CPT Senior Bioinformatics Scientist Jobs
Senior Bioinformatics Scientist roles sit at the intersection of computational biology and data science, making them a strong CPT fit for graduate students in bioinformatics, computational biology, or related programs. Your DSO must confirm the position is an integral part of your curriculum before you start work, so align your job search with your program's CPT authorization timeline.
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Get Access To All JobsAbout BOSTONGENE: BostonGene is redefining cancer patient care and drug development through the integration of omnimodal data and artificial intelligence. Built and validated through an extensive real-world clinical testing network, BostonGene’s Foundation Model of cancer and the immune system integrates genomic, transcriptomic, and immune data with clinical outcomes to generate biologically grounded, actionable insights. These insights enable biopharma partners to design and de-risk trials, identify novel targets, and optimize therapeutic response prediction across all stages of development while simultaneously improving patient care through clinically integrated innovation.
Position Overview
BostonGene is seeking a bench Scientist to join our R&D next-generation sequencing (NGS) team in our laboratory located in Waltham, MA. This candidate will support assay development and technical transfer in collaboration with immunology, production, and bioinformatics teams. The candidate will be expected to support NGS protocols, such as RNA and DNA isolation from tissue, cell-free DNA isolation from plasma, library preparation, QC, and other lab processes. The role will primarily require laboratory bench work (70-80%) in a BSL-2 laboratory.
Key Responsibilities:
- Perform assay and product development experiments of NGS workflows, including WGS, WES, and liquid biopsy assays for internal and external collaborators
- Troubleshoot and support the technical transfer of workflows to the production lab
- Maintain detailed and accurate records in LIMS, ELN, and in compliance with laboratory protocols and regulatory requirements
- Assist in the development of laboratory SOPs and batch records
- Execute and assist with validation studies, bridging studies, and technical reports
- Stay informed on emerging technologies and trends in NGS to support innovation in assay development
Qualifications
- Ph.D. in life sciences or related discipline with 0–3 years of relevant experience, OR M.S. with 3–6 years, OR B.S. with 6–10 years of hands-on experience. (The job title will be commensurate with experience.)
- Strong experience in nucleic acid extraction (DNA/RNA) from FFPE, blood, or other clinical samples
- Proficiency in NGS library prep (short-read and/or long-read), including WGS and WES
- Excellent problem-solving and troubleshooting skills
- Strong organizational skills with the ability to manage sample tracking, documentation, and inventory
Preferred Skills & Experience:
- Experience working with liquid biopsy samples (cfDNA/ctDNA, cfRNA, or exosomes)
- Familiarity with NGS QC metrics and analysis tools
- Understanding of assay validation in regulated environments (GCLP, ISO)
- Demonstrated experience in SOP development and process documentation
- Strong verbal and written communication skills, with the ability to work effectively in cross-functional teams
- Proven ability to work in a dynamic, fast-paced environment with shifting priorities
- Self-motivated and accountable, with a collaborative mindset
Additional Information
- Ability to stand for prolonged periods and perform repetitive tasks inherent to laboratory work.
About BOSTONGENE: BostonGene is redefining cancer patient care and drug development through the integration of omnimodal data and artificial intelligence. Built and validated through an extensive real-world clinical testing network, BostonGene’s Foundation Model of cancer and the immune system integrates genomic, transcriptomic, and immune data with clinical outcomes to generate biologically grounded, actionable insights. These insights enable biopharma partners to design and de-risk trials, identify novel targets, and optimize therapeutic response prediction across all stages of development while simultaneously improving patient care through clinically integrated innovation.
Position Overview
BostonGene is seeking a bench Scientist to join our R&D next-generation sequencing (NGS) team in our laboratory located in Waltham, MA. This candidate will support assay development and technical transfer in collaboration with immunology, production, and bioinformatics teams. The candidate will be expected to support NGS protocols, such as RNA and DNA isolation from tissue, cell-free DNA isolation from plasma, library preparation, QC, and other lab processes. The role will primarily require laboratory bench work (70-80%) in a BSL-2 laboratory.
Key Responsibilities:
- Perform assay and product development experiments of NGS workflows, including WGS, WES, and liquid biopsy assays for internal and external collaborators
- Troubleshoot and support the technical transfer of workflows to the production lab
- Maintain detailed and accurate records in LIMS, ELN, and in compliance with laboratory protocols and regulatory requirements
- Assist in the development of laboratory SOPs and batch records
- Execute and assist with validation studies, bridging studies, and technical reports
- Stay informed on emerging technologies and trends in NGS to support innovation in assay development
Qualifications
- Ph.D. in life sciences or related discipline with 0–3 years of relevant experience, OR M.S. with 3–6 years, OR B.S. with 6–10 years of hands-on experience. (The job title will be commensurate with experience.)
- Strong experience in nucleic acid extraction (DNA/RNA) from FFPE, blood, or other clinical samples
- Proficiency in NGS library prep (short-read and/or long-read), including WGS and WES
- Excellent problem-solving and troubleshooting skills
- Strong organizational skills with the ability to manage sample tracking, documentation, and inventory
Preferred Skills & Experience:
- Experience working with liquid biopsy samples (cfDNA/ctDNA, cfRNA, or exosomes)
- Familiarity with NGS QC metrics and analysis tools
- Understanding of assay validation in regulated environments (GCLP, ISO)
- Demonstrated experience in SOP development and process documentation
- Strong verbal and written communication skills, with the ability to work effectively in cross-functional teams
- Proven ability to work in a dynamic, fast-paced environment with shifting priorities
- Self-motivated and accountable, with a collaborative mindset
Additional Information
- Ability to stand for prolonged periods and perform repetitive tasks inherent to laboratory work.
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Get Access To All JobsSenior Bioinformatics Scientist CPT: Frequently Asked Questions
Does a Senior Bioinformatics Scientist role qualify for CPT authorization?
Yes, provided your degree program includes a bioinformatics, computational biology, or related curriculum and your DSO confirms the position is an integral part of your studies. Roles involving genomic data analysis, algorithm development, or pipeline engineering align well with graduate-level bioinformatics coursework. Your DSO makes the final determination, so bring the job description to your authorization meeting.
Can I work full-time as a Senior Bioinformatics Scientist on CPT?
Full-time CPT is allowed but affects your OPT eligibility. If you accumulate 12 or more months of full-time CPT, you lose your standard OPT and STEM OPT authorization entirely. Part-time CPT, defined as 20 hours or fewer per week, does not count against that limit. Many F-1 students in bioinformatics programs structure co-ops or internships as part-time CPT to preserve their post-graduation work authorization.
What documents does my employer need to process my CPT?
Your employer doesn't file anything with USCIS for CPT. The authorization happens entirely at your school. You'll need a written offer letter stating your start date, end date, employer name, job title, and specific duties. Your DSO uses that letter to issue an updated I-20 with CPT authorization. Bring both documents on your first day of work as proof of authorization.
How do I find Senior Bioinformatics Scientist roles where employers understand F-1 CPT?
Search Migrate Mate, which surfaces employers with verified bioinformatics hiring histories and filters for roles compatible with F-1 work authorization. Research universities, NIH-funded labs, and established biotech companies tend to have HR teams already familiar with CPT paperwork. Avoid startups without dedicated HR resources unless they've hired international students before.
Does CPT in a bioinformatics role count toward H-1B specialty occupation eligibility?
CPT work experience itself doesn't directly establish H-1B eligibility, but it does build the employment record that supports an H-1B petition later. A Senior Bioinformatics Scientist role requiring a bachelor's degree or higher in a directly related field qualifies as a specialty occupation under USCIS criteria. Document your CPT duties carefully, as that work history strengthens the employer's H-1B petition on your behalf.
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