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Transcriptomics Jobs in El Sobrante, CA (NOW HIRING)

Mithrl

Bioinformatics Engineer, Pipelines

San Francisco, CA · On-site

$150K - $200K/yr

These workflows include microarray, imaging, spatial transcriptomics, genomics, epigenomics, flow cytometry, and more. This role sits at the center of our technical stack. You will architect Nextflow ...

Vivodyne

Senior Bioinformatician

San Francisco, CA · On-site

We are expanding our capabilities to generate high-throughput -omics data across automated human tissue models, with a primary focus on single-cell and bulk transcriptomics, secretomics, and ...

Mithrl

Bioinformatics Engineer, Pipelines

San Francisco, CA · On-site

$150K - $200K/yr

These workflows include microarray, imaging, spatial transcriptomics, genomics, epigenomics, flow cytometry, and more. This role sits at the center of our technical stack. You will architect Nextflow ...

Nudge

Histotechnologist

San Francisco, CA · On-site

Prepare and process samples for spatial omics platforms, including multiplexed protein imaging and spatial transcriptomics, with both RNA- and protein-based tagging approaches * Develop, optimize ...

nudge

Histotechnologist

San Francisco, CA · On-site

Prepare and process samples for spatial omics platforms, including multiplexed protein imaging and spatial transcriptomics, with both RNA- and protein-based tagging approaches * Develop, optimize ...

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All JobsTranscriptomics JobsTranscriptomics Jobs in El Sobrante, CA

Transcriptomics information

See El Sobrante, CA salary details

$52.8K

$219.3K

$431.2K

How much do transcriptomics jobs pay per year?

As of Jul 15, 2026, the average yearly pay for transcriptomics in El Sobrante, CA is $219,350.00, according to ZipRecruiter salary data. Most workers in this role earn between $84,600.00 and $431,200.00 per year, depending on experience, location, and employer.

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 cities near El Sobrante, CA are hiring for Transcriptomics jobs? Cities near El Sobrante, CA with the most Transcriptomics job openings:
Transcriptomics jobs near you

Bioinformatics Engineer, Pipelines

Mithrl

San Francisco, CA • On-site

$150K - $200K/yr

Full-time

Medical, Dental, Vision, Retirement

Re-posted 16 days ago

Job description

ABOUT MITHRL
We imagine a world where new medicines reach patients in months, not years, and where scientific breakthroughs happen at the speed of thought.
Mithrl is building the world's first commercially available AI Co-Scientist. It is a discovery engine that transforms messy biological data into real insights in minutes. Scientists ask questions in natural language, and Mithrl responds with analysis, novel targets, hypotheses, and patent-ready reports.
Our traction speaks for itself:
  • 12X year-over-year revenue growth
  • Trusted by leading biotechs and big pharma across three continents
  • Driving real breakthroughs from target discovery to patient outcomes.

ABOUT THE ROLE
We are looking for a Lead Bioinformatics Pipeline Engineer to build and scale Mithrl's multi modal scientific processing pipelines. You will own the workflows that transform raw biological data into clean, reproducible outputs that power Mithrl's AI Co-Scientist. These workflows include microarray, imaging, spatial transcriptomics, genomics, epigenomics, flow cytometry, and more.
This role sits at the center of our technical stack. You will architect Nextflow and nf-core style pipelines, implement modality-specific validation and QC layers, and collaborate with the Tabular Data Team and Knowledge Curation Team to ensure downstream data harmonization, variable ID mapping, and schema alignment. Your work ensures that scientists can ask questions and receive accurate data-backed answers instantly.
If you enjoy building robust scientific workflows and want to work on high impact problems, you will thrive here.
WHAT YOU WILL DO
  • Design and maintain production grade bioinformatics pipelines for a wide range of data modalities, including microarray, cell painting, WGS and WES, spatial transcriptomics, flow cytometry, ATAC-seq, and methyl-seq
  • Build workflows using Nextflow, nf-core modules, or similar engines with a focus on reproducibility, validation, and scalability
  • Implement quality control, validation, and provenance tracking for all supported modalities
  • Collaborate with the Tabular Data Team to ensure pipeline outputs map cleanly into Mithrl's internal schemas, including variable ID coercions, metadata normalization, and feature name harmonization
  • Work with the Knowledge Curation Team to align outputs with reference genomes, annotations, and biological ontologies
  • Produce structured output artifacts so users can download processed data and supporting metadata directly through the platform

WHAT YOU BRING
Required Qualifications
  • 6 to 8 years of experience in bioinformatics workflow engineering or computational biology
  • Strong experience with Nextflow, nf-core, WDL, CWL, Snakemake, or similar workflow systems
  • Proficiency in Python or R for data processing, QC, and pipeline logic
  • Hands-on experience building pipelines for multiple biological data types, including genomics, single cell, imaging, flow cytometry, spatial data, or epigenomics
  • Ability to design pipelines that are reproducible and containerized using Docker or Singularity
  • Strong understanding of secondary and tertiary data layers and how they integrate with downstream analysis systems
  • Experience integrating pipeline outputs with data stores, schemas, or ML-ready formats

Nice to Have
  • Experience executing pipelines in cloud environments such as AWS Batch, ECS, Tower, or Nextflow Cloud
  • Experience with imaging workflows such as CellProfiler, DeepCell, or Squidpy
  • Familiarity with genomic reference databases, annotation formats, and biological ontologies
  • Previous work in a tech bio startup, biotech R&D group, or scientific software company

WHAT YOU WILL LOVE AT MITHRL
  • You will build the core pipelines that transform raw biological data into insights used by the AI Co-Scientist
  • Team: Join a tight-knit, talent-dense team of engineers, scientists, and builders
  • Culture: We value consistency, clarity, and hard work. We solve hard problems through focused daily execution
  • Speed: We ship fast (2x/week) and improve continuously based on real user feedback
  • Location: Beautiful SF office with a high-energy, in-person culture
  • Benefits: Comprehensive PPO health coverage through Anthem (medical, dental, and vision) + 401(k) with top-tier plans

We encourage you to apply even if you do not believe you meet every single qualification. Not all strong candidates will meet every single qualification as listed. Research shows that people who identify as being from underrepresented groups are more prone to experiencing imposter syndrome and doubting the strength of their candidacy, so we urge you not to exclude yourself prematurely and to submit an application if you're interested in this work. We think AI systems like the ones we're building have enormous social and ethical implications. We think this makes representation even more important, and we strive to include a range of diverse perspectives on our team.

Apply