Senior DL/Bioinformatics scientist (to Yerevan)

About BostonGene

Since our inception in Boston in 2015, we've led the charge in oncology personal healthcare, offering an extensive array of diagnostic tools that empower clinical decisions and advance patient care. Our culture is our foundation—fueled by innovation, a commitment to transformation, and a team of authentic, driven individuals worldwide. At BostonGene, you'll find a community that's not just about the work but about making a difference, together. Join us to be a part of a future where your work contributes to transformative cancer treatments and shapes the lives of patients globally. We develop a distributed information and analytical system that provides oncologists with the necessary data for diagnosis and personalized treatment of patients.

Position Summary

BostonGene is seeking a Senior Deep Learning/Bioinformatics Scientist to lead multi-omics and NGS analyses in oncology, develop reproducible workflows, ensure GCLP/CAP compliance, mentor junior staff, and drive R&D initiatives. The role involves collaborating with cross-functional teams and representing the department in scientific and client-facing settings.

The ideal candidate for this role will have one of two profiles:

Deep Learning Specialist: High proficiency in Python and deep learning frameworks (e.g., PyTorch, with experience in multimodal approaches) is required, even without extensive background knowledge in biology and bioinformatics.

Bioinformatics Expert: High proficiency in bioinformatics is required, proficiency in scRNA/MxIF/H&E analysis as a plus, coupled with a solid understanding of deep learning methodologies.

Job responsibilities

Own the full analytical life cycle for complex oncology studies: clarify scope with internal/external clients, design analysis plan, agree QC metrics, schedule iterations and deliver publication-ready results.

Perform integrative NGS analyses (WGS/WES, RNA-seq, scRNA-seq, TCR/BCR, methylation) and advanced statistics (survival, pathway enrichment).

AI Pipeline Enhancement and Optimization: Develop and refine AI pipelines, focusing on designing neural network architectures, managing training and finetuning processes, and rigorous validation.

MLOps Implementation: Oversee the implementation and maintenance of MLOps practices.

Drive R&D initiatives: assess emerging tools, prototype novel approaches, standardize best practices across the department.

Write detailed, testable technical specifications for new workflow steps; validate delivered components from the Pipeline Development group.

Ensure traceability and regulatory compliance (GCLP/CAP): maintain audit trails, SOP alignment, participate in internal QA audits.

Contribute to internal processes improvement.

Represent the department externally: author conference abstracts, support business-development meetings.

Optional

• Delegate tasks and mentor team members; review notebooks, pull requests and slide decks, ensuring scientific rigor and timely delivery.
• Lead client communication: explain methodology to clinicians, negotiate timelines, manage expectations and resolve conflicts.

Required qualifications

• M.Sc. or PhD in Bioinformatics, Data Science, Computer Science, Computational Biology, Biostatistics or a related discipline.
• 3+ years of hands-on NGS/omics data analysis experience; for lead roles - at least 1 year in a leadership capacity overseeing analysts and managing analytical projects.
• Strong understanding of molecular oncology, tumor biology and heterogeneity; proficiency in advanced statistics; familiarity with GCLP/CAP guidelines for bioinformatics reporting and data integrity.
• Expertise in Python and R; strong Bash. Practical experience with Gitflow, Docker/Singularity, CWL/Snakemake. Confident user of standard NGS tools (e.g., bwa-mem, strelka, sequenza, STAR/STAR-Fusion, etc.).
• Ability to design, execute and validate multi-omics workflows; interpret alignment and variant-calling QC metrics; implement automated reproducibility and consistency checks.
• Hands-on experience with Jira/Confluence and agile project practices; risk tracking; preparation of client-facing technical documentation.
• English level B2 or higher: capable of writing manuscripts, preparing scientific/technical documentation, negotiating timelines and presenting to international audiences.

Skills and Abilities

• Ability to guide analysis direction, coach junior and mid-level specialists, provide structured feedback, and participate in performance reviews and talent development.
• Designs statistically rigorous studies, critically evaluates literature, and justifies analytical choices before scientific and clinical committees.
• Implements GCLP-compliant data integrity controls; prepares documentation for QA audits; coordinates with Legal teams on data-sharing and compliance topics.
• Writes optimized and scalable code; sets up and maintains CI tests; reviews complex pull requests; containerizes and deploys workflows on HPC/cloud infrastructures.
• Explains complex bioinformatics methods to clinicians and business stakeholders; prepares SoWs and change requests; resolves scope, expectation, or timeline discrepancies.
• Identifies and evaluates emerging algorithms or tools, benchmarks performance on internal datasets, and leads integration of promising solutions into production workflows.
• Aligns analytical roadmaps with broader research goals; identifies operational bottlenecks; drives cross-functional and department-wide process improvements.

Why Join Us?

Join our team at BostonGene, where your work makes a real difference! As a pioneering biotech company with a global footprint, we're passionate about improving lives through groundbreaking oncology personal healthcare. With a team of over 500 dedicated professionals, we foster an empowering environment where your unique skills contribute to a healthier, better world. At BostonGene, you're not just choosing a career; you're stepping into a role that leverages your talents to create a positive change. Discover a workplace that values you as its most precious asset, offering a competitive benefits package designed to enhance your life and those around you.

We offer:

• Full-time position with a permanent contract and flexible working hours, with hybrid work options.
• Competitive salary and comprehensive healthcare insurance.
• Convenient office location in Yerevan (1-minute walk from the metro) with on-site snacks.
• Relocation package for candidates and their immediate family members, including full documentation and bureaucracy support (bank accounts, residence permits, school contacts, etc.).
• Corporate benefits, including English language lessons and gym membership.
• Dynamic and versatile professional environment with a diverse team of bioinformaticians, biologists, physicians, and software developers committed to improving oncological healthcare.
• Careful, structured, and responsible supervision to support professional growth.