team and lead computational development for epigenomics and molecular assay research. The scientist will curate datasets, discover and evaluate candidate methylation biomarkers, develop statistical models, and build reproducible analysis pipelines in close collaboration with experimental scientists.
This role combines epigenomics, statistical modeling, and software development. The scientist will guide computational strategy, define analytical performance criteria, and support targeted assay development, independent validation, and transfer into scalable research products.
Join us in making a meaningful impact!
Essential Duties and Responsibilities
- Own the computational roadmap for assigned research and assay development projects, defining deliverables, milestones, acceptance criteria, data needs, and technical risks. Coordinate priorities and dependencies with experimental scientists and support bioinformatics teams.
- Curate public and internal epigenomic datasets (methylation, hydroxymethylation). Document sample provenance, quality, relevant metadata, assay platform, genome build, and usage permissions; maintain versioned datasets with clear inclusion and quality criteria.
- Discover and prioritize candidate molecular markers and differentially methylated regions. Evaluate specificity, biological variability, common sequence variants, repetitive regions, assay compatibility, and stability across relevant sample and biological conditions.
- Develop and benchmark statistical models for molecular profiling and epigenetic biomarker analysis. Evaluate feature selection, model assumptions, uncertainty and performance supported by the available data.
- Contribute to other projects requiring relevant scientific and technical expertise.
Pipeline Development and Validation
- Build reproducible pipelines for methylation sequencing and relevant reference array datasets, covering quality control, alignment, methylation quantification, filtering, annotation, and reporting. Evaluate conversion efficiency, mapping ambiguity, duplicates, coverage, and batch effects using controls appropriate to each assay.
- Co-design targeted methylation panels with the assay team. Perform in silico assessment of primers, probes, and hybridization capture baits for sequence specificity, common variants, conversion-related sequence changes, and cross-hybridization; use empirical enrichment and coverage data to refine panel design.
- Benchmark analytical methods using reference standards, simulations, and independent sample sets. Separate model development, marker selection, and validation by biological source; assess bias, error, agreement, reproducibility, and robustness.
- Assess robustness to sequencing depth, missing data, DNA input, dataset selection, platform differences, batch effects, and relevant biological variation. Use validated harmonization approaches and prevent information leakage across development and validation datasets.
- Define quantitative reporting metrics, calibration approaches, quality thresholds, and validated reporting ranges. Document uncertainty, investigate unexpected results, and communicate analytical limitations.
- Implement automated quality checks, failure flags, versioned reports, and traceable software releases. Use code review, tests, workflow automation, and documented environments to support reproducibility and technical transfer; communicate model limitations clearly to scientific and product teams.
Additional Responsibilities
- Provide technical guidance and code review for collaborating scientists and junior bioinformatics staff. Maintain clear analysis documentation, contribute to publications and invention disclosures, and support product and customer-facing technical discussions as needed for relevant projects.
Education and Experience:
- Ph.D. in bioinformatics, computational biology, computer science, genomics, or a related discipline, with demonstrated independent ownership of substantial computational research or product development projects.
- Strong experience analyzing DNA (hydroxy)methylation or epigenomic data, including sequencing-based quantification, quality control, and biological interpretation.
- Experience with statistical modeling, biomarker discovery, or closely related quantitative methods, including rigorous study design, feature selection, and independent model validation.
Required Technical Skills
- Proficiency in Python and R, Linux or Unix, statistical analysis, and scientific visualization. Experience building maintainable analysis code with version control, automated tests, and documented workflows.
- Experience processing Illumina sequencing data, managing large genomic datasets, and developing scalable workflows using high-performance or cloud computing environments.
- Experience with epigenomic biomarker discovery, dataset curation, method benchmarking, or statistical model optimization.
- Strong communication skills and evidence of original scientific contributions through publications/posters, validated analytical methods, or deployed analysis tools (e.g. GitHub). Ability to explain uncertainty and analytical tradeoffs to multidisciplinary collaborators.
Preferred Qualifications
- Experience with targeted methylation sequencing, hybridization capture panel design, multiplex primer or probe design, or analysis of methylation-sensitive qPCR or digital PCR data.
- Experience analyzing DNA variants/SNPs using NGS data and appropriate quality control and validation methods.
- Experience comparing molecular assay results with independent measurements and assessing analytical agreement, bias, and reproducibility.
- Experience with cross-platform methylation analysis (Nanopore/PacBio), low-input assays, uncertainty estimation, workflow engines, or transfer of analytical methods into supported research products.
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 $85,000-115,000 per annum 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
- 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
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
Disclaimer:
At Zymo, we take the integrity of our hiring process seriously. Please be aware of fraudulent recruitment activities that may use our name to deceive job seekers. We will never ask for payment, sensitive personal information, or financial details during the recruitment process. All legitimate communications will come from an official Zymo or TriNet Hiring email address. If you are contacted by anyone claiming to represent us using a free email service (e.g., Gmail, Yahoo, Hotmail) or asking for payment, please treat this as fraudulent and report it immediately to careers@zymoresearch.com.
Job Summary:
Zymo Research is seeking a Bioinformatics Scientist to join the Epigenetics Technology team and lead computational development for epigenomics and molecular assay research. The scientist will curate datasets, discover and evaluate candidate methylation biomarkers, develop statistical models, and build reproducible analysis pipelines in close collaboration with experimental scientists.
This role combines epigenomics, statistical modeling, and software development. The scientist will guide computational strategy, define analytical performance criteria, and support targeted assay development, independent validation, and transfer into scalable research products.
Join us in making a meaningful impact!
Essential Duties and Responsibilities
- Own the computational roadmap for assigned research and assay development projects, defining deliverables, milestones, acceptance criteria, data needs, and technical risks. Coordinate priorities and dependencies with experimental scientists and support bioinformatics teams.
- Curate public and internal epigenomic datasets (methylation, hydroxymethylation). Document sample provenance, quality, relevant metadata, assay platform, genome build, and usage permissions; maintain versioned datasets with clear inclusion and quality criteria.
- Discover and prioritize candidate molecular markers and differentially methylated regions. Evaluate specificity, biological variability, common sequence variants, repetitive regions, assay compatibility, and stability across relevant sample and biological conditions.
- Develop and benchmark statistical models for molecular profiling and epigenetic biomarker analysis. Evaluate feature selection, model assumptions, uncertainty and performance supported by the available data.
- Contribute to other projects requiring relevant scientific and technical expertise.
Pipeline Development and Validation
- Build reproducible pipelines for methylation sequencing and relevant reference array datasets, covering quality control, alignment, methylation quantification, filtering, annotation, and reporting. Evaluate conversion efficiency, mapping ambiguity, duplicates, coverage, and batch effects using controls appropriate to each assay.
- Co-design targeted methylation panels with the assay team. Perform in silico assessment of primers, probes, and hybridization capture baits for sequence specificity, common variants, conversion-related sequence changes, and cross-hybridization; use empirical enrichment and coverage data to refine panel design.
- Benchmark analytical methods using reference standards, simulations, and independent sample sets. Separate model development, marker selection, and validation by biological source; assess bias, error, agreement, reproducibility, and robustness.
- Assess robustness to sequencing depth, missing data, DNA input, dataset selection, platform differences, batch effects, and relevant biological variation. Use validated harmonization approaches and prevent information leakage across development and validation datasets.
- Define quantitative reporting metrics, calibration approaches, quality thresholds, and validated reporting ranges. Document uncertainty, investigate unexpected results, and communicate analytical limitations.
- Implement automated quality checks, failure flags, versioned reports, and traceable software releases. Use code review, tests, workflow automation, and documented environments to support reproducibility and technical transfer; communicate model limitations clearly to scientific and product teams.
Additional Responsibilities
- Provide technical guidance and code review for collaborating scientists and junior bioinformatics staff. Maintain clear analysis documentation, contribute to publications and invention disclosures, and support product and customer-facing technical discussions as needed for relevant projects.
Education and Experience:
- Ph.D. in bioinformatics, computational biology, computer science, genomics, or a related discipline, with demonstrated independent ownership of substantial computational research or product development projects.
- Strong experience analyzing DNA (hydroxy)methylation or epigenomic data, including sequencing-based quantification, quality control, and biological interpretation.
- Experience with statistical modeling, biomarker discovery, or closely related quantitative methods, including rigorous study design, feature selection, and independent model validation.
Required Technical Skills
- Proficiency in Python and R, Linux or Unix, statistical analysis, and scientific visualization. Experience building maintainable analysis code with version control, automated tests, and documented workflows.
- Experience processing Illumina sequencing data, managing large genomic datasets, and developing scalable workflows using high-performance or cloud computing environments.
- Experience with epigenomic biomarker discovery, dataset curation, method benchmarking, or statistical model optimization.
- Strong communication skills and evidence of original scientific contributions through publications/posters, validated analytical methods, or deployed analysis tools (e.g. GitHub). Ability to explain uncertainty and analytical tradeoffs to multidisciplinary collaborators.
Preferred Qualifications
- Experience with targeted methylation sequencing, hybridization capture panel design, multiplex primer or probe design, or analysis of methylation-sensitive qPCR or digital PCR data.
- Experience analyzing DNA variants/SNPs using NGS data and appropriate quality control and validation methods.
- Experience comparing molecular assay results with independent measurements and assessing analytical agreement, bias, and reproducibility.
- Experience with cross-platform methylation analysis (Nanopore/PacBio), low-input assays, uncertainty estimation, workflow engines, or transfer of analytical methods into supported research products.
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 $85,000-115,000 per annum 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
- 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
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
Disclaimer:
At Zymo, we take the integrity of our hiring process seriously. Please be aware of fraudulent recruitment activities that may use our name to deceive job seekers. We will never ask for payment, sensitive personal information, or financial details during the recruitment process. All legitimate communications will come from an official Zymo or TriNet Hiring email address. If you are contacted by anyone claiming to represent us using a free email service (e.g., Gmail, Yahoo, Hotmail) or asking for payment, please treat this as fraudulent and report it immediately to careers@zymoresearch.com.
See all STEM OPT Bioinformatics Jobs
Sign up for free to unlock all listings, filter by visa type, and get alerts for new STEM OPT Bioinformatics Jobs.
Get Access To All JobsTips for Finding STEM OPT Authorization in Bioinformatics
Verify your CIP code matches bioinformatics
Your degree's Classification of Instructional Programs code must map to a STEM-designated field. Check your I-20 and confirm with your DSO that your program qualifies, since bioinformatics, computational biology, and related fields each have distinct CIP codes.
Confirm E-Verify enrollment before accepting offers
Before signing, ask your hiring contact to confirm their E-Verify Company ID or look it up through E-Verify's employer search. Smaller biotech startups and university-affiliated labs frequently lack E-Verify enrollment, which disqualifies them from hosting STEM OPT extensions.
Use Migrate Mate to target verified bioinformatics employers
Search Migrate Mate to find bioinformatics roles at employers already confirmed as E-Verify participants. Filtering for verified employers at the research stage saves time and prevents late-stage offer complications once your STEM OPT extension timeline is already in motion.
Build your I-983 training plan around job duties
Your Form I-983 must list specific learning objectives tied to your actual role, not a generic job description. For bioinformatics positions, map duties like pipeline development, variant calling, or RNA-seq analysis directly to the STEM learning goals your DSO must sign off on.
Check O*NET to align your job title with STEM criteria
USCIS expects the offered role to require a STEM degree. Cross-referencing your job title against O*NET confirms whether the occupation is classified as STEM-qualifying, which strengthens your extension application and gives your employer documentation support if questions arise.
File your STEM OPT extension application 90 days early
USCIS requires your I-765 extension application to be filed at least 90 days before your initial OPT expires. Bioinformatics job timelines can stretch, so starting this process while still interviewing protects your authorization gap and preserves your full 24-month extension window.
Frequently Asked Questions
Does my bioinformatics degree qualify me for the STEM OPT extension?
Your degree qualifies if its CIP code appears on the STEM Designated Degree Program List maintained by the Department of Homeland Security. Degrees in bioinformatics, computational biology, biostatistics, and related fields typically qualify, but the determining factor is your specific program's CIP code on your I-20, not the degree title. Confirm with your DSO before applying.
Do bioinformatics employers need to be on E-Verify for STEM OPT?
Yes. E-Verify enrollment is a hard requirement for any employer hosting a STEM OPT extension student, not a preference. If your employer isn't enrolled, your extension cannot be approved regardless of how well the role matches your degree. Before you reach the offer stage, search E-Verify's employer directory or ask your recruiter directly for their Company ID.
What goes into the I-983 training plan for a bioinformatics role?
The I-983 requires a structured training plan that links your specific job duties to concrete STEM learning goals. For bioinformatics, this means documenting how tasks like genomic data analysis, algorithm development, or database pipeline work advance skills in your field. Both you and your employer supervisor must sign it, and your DSO must receive a copy before your extension is filed with USCIS.
How does cap-gap work if my H-1B is selected while I'm on STEM OPT?
If your H-1B visa petition is filed and accepted before your STEM OPT authorization expires, cap-gap automatically extends your work authorization through September 30 of that year. This keeps you employed continuously while USCIS adjudicates your H-1B. Your employer doesn't need to take any separate action, but your DSO should update your SEVIS record to reflect the cap-gap status.
Where can I find bioinformatics jobs at E-Verify enrolled employers?
Migrate Mate lists bioinformatics roles filtered for E-Verify compliance, which removes the most common early-stage obstacle for STEM OPT students. Many postings on general platforms don't disclose E-Verify status, forcing you to find out late in the process. Searching through Migrate Mate surfaces employers already confirmed as eligible hosts before you invest time in applications.