Functional Genomics Senior Scientist / Assistant Director

Headquartered in Carlsbad, California, and with offices in Boston, Massachusetts, and Dublin, Ireland, Ionis has been at work for more than three decades discovering medical breakthroughs that have redefined life for people with serious diseases. We're pioneers in RNA-targeted medicines, and our platform continues to revolutionize drug discovery and transform lives for patients with unmet needs. With multiple marketed medicines and a leading pipeline in neurology, cardiology and select areas of high patient needs, we continue to drive innovation in RNA therapies in addition to advancing new approaches in gene editing to provide greater value to patients and are well positioned financially to deliver on our strategic goals.

At Ionis, we pride ourselves on cultivating a challenging, motivating and rewarding environment that fosters innovation and scientific excellence. We know that our success is a direct result of the exceptional talents and dedication of our employees.

With an unprecedented opportunity to change the course of human health, we look to add diverse individuals, skill sets and perspectives to our exceptional team. We continue to invest time, money and energy into making our onsite, hybrid and remote work environments a place where solid and lasting relationships are built and where our culture and employees can thrive.

We're building on our rich history, and we believe our greatest achievements are ahead of us. If you're passionate about the opportunity to have meaningful impact on patients in need, we invite you to apply and join us. Experience and contribute to our unique culture while you develop and expand your career!

FUNCTIONAL GENOMICS SENIOR SCIENTIST / ASSISTANT DIRECTOR

SUMMARY:

We are currently seeking a qualified and highly motivated Senior Scientist or Assistant Directorto join our Functional Genomics group. The successful candidate will be an integral leader within a dynamic and collaborative research team,providing scientific and technical leadershipto support the development and maintenance of robust production pipelines for next-generation sequencing (NGS) data generation and analysis, as well as leading the integrative analysis of multi-omics data.

The ideal candidate will possess a systems-level perspective on biology, combining expertise in transcriptional regulation, protein function, and higher-order cellular and tissue biochemical interactions. This dual focus on advanced computational pipeline development and biological insight will directly support the discovery of novel therapeutics.

RESPONSIBILITIES:

• Design, build and optimize robust, production-grade pipelines for next-generation sequencing (NGS) data processing and analysis, with emphasis on reproducibility, scalability, and accuracy.
• Apply deep expertise in NGS library preparation and analysis strategies, including indexing, barcoding, and duplicate marking/removal, to support diverse experimental platforms.
• Document and organize pipeline workflows, analysis strategies, and results to facilitate knowledge sharing and reproducibility across teams.
• Collaborate with research scientists to shape biological hypotheses, design NGS-based experiments, and analyze complex multi-modal datasets to derive actionable biological insights.
• Lead cross-disciplinary teams, providing scientific guidance and facilitating effective communication of technical and biological findings to diverse stakeholders.
• Regularly present research findings, analytical strategies, and experimental results to internal scientific peers, fostering collaboration, transparency, and critical feedback.
• Participate in strategic planning and contribute to the continuous improvement of computational infrastructure and workflows within the Functional Genomics group.

REQUIREMENTS:

• Ph.D. in Computational Biology, Biological Sciences, Bioinformatics, Biostatistics, or related fields with at least 3 years of relevant industry experience (or M.Sc. with at least 6 years industry experience).
• Expertise in NGS data analysis, including end-to-end understanding of library preparation protocols, indexing schemes, and handling of technical artifacts such as PCR duplicates and barcode collisions.
• Extensive experience processing and analyzing a wide range of NGS data types, such as RNA-seq, ATAC-seq, ChIP-seq, WGS, and single-cell omics.
• Proven ability to partner with biologists to define scientific questions, design sequencing-based experiments, and interpret results in a biological context.
• Fluency in workflow development using modern frameworks (e.g., Nextflow, Snakemake, WDL, CWL) and version control (e.g., git); experience with containerization (Docker/Singularity) is a plus.
• Strong programming skills in Python and/or R, with comfort operating in Unix-based environments and using tools such as Jupyter, RStudio, or VSCode.
• Familiarity with advanced analysis methods such as differential expression, transcript isoform quantification, network analysis, and integration of multi-omic data; experience with machine learning approaches is a plus.
• Prior experience using cloud computing environments such as AWS or GCP is desirable.
• Strong written and verbal communication skills, with a demonstrated ability to mentor junior staff and lead technical projects across cross-disciplinary teams.

Please visit our website, for more information about Ionis and to apply for this position; reference requisition # IONIS003809

Ionis offers an excellent benefits package! Follow this link for more details: Ionis Benefits

Full Benefits Link:

The pay scale for this position is $115,203 to $182,354

NO PHONE CALLS PLEASE. PRINCIPALS ONLY.

Ionis Pharmaceuticals, Inc. and all its subsidiaries are proud to be EEO employers.