Bioinformatics Scientist

Axle is seeking a highly ambitious, adaptable, structured, and detail-oriented Bioinformatics Scientist to join our vibrant team at the National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID), Division of Intramural Research (DIR), Research Technologies Branch (RTB), Integrated Data Sciences Section (IDSS) in Bethesda, MD. 

 Responsibilities:

• Address bioinformatics, scientific computing, and data analysis needs of users within the Division of Intramural Research (DIR) at NIAID and their collaborators by lending expertise in the proper statistical design of biological experiments involving high-throughput genome-scale technologies, data mining and knowledge discovery techniques, automated workflow development, statistical and scientific experimental design consulting.

• Provide bioinformatics support to include somatic and germline variant calling and analysis, single-cell and bulk gene expression analysis, de novo assembly of genomes and transcriptomes, comparative genomics of model and non-model organisms, proteomics, ChIP-seq, ATAC-seq, and the development of high-throughput pipelines for the analysis of the above data modalities.

• Provide programming and troubleshooting support to the Research Technologies Branch (RTB) of the National Institute of Allergy and Infectious Diseases (NIAID) and collaborating Institutes in the dissemination of research data.

• Perform computational data analysis on genomic and clinical research data.

• Work with staff on scientific programming and experimental design. Provide statistical support/analysis on research data.

• Contribute to and co-author scientific publications in leading peer-reviewed journals.

• Contribute to the development of a scalable and flexible resource to provide NGS bioinformatics, structural biological and computational, machine learning data support to NIAID scientists and investigators.

• It is expected that the bioinformatics scientist will need strong skills in the following:

  • NGS analysis (whole-exome, whole-genome, RNA-seq, ChIP-Seq, both long- and short-read technologies, etc.)

  • Statistical modeling

  • Scripting

  • Biological interpretation

 Specific Qualifications:

• Ability to obtain and maintain a Public Trust Security clearance

• Minimum Bachelor’s degree in related field, Master’s or Ph.D. preferred

• 4+ years of experience in bioinformatics

• 2+ years of experience developing and maintaining production bioinformatics pipelines

• Expert in two (2) of the following languages: Python, R, C/C++, sh/bash

• Experience building images using one (1) of the following: Docker, Podman, Singularity/Apptainer

• Expert in one (1) pipeline framework: Snakemake, Nextflow, CWL/WDL

• Expertise building technical and user documentation for tools, pipelines, and applications

• Experience building pipelines locally on-premise using available HPC infrastructure

• Experience building pipelines/applications in the Cloud with AWS/GCP/Azure is a plus

• Experience building applications using one (1) of the following frameworks is a plus: Django, Flask, RShiny, Electron, Flutter, React

• Experience working in a laboratory setting is a plus but not required

Please submit a cover letter with your resume that addresses the following questions:

1. What experience do you have working with large datasets and compute clusters?
2. Describe your experience building workflows/pipelines and/or using bioinformatics software and tools to analyze data.
3. What programming languages are you comfortable using for bioinformatics data analysis?
4. What bioinformatics areas are you familiar with? (e.g., single cell, bulk genomics, transcriptomics, epigenetics, flow, spatial, metagenomics, etc.)
5. What life science disciplines do you have experience in? (e.g., immunology, infectious disease, cancer research, etc.)
6. Provide examples of basic machine learning/AI concepts and/or how you've applied them in bioinformatics data analysis.