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Transcriptomics Jobs in California (NOW HIRING)

Ionis

Director, Computational Biology

Carlsbad, CA · On-site +1

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 ...

Novartis

Senior Expert I, Data Science

San Diego, CA

$126K - $234K/yr

Integrate multi-modal internal and external preclinical datasets (e.g., genomics, transcriptomics, pharmacology, and functional screens) to produce translationally relevant insights. Apply advanced ...

Valius Sciences

Medical Director

San Francisco, CA · On-site

$400K - $800K/yr

This coming year, we're on track to scale our patient volume significantly, all while bringing new diagnostic modalities (e.g., single-cell transcriptomics) and analytical approaches into clinical ...

Valius Sciences

Medical Director

San Francisco, CA · On-site

$200 - $300/hr

This coming year, we're on track to scale our patient volume significantly, all while bringing new diagnostic modalities (e.g., single-cell transcriptomics) and analytical approaches into clinical ...

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All JobsTranscriptomics JobsTranscriptomics Jobs in California

Transcriptomics information

What are the key skills and qualifications needed to thrive as a Transcriptomics Scientist, and why are they important?

To thrive as a Transcriptomics Scientist, you need a strong background in molecular biology, genomics, and bioinformatics, typically supported by an advanced degree in a relevant field. Familiarity with next-generation sequencing (NGS) platforms, RNA-seq analysis pipelines, and programming languages like R or Python is essential. Attention to detail, problem-solving abilities, and effective communication skills set outstanding candidates apart. These competencies are vital for generating accurate transcriptomic data, interpreting complex results, and collaborating within multidisciplinary research teams.

What does transcriptomics do?

Transcriptomics is a field within molecular biology that studies the complete set of RNA transcripts produced by a genome under specific conditions. Professionals in this area analyze gene expression patterns using tools like RNA sequencing to understand cellular functions and disease mechanisms.

What biology jobs pay over $100k?

In the field of transcriptomics, roles such as senior research scientist, bioinformatics director, and molecular biology manager often have salaries exceeding $100,000 annually. These positions typically require advanced degrees, extensive experience, and skills in data analysis, programming, and laboratory techniques.

What is transcriptomics?

Transcriptomics is the study of the complete set of RNA transcripts produced by the genome under specific circumstances or in a specific cell. It provides insights into gene expression patterns, how genes are regulated, and how cells respond to various conditions. By analyzing the transcriptome, researchers can better understand biological processes, disease mechanisms, and identify potential targets for therapy. Technologies such as RNA sequencing (RNA-seq) are commonly used in transcriptomics research.

What are some common challenges faced by professionals working in transcriptomics, and how can they be addressed?

Professionals in transcriptomics frequently encounter challenges such as handling large and complex datasets, ensuring data quality, and staying current with rapidly evolving analytical tools and technologies. Working closely with bioinformaticians and statisticians is essential for effective data analysis and interpretation. Additionally, clear communication and collaboration with wet-lab biologists and clinicians help bridge the gap between raw data and meaningful biological insights. Regular training and professional development can help transcriptomics professionals stay updated with the latest best practices and software advancements.

What is the highest paying job in genetics?

In genetics, roles such as genetic counselors, research directors, and senior clinical geneticists tend to have the highest salaries, often exceeding six figures annually. Positions requiring advanced degrees, specialized skills, and leadership responsibilities typically offer the highest compensation in the field.

What is the highest paying job in bioinformatics?

In bioinformatics, senior roles such as bioinformatics directors, principal scientists, or lead data scientists tend to have the highest salaries, often exceeding $150,000 annually. These positions typically require advanced skills in programming, data analysis, and experience with large-scale genomic or transcriptomic data, along with leadership responsibilities.

What is the difference between Transcriptomics vs Bioinformatics?

AspectTranscriptomicsBioinformatics
Required credentialsBachelor's or Master's in Biology, Genetics, or related fields; experience with sequencing technologiesBachelor's or Master's in Computer Science, Bioinformatics, or related fields; programming skills
Work environmentLaboratories, research institutions, biotech companiesResearch labs, biotech firms, academic institutions, data analysis centers
Industry usageGenomics, molecular biology, medical researchData analysis, software development, computational biology

While both Transcriptomics and Bioinformatics involve analyzing biological data, Transcriptomics focuses on studying gene expression profiles using sequencing technologies, whereas Bioinformatics encompasses a broader range of computational methods to analyze various biological datasets. Professionals in both fields often collaborate but have distinct skill sets and work environments.

What are popular job titles related to Transcriptomics jobs in California? For Transcriptomics jobs in California, the most frequently searched job titles are:
What job categories do people searching Transcriptomics jobs in California look for? The top searched job categories for Transcriptomics jobs in California are:
What cities in California are hiring for Transcriptomics jobs? Cities in California with the most Transcriptomics job openings:
Transcriptomics jobs near you
Infographic showing various Transcriptomics job openings in California as of July 2026, with employment types broken down into 93% Full Time, 4% Part Time, 1% Temporary, and 2% Contract. Highlights an 93% Physical, 3% Hybrid, and 4% Remote job distribution.

Director, Computational Biology

Ionis

Carlsbad, CA • On-site, Remote

Full-time

Re-posted 10 days ago

Job description

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!
DIRECTOR, COMPUTATIONAL BIOLOGY
SUMMARY:
We are 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 which will align 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 - statistical rigor and reproducibility are paramount.
  • Develop and maintain scalable, reproducible analytical pipelines, including human-in-the-loop-AI workflow as required. 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 the 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 required.
  • Proven experience in target identification and validation using multi-omics approaches in a pharma or biotech.
  • Experience in multi-omics analyses and integration (including RNA-seq, ATAC-seq - bulk, single cell - spatial transcriptomics, proteomics, metabolomics, ChIP-seq and similar, 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 (fine-tuning, interpretability, efficient deployment) and the judgment to match method to biological question and data.
  • Proficiency in Python and/or R, plus working knowledge of Bash and Docker is required, 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 etc.) is preferred.
  • Experience directly managing PhD-level scientists is required.
  • Excellent communication skills across audiences, with a track record of influencing cross-functional teams (including non-computational partners) and translating complex computational findings into clear, actionable recommendations that inform senior leadership on portfolio and target decisions.

Please visit our website, http://www.ionis.com for more information about Ionis and to apply for this position; reference requisition # IONIS004015
Ionis offers an excellent benefits package! Follow this link for more details: Ionis Benefits
Full Benefits Link: https://ionis.com/careers#:~:text=Highly%20competitive%20benefits
The pay scale for this position is $200,385 to $250,332
NO PHONE CALLS PLEASE. PRINCIPALS ONLY.
Ionis Pharmaceuticals, Inc. and all its subsidiaries are proud to be EEO employers.
Equal Opportunity Employer
This employer is required to notify all applicants of their rights pursuant to federal employment laws.
For further information, please review the Know Your Rights notice from the Department of Labor.

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