Senior R&D Scientist, Algorithm Developer

Baylor Genetics; United States; On-site; USD 150,000 - 190,000; Full time

Job summary

Baylor Genetics seeks a Senior Scientist in NGS Algorithm Development to lead computational design and optimization of algorithms for detecting diverse genomic features, including trisomy, small variants, CNVs, STRs, methylation, and PGx variants.

The role drives development, validation, and integration of analysis pipelines, collaborating with assay development, bioinformatics, and partner teams to enable robust, scalable solutions and publications.

Qualifications

• PhD in Bioinformatics, Computational Biology, Genomics, or a related field.
• Minimum 5 years of hands-on experience in NGS algorithm development.
• Proficiency in Python, R, C++, and workflow orchestration tools.
• Experience with read alignment and variant calling and with CNV modelling/STR/methylation callers.

Responsibilities

• Lead design, optimization, and implementation of scalable NGS algorithms and pipelines.
• Lead design and optimization of targeted NGS panels for products.
• Drive end-to-end development, validation, benchmarking, and integration of NGS pipelines.
• Collaborate with assay scientists, bioinformatics, and software engineers to translate requirements into computational solutions.
• Provide technical and project leadership to ensure accuracy and scalability across products.

Skills

Python

R

C++

Workflow orchestration

Nextflow

Docker

GitHub

Read alignment

Variant calling

PGx interpretation

Education

PhD in Bioinformatics/Computational Biology/Genomics

Tools

Linux HPC

Docker

Nextflow

GitHub

Groovy

Cloud platforms

FASTQ/BAM/VCF

Job description

We are seeking a highly experienced and innovative Senior Scientist in NGS Algorithm Development to lead the design, optimization, and implementation of computational algorithms for next-generation sequencing (NGS) data. This role focuses on detecting and interpreting a wide range of genomic features and chromosomal abnormalities, including trisomy, small variants, copy number variants, short tandem repeats, methylation patterns, and variants in homologous and homopolymer regions.

The Senior Scientist will also lead the design and optimization of targeted NGS panels for existing and new products and drive the development, validation, and integration of NGS algorithms and analysis pipelines. As a technical and project lead, this role ensures analytical accuracy, robustness, and scalability across products, supports technology transfer and pipeline updates, and collaborates cross-functionally with assay development, bioinformatics, and partner teams to provide technical guidance and inform strategic decisions.

The ideal candidate will hold a Ph.D. in Bioinformatics, Computational Biology, Genomics, or a related field, and have at least 5 years of hands‑on experience in algorithm development for NGS applications. Experience in pharmacogenomics (PGx) variant calling, including complex loci such as CYP2D6, is strongly preferred.

Preferred experience with Linux/HPC, Docker containerization, Nextflow workflow development, GitHub-based software engineering, and Python/Groovy programming. Familiarity with cloud platforms and NGS data formats (FASTQ, BAM, VCF), along with CI/CD, workflow automation, troubleshooting, and developing reproducible bioinformatics pipelines.

Key Responsibilities

• Lead the design, optimization, and implementation of scalable NGS algorithms and pipelines for detection and interpretation of complex genomic features, including SNVs/Indels, CNVs, STRs, methylation, trisomy, PGx variants, and variants in homologous and homopolymer regions
• Lead the design and optimization of targeted NGS panels for existing and new products
• Drive end-to-end development, validation, benchmarking, and integration of NGS algorithms and analysis pipelines using internal and public truth sets
• Collaborate closely with assay scientists, bioinformatics teams, software engineers, and other partners to translate biological and product requirements into computational solutions
• Provide technical and project leadership to ensure analytical accuracy, robustness, scalability, and continuous improvement across products
• Support technology transfer, pipeline updates, and production deployment, and contribute to scientific publications, conference presentations, and intellectual property development.

Required Qualifications

• Ph.D. in Bioinformatics, Computational Biology, Genomics, or a related discipline
• Minimum 5 years of experience in NGS algorithm development
• Proficiency in Python, R, C++, and workflow orchestration tools
• Deep understanding of:
  • Read alignment and variant calling (e.g., BWA-MEM, minimap2, GATK, DeepVariant) for germline or/and somatic variants
  • CNV modeling, STR detection tools and methylation callers
  • Homologous region analysis and control gene normalization
  • PGx variant interpretation and allele resolution
• Experience with long-read technologies (ONT, PacBio) and signal-level data
• Strong analytical, problem‑solving, and communication skills

Preferred Qualifications

• Somatic variant calling by short‑reads or/and long‑reads sequencing
• Experience with machine learning models for variant classification
• Knowledge of clinical genomics and regulatory standards
• Familiarity with pharmacogenomic databases (e.g., PharmGKB, CPIC)

PHYSICAL DEMANDS AND WORK ENVIRONMENT

• Frequently required to sit or stand for extended periods.
• Frequently required to use hand and finger dexterity to operate laboratory equipment.
• Frequently required to communicate verbally and visually interpret technical data.
• Occasionally exposed to bloodborne or airborne pathogens or infectious materials.
• Work is primarily performed in a laboratory and office environment.

EEO Statement:

Baylor Genetics is proud to be an equal opportunity employer dedicated to building an inclusive and diverse workforce. We do not discriminate based on race, religion, color, national origin, sex, sexual orientation, age, gender identity, veteran status, disability, genetic information, pregnancy, childbirth, or related medical conditions, or any other status protected under applicable federal, state, or local law.

This employer is required to notify all applicants of their rights pursuant to federal employment laws. For further information, please review the Know Your Rights notice from the Department of Labor.