Sr. Clinical Bioinformatics Scientist

Position Overview

Gene By Gene is seeking a senior-level Clinical Bioinformatics Scientist to develop and maintain high-throughput genomic pipelines in a regulated clinical laboratory environment (CLIA/CAP). The position will involve transforming raw next generation sequencing (NGS) data into actionable clinical insights, ensuring the accuracy, scalability, and security of diagnostic assays.

Accountabilities and Responsibilities

• Pipeline Development: Design, optimize, and validate new automated bioinformatics  workflows for genetic variant calling, including the following: 
• • Using or developing software to receive, process, and analyze genetic data.
  • Assessing software and programs for suitability to achieve desired analysis goals 
  • Determination of appropriate analysis parameters and thresholds for identification and  evaluation of genetic markers of interest 
  • Designing defined analysis protocols within the software for routine use by other data  analysts, including pre-set filters and settings 
  • Validation of developed protocols to demonstrate accurate generation and reporting of  results 
  • Writing or revising code to aid in the processing or analysis of samples though the lab
• Variant Analysis: Use developed analysis pipelines to implement algorithms for detection of  SNV’s, Indels, CNV’s, and structural variants from genetic data.
• Clinical Validation: Complete and document the analytical validation of bioinformatics tools to  meet regulatory requirements for clinical use, including the analytical validity of risk models to  satisfy CLIA / CAP / ACMG requirements.
• Data Management: Oversee large-scale genomic datasets, ensuring data integrity, security, and  HIPAA compliance
• Quality Control: Establish automated QC metrics to monitor run performance and data integrity.
•  Collaboration: Work with laboratory directors, clinical geneticists, the research and  development team, and IT professionals to integrate and implement bioinformatics tools to  fulfill client reporting requirements. 
• Report Generation: Work with laboratory directors, clinical geneticists, and IT professionals to  create clinically validated reporting pipelines for genetic data interpretation, including  Monogenic and Polygenic Risk Scores, Pharmagogenomics (PGx) interpretation, and Carrier  Screening.
• Troubleshooting: Resolve technical issues in production pipelines to prevent delays in client  report generation and delivery.

Position Requirements

• Doctoral Degree in Bioinformatics, Computational Biology, Statistical Genetics, or a related field with 5+ years post-graduate experience. 
• Understanding of general molecular biology and genetic laboratory procedures. 
• Ability to apply theoretical knowledge of genetics towards interpretation of genetic data to  generate clinical reports.
• Expertise with bioinformatics principles and ability to apply this knowledge towards  implementation of genetic analysis programs and clinical report generation pipelines.
• Knowledge of clinical laboratory regulatory requirements for clinical diagnostics and reporting,  including familiarity with HIPAA, CLIA, NYSDOH CLEP standards, and ACMG variant  interpretation classifications.
• Understanding of population genetics and statistical modeling to account for ancestry, ethnicity,  and environmental factors in the calculation of risk scores for complex traits.
• Understanding of genetic imputation and haplotype phasing determination, and ability to  ensure that imputed data meets strict quality control thresholds for clinical use.
• Familiarity with machine learning for genomic functional prediction and pattern recognition.
• Familiarity with multiple NGS instrumentation platforms and their file formats (eg. Illumina,  Ultima Genomics, Complete Genomics, Oxford Nanopore, etc.) and ability to create platform agnostic analysis pipelines, adaptable to various platforms.
• Expertise or Familiarity with the following (or similar) environments, databases, coding  languages, software suites, data analysis tools, etc.: 
• • Command Line, Python, R, Java, shell scripting (Bash) 
  • SQL and database administration 
  • Strong command of Linux/Unix environments 
  • Cloud computing (AWS, Google Cloud, or Azure) 
  • Containerization (Docker, Kubernetes) 
  • Software version control tools (Git) 
  • NGS analysis tools and variant annotation databases: FastQC, Samtools, Bamtools,  VCFTools, BWA, GATK, ClinVar, gnomAD  
  • Bioinformatics tools for analysis of large-scale genomic data (PLINK, Eagle2, Beagle, etc.)
  • Workflow managers (Nextflow or similar) 
  • Genetic databases and reference standard repositories (NCBI GenBank, RefSeq,  ENSEMBL, Genome Reference Consortium etc.) 
  • Global and population-specific genetic reference panels (TOPMed, 1000 Genomes  Project, Haplotype Reference Consortium, GenomeAsia, African Genome Resource,  etc.)

Why Join Us

At Gene by Gene, you’ll join a mission-driven team advancing the science of genetics and discovery. You’ll have the opportunity to shape meaningful campaigns, tell compelling brand stories, and collaborate with talented professionals who share your passion for creativity, curiosity, and impact.

Comprehensive Benefits

• Medical & Health Savings: Choice of 3 medical tiers generously sponsored by the company, with a monthly $50–$100 employer HSA contribution based on plan type and dependent level.
• 100% Covered Dental & Vision: No premium costs for employees or dependents.
• 401(k) Matching: Generous 50% company match up to 6% of annual base salary.
• Diverse PTO Framework: Structured time off incorporating vacation, sick leave, mental health days, personal days, company holidays, and a flexible floating holiday.
• Income Protection & Family Leave: Full company sponsorship of Short-Term and Long-Term Disability (STD/LTD) alongside Paid Family Leave offerings.