Please note that this position is contingent upon the successful award of a contract currently under bid.

Summary:

GbILS is seeking a Senior Bioinformatician to serve as the technical lead for sequencing analytics, bioinformatics pipeline development, and computational infrastructure. This individual will provide scientific leadership in the design, implementation, optimization, and maintenance of scalable bioinformatics workflows supporting national wastewater surveillance efforts. The Senior Bioinformatician will collaborate with epidemiologists, laboratory scientists, software engineers, and public health partners to develop innovative analytical solutions that translate complex sequencing data into actionable public health intelligence.

Essential Job Functions:

The Senior Bioinformatician serves as a technical lead and subject matter expert supporting advanced genomic surveillance, outbreak response, and pipeline architecture across multiple program areas. This role requires independent judgment, cross-functional collaboration, and the ability to design scalable, reproducible solutions for complex public health challenges.

• Technical Leadership:
  • Lead the design, development, validation, and maintenance of scalable bioinformatics workflows for wastewater sequencing analyses
  • Serve as the subject matter expert for computational genomics and metagenomic analyses
  • Establish coding standards, workflow documentation, and quality assurance processes for bioinformatics analyses
  • Mentor junior bioinformaticians and provide technical oversight on analytical projects 
  • Review analytical methods, code, and computational workflows to ensure reproducibility and scientific rigor.
• Scientific Leadership:
  • Collaborate with epidemiologists, laboratorians, statisticians, and software developers to translate surveillance needs into computational solutions
  • Recommend new analytical methods, software tools, and emerging technologies that improve wastewater surveillance capabilities
  • Lead development of novel algorithms and computational approaches for variant detection and pathogen characterization
  • Support publication of scientific findings through manuscripts, presentations, and technical reports. 
  • Design and maintain scalable cloud-based bioinformatics infrastructure capable of supporting national surveillance data
  • Optimize computational performance for high-volume sequencing datasets. 
  • Implement automated quality assurance and quality control monitoring throughout analytical pipelines
  • Develop statistical methods to identify variants and potential abundance based on mutations sequencing data sets
  • Develop standardized bioinformatics outputs for integration into the platform 
  • Performs quality control, assembly and analysis of environmental metagenomic sequencing samples 
  • Manages high-throughput sequencing raw and analytic data files, databases, including uploads to sequencing repositories
  • Prepares and delivers clear, concise and accurate reports, presentations, and scientific manuscripts
  • Assists with outbreak response
• Wastewater Surveillance & Metagenomics:
  • Lead the design, implementation, and optimization of end-to-end bioinformatics pipelines for wastewater metagenomic sequencing in support of domestic wastewater surveillance for infectious diseases and related environmental monitoring programs
  • Develop and curate reference databases for detection and characterization of microbial, viral, fungal, and eukaryotic organisms from environmental and wastewater sample types, including source-specific databases for source attribution analyses
  • Develop and validate statistical models to identify variant composition and estimate relative pathogen abundance from wastewater sequencing datasets, integrating mutation profiling and deconvolution approaches
• Synthetic Construct & Bio-surveillance:
  • Lead in silico screening efforts to detect synthetic genomic constructs and engineered sequence features within metagenomic and Whole Genome Sequencing (WGS) datasets, coordinating with biosecurity and laboratory partners to define detection criteria and validate findings.
  • Design and maintain specialized sequence databases incorporating virulence markers, resistance determinants, strain-type markers, and curated exclusion sequences (e.g., host DNA) to support bio surveillance workflows
• Whole Genome Sequencing of Viral Pathogens
  • Provide expert bioinformatics support for Whole Genome Sequencing (WGS) of viral pathogens including measles virus and other priority pathogens, encompassing quality control, reference-based assembly, consensus genome generation, variant calling, and phylogenetic analysis.
  • Support evolutionary modeling of viral genomic data using Bayesian, maximum likelihood, and/or machine learning approaches to inform outbreak investigations and transmission network reconstruction
• Pipeline Development & HPC/Cloud Architecture:
  • Architect, develop, optimize, refactor, and maintain modular, containerized Nextflow pipelines for sequence analysis spanning wastewater metagenomics, isolate Whole Genome Sequencing (WGS), and metagenomic source attribution, ensuring portability across HPC and cloud/hybrid-cloud environments (e.g., AWS, Azure, GCP).
  • Consult on scaling workflows from desktop to HPC and cloud environments using containerization tools (Docker, Singularity) and workflow management best practices; implement parallelized architectures where appropriate.
  • Champion code versioning standards and reproducibility practices using Git/GitHub/GitLab; author and maintain comprehensive technical documentation, SOPs, and workflow specifications
• Artificial Intelligence/Machine Learning (AI/ML) Integration
  • Investigate and implement AI/ML algorithms — including deep learning and Natural Language Processing (NLP)-based approaches — for large-scale genomic pattern recognition, pathogen characterization, and automated feature extraction from scientific literature and surveillance reports.
  • Advise program staff on novel applications of AI/ML to public health genomic surveillance and recommend approaches appropriate to data scale and biological context

Necessary Skills and Knowledge:

• Expertproficiencyin Python, R, Bash, and Perl in Linux/HPC environments
• Containerization: Docker, Singularity
• NGS tools: Bowtie2,SPAdes, Velvet, Prodigal, GATK, QUAST, and related open-source platforms
• Phylogenetics: IQ-TREE, BEAST,RAxML, or equivalent
• Cloud computing platforms and NoSQL/relational database design
• Code versioning: Git, GitHub, GitLab

Minimum Qualifications:

• Minimum 5-8 years of related years of experience
• Advanced experience with Nextflow; familiarity with Snakemake and WDL

Preferred Qualifications:

• Master's or Ph.D. in Bioinformatics, Computational Biology, Computer Science, Genomics, Biology, Microbiology, Public Health, Biostatistics, or closely related scientific discipline
• Experience with PySpark preferred
• Excellent problem-solving and analytical skills
• Strong communication skills, capable of effectively interacting with both technical teams and non-technical stakeholders.
• Ability to work independently as well as collaboratively in a team-oriented environment
• At least five (5) years of experience in relevant work or related areas
• Previous experience with federal government agencies; preferably with CDC

Pay and BenefitsAt Goldbelt, we value and reward our team's dedication and hard work. We provide a competitive base salary commensurate with your qualifications and experience. As an employee, you'll enjoy a comprehensive benefits package, including medical, dental, and vision insurance, a 401(k) plan with company matching, tax-deferred savings options, supplementary benefits, paid time off, and professional development opportunities.