Staff Scientist

Overview

Black Canyon Consulting is seeking a Staff Scientist to work with a Principal Investigatory in the National Institutes of Health at the National Library of Medicine to support the development of high-fidelity artificial intelligence models designed to decode the functional landscape of the human and mouse genomes. This effort will leverage Telomere-to-Telomere (T2T) reference assemblies to advance understanding of gene regulation, particularly within complex and repetitive genomic regions.

This position requires a unique combination of computational genomics expertise, machine learning proficiency, and scalable software engineering capabilities to support large-scale data integration and model development.

Responsibilities

Lead the design, development, and implementation of AI-driven models for gene regulation analysis

Architect and scale a TREDNet-based framework for cloud-native execution

Optimize models for distributed, multi-GPU training environments

Integrate and analyze large-scale genomic and epigenomic datasets, including:

ENCODE / modENCODE

NIH Roadmap Epigenomics

UCSC Genome Database

Apply AI methodologies to functionally annotate repetitive genomic regions, including centromeres and telomeres

Develop and maintain scalable, containerized pipelines using Docker and/or Singularity

Implement MLOps best practices, including experiment tracking, model versioning, and reproducibility

Deploy and manage workflows in cloud environments (AWS, GCP, or Azure)

Collaborate with interdisciplinary teams across computational and life sciences domains

Required Qualifications

PhD in Computer Science, Computational Biology, Bioinformatics, or a related field

Minimum of 5 years of experience developing and deploying machine learning or deep learning models

Strong experience with cloud platforms (AWS, GCP, or Azure)

Proficiency in deep learning frameworks (PyTorch preferred; TensorFlow or HuggingFace acceptable)

Deep understanding of neural network architectures (CNNs, transformers, sequence models)

Strong programming skills in Python and experience working in Linux-based environments

Experience with MLOps practices, including experiment tracking and model versioning

Experience building and deploying containerized workflows (Docker and/or Singularity)

Experience with distributed training across GPUs or multi-node environments

Strong knowledge of genomics, gene regulation, and epigenomics

Experience working with large-scale biological datasets (e.g., ENCODE, Roadmap Epigenomics, UCSC Genome Browser)

Familiarity with genomics data formats (FASTA, VCF, BAM/CRAM, BED)

Preferred Qualifications

Experience with Telomere-to-Telomere (T2T) genome assemblies

Experience analyzing repetitive genomic regions (e.g., centromeres, telomeres)

Background in regulatory, functional, or comparative genomics (e.g., human vs. mouse)

Experience with hyperparameter tuning and large-scale model optimization

Familiarity with genomic foundation models or sequence-based deep learning approaches

Experience running ML workloads on GPU-enabled cloud or HPC environments

Familiarity with workflow orchestration tools (e.g., Nextflow, Snakemake, Airflow)

Experience transitioning research models into production-grade pipelines

Familiarity with CI/CD and infrastructure-as-code tools (e.g., Terraform)

Experience working in interdisciplinary teams

Deliverables

Develop a containerized (Docker/Singularity) TREDNet pipeline capable of scaling across multiple GPU nodes in a cloud environment

Produce a comprehensive functional map of the T2T reference genome, identifying regulatory motifs in previously unresolved regions

Develop comparative models between human and mouse cell lines to identify conserved regulatory mechanisms

Benefits and Salary

We attract the best people in the business with our competitive benefits package, including medical, dental, and vision coverage; a 401(k) plan with employer contribution; paid holidays, vacation, and tuition reimbursement.

We offer a competitive salary commensurate with experience and location. The targeted range for this position is $110,000 - $140,000.

If you enjoy being part of a high-performing, professional, technology-focused organization, please apply today!