Bioinformatics Scientist -- NGS Assay Development (Remote)

Pillar Biosciences Incorporated; United States; On-site; USD 90,000 - 120,000; Full time

Job summary

Pillar Biosciences Incorporated is seeking a hands‑on Bioinformatics Scientist to design, evaluate, and improve targeted NGS assays. You will combine programming with human genomics to analyze sequencing data and translate findings into actionable improvements.

You will collaborate across molecular biology, software, product development, regulatory, and clinical teams to deliver robust, reproducible analyses and clear technical conclusions.

Qualifications

• MS or PhD in bioinformatics, computational biology, genetics, genomics, or related field.
• Hands‑on programming experience in Python, R, or similar language.
• Strong knowledge of human genomics and variation.
• Experience analyzing human NGS data, including alignment and variant analysis.
• Familiarity with FASTQ/BAM/CRAM/VCF formats and common tools (BWA, samtools, GATK).
• Ability to independently investigate complex datasets and communicate conclusions.
• Proven ability to produce reproducible analyses and technical documentation.
• Strong organizational skills and cross‑functional collaboration.

Responsibilities

• Develop reproducible analyses and computational workflows in Python, R, and Bash.
• Analyze sequencing data (SNVs, indels, CNVs, fusions) and performance metrics.
• Investigate assay failures using sequencing data and genomic context.
• Support development of targeted amplicon‑based NGS workflows.
• Research genomic targets using ClinVar, gnomAD, TCGA, dbSNP, and literature.
• Collaborate with molecular biology, software, product, and regulatory teams.
• Develop scripts and methods to improve assay development efficiency.
• Maintain well‑documented analyses with version control and provenance.
• Communicate findings through concise reports and presentations.
• Manage multiple projects with clear records of methods and results.

Skills

Python

R

Education

MS/PhD in bioinformatics

Tools

GATK

samtools

bedtools

BWA

VCF

Job description

Our bioinformatics team develops and supports next-generation sequencing assays for oncology and other human genomic applications. We are seeking a hands‑on bioinformatics scientist who can combine strong programming skills with human genomics expertise to support the design, evaluation, and improvement of targeted NGS assays. This role is well suited to someone who enjoys working directly with sequencing data, investigating unexpected assay behavior, developing reproducible analyses, and translating complex findings into clear technical conclusions. The scientist will work closely with molecular biology, software, product development, regulatory, and clinical teams.

Responsibilities

• Develop reproducible analyses and computational workflows in Python, R, and/or Bash to evaluate NGS assay performance.
• Analyze DNA and RNA sequencing data generated from targeted assays, including SNVs, indels, CNVs, fusions, coverage, assay artifacts, and other performance characteristics.
• Investigate assay failures and unexpected results using sequencing data, genomic context, experimental metadata, and appropriate statistical or computational approaches.
• Support development and optimization of targeted amplicon-based NGS assay workflows.
• Use public genomic and oncology resources such as ClinVar, gnomAD, TCGA/cBioPortal, dbSNP, and primary literature to research genomic targets and interpret assay results.
• Work closely with molecular biology scientists to translate experimental observations into testable computational analyses and assay improvements.
• Develop tools, scripts, and analytical methods that improve the efficiency, robustness, or interpretability of assay development.
• Maintain well-organized, reproducible analyses with clear version control, data provenance, and documentation.
• Communicate findings through concise technical reports, figures, presentations, protocols, and other documentation that can be understood by both computational and non-computational collaborators.
• Manage multiple development projects and analyses while maintaining clear records of assumptions, methods, results, and outstanding questions.

Qualifications

• MS or PhD in bioinformatics, computational biology, genetics, genomics, or a related field.
• Demonstrated hands‑on programming experience in Python, R, or another general‑purpose scientific programming language. Candidates should be comfortable writing their own analysis code rather than relying primarily on graphical or preconfigured analysis tools.
• Strong knowledge of human genomics and genetic variation.
• Experience analyzing human NGS data, including alignment, QC, variant analysis, and interpretation.
• Familiarity with common genomics file formats and tools such as FASTQ, BAM/CRAM, VCF, BED, BWA, samtools, bedtools, GATK, or equivalent tools.
• Demonstrated ability to independently investigate complex datasets, identify the source of analytical or experimental problems, and communicate conclusions.
• Strong scientific writing and documentation skills, with evidence of producing reproducible analyses, technical documentation, protocols, reports, publications, or similar work.
• Strong organizational skills and ability to manage multiple analyses and development activities with appropriate documentation and follow-through.
• Ability to communicate effectively with molecular biologists, software engineers, and other cross‑functional collaborators.

Preferred Qualifications

• Experience developing or analyzing targeted NGS assays using amplicon sequencing or hybrid capture.
• Experience with oncology genomics, somatic variant analysis, low‑input DNA, FFPE, cfDNA, or other clinically relevant sample types.
• Experience evaluating assay performance metrics such as coverage, uniformity, sensitivity, specificity, background error, limit of detection, or variant‑calling performance.
• Experience with primer/probe design, target‑region design, or computational support of molecular assay development.
• Experience developing new algorithms or analytical methods for genomic data.
• Experience with reproducible development practices using Git, Jira, containers, or similar tools.

$90,000 - $120,000 a year

Please note: You must complete all application questions to be considered for the role

Pillar Biosciences is an equal opportunity employer

We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses and identifying potential inconsistencies or verification signals in application materials based on available information. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.