Ionis Pharmaceuticals, Inc.
Functional Genomics Senior Scientist / Assistant Director
Ionis Pharmaceuticals, Inc., Carlsbad, California, United States, 92002
Overview
Ionis Pharmaceuticals, Inc. is headquartered in Carlsbad, California, with offices in Boston, Massachusetts, and Dublin, Ireland. Ionis is a leader in RNA-targeted medicines with a growing pipeline in neurology, cardiology and high-need areas, and is advancing gene editing approaches to deliver value to patients. We are building a challenging, motivating and rewarding environment that fosters innovation and scientific excellence. We value diverse talents and perspectives and support onsite, hybrid and remote work environments to foster collaboration and growth. If you’re passionate about meaningful impact on patients, apply to join us. Functional Genomics Senior Scientist / Assistant Director
Summary We are currently seeking a qualified and highly motivated Senior Scientist or Assistant Director to join our Functional Genomics group. The successful candidate will be an integral leader within a dynamic and collaborative research team, providing scientific and technical leadership to 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. Qualifications
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. Ionis offers an excellent benefits package. The pay scale for this position is $115,203 to $182,354. No phone calls. Principals only. Ionis is an equal opportunity employer.
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Ionis Pharmaceuticals, Inc. is headquartered in Carlsbad, California, with offices in Boston, Massachusetts, and Dublin, Ireland. Ionis is a leader in RNA-targeted medicines with a growing pipeline in neurology, cardiology and high-need areas, and is advancing gene editing approaches to deliver value to patients. We are building a challenging, motivating and rewarding environment that fosters innovation and scientific excellence. We value diverse talents and perspectives and support onsite, hybrid and remote work environments to foster collaboration and growth. If you’re passionate about meaningful impact on patients, apply to join us. Functional Genomics Senior Scientist / Assistant Director
Summary We are currently seeking a qualified and highly motivated Senior Scientist or Assistant Director to join our Functional Genomics group. The successful candidate will be an integral leader within a dynamic and collaborative research team, providing scientific and technical leadership to 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. Qualifications
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. Ionis offers an excellent benefits package. The pay scale for this position is $115,203 to $182,354. No phone calls. Principals only. Ionis is an equal opportunity employer.
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