Mithrl · 1 week ago
Bioinformatics Engineer, Pipelines
San Francisco
Full-time
Onsite
Senior Level
$150K/yr - $200K/yr
6+ years expMithrl is building the world’s first commercially available AI Co-Scientist, transforming biological data into insights. The Lead Bioinformatics Pipeline Engineer will architect and maintain scientific processing pipelines to ensure accurate data outputs for the AI Co-Scientist.
Artificial Intelligence (AI)Data Center AutomationLife ScienceMedicalSoftware
Responsibilities
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
Qualification
Required
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
Preferred
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
Benefits
Comprehensive PPO health coverage through Anthem (medical, dental, and vision)
401(k) with top-tier plans
Company
Mithrl
Mithrl is a software development company that builds the custom workflows for NGS data on-demand.
11-50 employees
Funding
Current Stage
Early StageTotal Funding
$4MKey Investors
Bonfire Ventures
2024-11-14Seed· $4M
Leadership Team
Shara Balakrishnan, Ph.D.
Chief Technology Officer
Company data provided by crunchbase