Bioinformatics Engineer, Pipelines

Department: Engineering

Location: San Francisco

Compensation: $150K – $200K • Offers Equity

Employment Type: FullTime

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.