Microbiome Computational Scientist

About the role

The Microbiome AI/Deep Learning Lab in the Massachusetts Host-Microbiome Center and Division of Computational Pathology at Brigham and Women’s Hospital/Harvard Medical School is seeking a computational scientist with experience in microbiome bioinformatics and machine learning.

Responsibilities

• Engage in research developing and applying bioinformatic and machine learning approaches, for a variety of microbiology data sources, including next generation sequencing and metabolomic data.
• Substantially contribute to scientific publications and grant applications.
• Analyze datasets and produce visualizations and written reports about scientific findings.
• Deploy computational pipelines on local workstations and on high performance CPU and GPU clusters.
• Organize and curate large datasets using structured approaches, including database systems.
• Engage with trainees and other users of the MHMC to facilitate use of computing resources and application of machine learning technologies for the microbiome.

Qualifications

• PhD in Computational Biology, Computer Science, or related quantitative discipline.
• Experience analyzing microbiome data and machine learning applications demonstrated through authorship on high-quality, peer-reviewed scientific publications.
• 3+ years minimum Python programming experience.
• 3+ years minimum experience working in high-performance computing environments.
• Experience with microbiome bioinformatics methods and pipelines for next generation sequencing data analysis.
• Experience with organizing and managing large multi-omics datasets.
• Strong verbal and written communication, and interpersonal skills.
• Experience with deep learning and PyTorch is highly desired.

Skills/Abilities/Competencies

• Must be capable of contributing within an interdisciplinary team, exhibit a high level of initiative, and have an eagerness to learn new technologies.
• Ability to manage entire projects in a research environment, from design to implementation, and interpretation of final results.
• Must have experience analyzing microbiome data.
• Demonstrated ability to develop and implement computational approaches for analyzing complex biomedical datasets including next generation sequencing data.
• Demonstrated ability to manage large and complex biomedical datasets, using tools such as databases.
• Excellent written and verbal communication skills with demonstrated ability to communicate complex results to both technical and non-technical audiences, through publications and presentations.
• Experience with deep learning and using PyTorch is highly desired.
• Knowledge of software engineering best practices, including source code management/control (e.g., Git) and containerization approaches.
• Experience with high-performance computing environments, including scheduling systems, e.g., SLURM.
• Ability to multitask and prioritize work, to achieve desired goals and deliverables.
• Ability to share expertise, coach, and give general direction to others of different skill sets, backgrounds and levels.