Senior DL/Bioinformatics scientist (to Yerevan)

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.

Requirements

• 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.

We offer:

• Relocation support for candidates (and their immediate family members) to Armenia.
• Complete documentation and bureaucracy support on-site (bank accounts, residence permit, school contacts, etc.).
• Full-time position, permanent contract, flexible working hours, hybrid work.
• The office is located in Yerevan, within a 1-minute walk from the metro, and on-site snacks.
• Competitive salary.
• Healthcare insurance, corporate plans for English language lessons, and gym.
• Versatile professional environment: bioinformatics, biologists, physicians, and software developers who united to save people’s lives.