Job Details

Overview

ClearNote Health is seeking a motivated and detail-oriented Bioinformatics Engineer to join our team. In this role, you will support internal research initiatives and help drive successful external collaborations through the development, maintenance, and execution of bioinformatics workflows. You will work closely with other research and development personnel in the Company to understand scientific requirements and to identify bioinformatics solutions. You will incorporate a range of existing and custom software to develop robust, scalable, and reproducible bioinformatic workflows in a timely manner. The ideal candidate should have a strong working knowledge of bioinformatics tools and pipelines, excellent organization skills, and good understanding of software engineering best-practices.

Responsibilities

• Develop and maintain cloud-based bioinformatics pipelines for next-generation sequencing (NGS) data in support of the research & development team
• Collaborate with the R&D team to identify and evaluate bioinformatics tools
• Collaborate with the R&D team to develop new machine learning features suitable for machine learning models trained to detect cancer and monitor treatment response
• Document requirements including expected input and output data types and example use cases
• Develop unit tests to ensure reproducible workflows
• Track development plans and progress of sprints
• Work with the rest of the engineering team to transition computational pipelines in the research environment to use in the clinical environment
• Survey current industry practices to identify opportunities for improving our code base
• Assist with servicing of customers, including the timely execution of in-house data processing and analysis pipelines and the transfer of these data to customers

Requirements

• Experience with developing scientific workflow system (e.g. Nextflow, Snakemake) for bioinformatics analysis
• Familiarity with best practices in software engineering and strong organizational skills
• Proficiency in Unix, SQL, Python and R
• Experience with working in a cloud computing environment (e.g. AWS, Azure)
• Working knowledge of molecular biology concepts and the principles of genomics technology
• Team player with excellent communication skills
• Ability to meet deadlines
• Attentive to detail with the ability to independently investigate/troubleshoot complex computational workflows
• Strong knowledge of file formats and tools commonly used in NGS bioinformatics workflows such as fastq, BAM, vcf, bed, bedtools, reference genome, annotations, bwa, WGS, samtools
• Familiarity with containerization technology (e.g. Docker, Singularity)
• Familiarity with Git and best practices in software version control

Preferred

• Exposure to JIRA
• Experience creating visualizations for bioinformatics analysis
• Experience with differential gene expression analysis

Compensation

Compensation is based on skills, experience, and qualifications. The estimated base salary range for this position is $121,667 - $187,833, with potential variation based on depth of experience and location. This role includes stock options and generous benefits.

Location

San Mateo (Preferred), San Diego or Remote

FLSA

Exempt

Equal Opportunity

ClearNote Health is an equal opportunity employer and values diversity at our company.