Director, Computational Biology

Ionis Pharmaceuticals is seeking an exceptional computational biologist to lead target identification and multi-omics research efforts. In this role, you will drive the use of high-throughput transcriptomics, epigenomics, proteomics, and functional genomics data to identify and prioritize novel therapeutic targets. You will bring a strategic, industry-wide perspective on the field — staying ahead of where it is moving and translating that into a differentiated approach aligned with Ionis's RNA-targeting and oligonucleotide platforms. You will lead a team of computational biologists, shape analytical strategy, and partner tightly with biology, human genetics, and drug discovery colleagues to bring forward the next wave of therapeutic targets.

Responsibilities

• Lead the development of a target identification and prioritization pipeline using multi-omics data (transcriptomics, proteomics, metabolomics, chromatin conformation, and functional genomics – e.g. CRISPR screens)
• Define internal standards for validation of target discovery methods, including benchmarking against orthogonal datasets
• Apply rigorous model-to-human translation, evaluating cross-species conservation, model fidelity, and translational risk when nominating and de-risking targets
• Partner with the Human Genetics group to integrate genetic evidence into target identification and prioritization
• Propose targets with clear mechanistic hypotheses, building evidence packages that draw on orthogonal data and analyses
• Assess data quality, batch effects, and biological confounders throughout the analytical cycle
• Develop and maintain scalable, reproducible analytical pipelines, including human-in-the-loop-AI workflows. Use best practices in software engineering and ensure appropriate data governance and infrastructure for large-scale omics data
• Lead or contribute to cross-functional target assessment documents and portfolio decision-making meetings with clear, evidence-based scientific recommendations
• Lead a team of computational biologists fostering a culture of scientific rigor, reproducibility, and continuous learning
• Maintain working knowledge of current literature on computational biology and stay current with novel methodologies, including applicable advances in AI

Requirements

• PhD in computational biology, bioinformatics, genomics, systems biology, or a closely related quantitative field and 8+ years of relevant experience
• Proven experience in target identification and validation using multi-omics approaches in pharma or biotech
• Experience in multi-omics analyses and integration (RNA-seq, ATAC-seq, single cell, spatial transcriptomics, proteomics, metabolomics, ChIP-seq, long read RNA-seq, small RNA-seq, and functional genomics perturbation screens)
• Methodological breadth across comp-bio modeling spectrum – classical and hierarchical statistics, causal inference, Bayesian modeling, network-based and mechanistic approaches, and modern deep learning – with hands-on depth in biological foundation models
• Proficiency in Python and/or R, plus working knowledge of Bash and Docker; proficiency or familiarity with Nextflow workflows and AWS cloud stack strongly preferred
• Knowledge of human genetic analyses methods (e.g. GWAS, rare variant analyses, QTL colocalization) preferred
• Experience directly managing PhD-level scientists required
• Excellent communication skills with a track record of influencing cross-functional teams and translating complex computational findings into actionable recommendations