Bioinformatics Engineer, Pipelines

About the Company

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, helping scientists move from target discovery to patient outcomes at unprecedented speeds.

Responsibilities

• Design and maintain production grade bioinformatics pipelines for data modalities including microarray, cell painting, WGS, 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 internal schemas, including 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 for platform downloads

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 (genomics, single cell, imaging, flow cytometry, spatial data, or epigenomics)
• Ability to design reproducible and containerized pipelines using Docker or Singularity
• Strong understanding of secondary and tertiary data layers and integration with downstream analysis systems
• Experience integrating pipeline outputs with data stores, schemas, or ML-ready formats

Preferred Qualifications

• 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