(Senior) Bioinformatician, Foundation Models and Discovery
Deep Genomics
Toronto, ON, Canada
Posted on Sep 13, 2025
About Us
Deep Genomics is at the forefront of using artificial intelligence to transform drug discovery. Our proprietary AI platform decodes the complexity of RNA biology to identify novel drug targets, mechanisms, and therapeutics inaccessible through traditional methods. With expertise spanning machine learning, bioinformatics, data science, engineering, and drug development, our multidisciplinary team in Toronto and Cambridge, MA is revolutionizing how new medicines are created.
About the Role
Join us in building the future of AI-driven target discovery as a (Senior) Bioinformatician in our Systems and Target Biology (STB) group. In this role, you will be responsible for leveraging large-scale genomics and transcriptomic datasets to aid in the construction and application of foundation models (FMs). You will also contribute across teams to help process, analyze, and draw conclusions from multi-modal functional genomics data for target discovery. You will be building, executing, and maintaining automated pipelines for the analysis of large-scale -omics data. You will work collaboratively with our statistical genetics, machine learning science, engineering, and biology teams to support and accelerate scientific discovery.
Key Responsibilities
- Develop workflows for -omics data processing and analyses; this may include whole genome, whole exome, array, RNA-seq, proteomic data, single-cell -omics, etc.
- Interpret complex -omics analyses to generate novel biological hypotheses & insights.
- Work closely with ML scientists to develop workflows for ML model evaluation.
- Work collaboratively with engineering teams to develop robust tools and software packages.
- Generate effective data interfaces, such as data visualization and dashboards, as needed.
- Implement novel computational tools and technologies, as needed.
Basic Qualifications
- Masters in bioinformatics, data science, computer science or related fields.
- 2 to 4+ years of hands-on experience with -omics data processing and developing standardized reproducible processing pipelines (Mid-Level or Senior level position determined by the candidate’s level of experience).
- Knowledge of core biological concepts, including human genetics, RNA biology and genomics.
- Basic knowledge of common bioinformatics tools (e.g. SAMTools, BCFTools, DESeq2 and aligners BWA/STAR) and file format (BAM, VCF etc.).
- Strong programming (Python preferred) and command line (shell) skills.
- Experience with high-throughput or cloud based computing.
- Excellent documentation, communication and interpersonal skills
Preferred Qualifications
- Familiarity with machine learning or AI models in the context of -omics.
- Experience in applying AI models to large-scale datasets and some knowledge of target discovery or population genomics.
- Experience with a version control system like Git.
- Direct experience with public datasets with human -omic or genetic data e.g., GTEx, gnomAD.
- Experience with containerization technologies (e.g., Docker) and workflow management systems (e.g., Cromwell / WDL, NextFlow) is a plus
What we offer
- A collaborative and innovative environment at the frontier of computational biology, machine learning, and drug discovery.
- Highly competitive compensation, including meaningful stock ownership.
- Comprehensive benefits - including health, vision, and dental coverage for employees and families, employee and family assistance program.
- Flexible work environment - including flexible hours, extended long weekends, holiday shutdown, unlimited personal days.
- Maternity and parental leave top-up coverage, as well as new parent paid time off.
- Focus on learning and growth for all employees - learning and development budget & lunch and learns.
- Facilities located in the heart of Toronto - the epicenter of machine learning and AI research and development, and in Kendall Square, Cambridge, Mass. - a global center of biotechnology and life sciences
Deep Genomics welcomes and encourages applications from people with disabilities. Accommodations are available on request for candidates taking part in all aspects of the selection process.
Deep Genomics thanks all applicants, however only those selected for an interview will be contacted.
