Bioinformatics Engineer, Pipelines

Mithrl•San Francisco, CA

1d•Onsite

About The Position

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.

Requirements

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 Haves

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

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