Microbiome Postdoctoral Fellow

What You Will Do

• Develop computational, statistical, and machine-learning methods for large-scale comparative analysis of microbial genomes and metagenomes.
• Build predictive models to identify genomic, metabolic, phylogenetic, ecological, and environmental factors associated with microbial cultivability.
• Design scalable workflows for integrating and analyzing large genomic, metagenomic, and environmental datasets using HPC.
• Apply microbial metabolic and physiological knowledge to characterize genomes and distinguish cultivated from uncultivated lineages.
• Implement analytical methods for feature extraction, classification, clustering, dimensionality reduction, and network analysis.
• Develop, optimize, document, and maintain reproducible research software and computational workflows.
• Integrate multi-omics and environmental data to predict cultivation potential and generate experimentally testable hypotheses.
• Collaborate with JGI's cultivation community to prioritize microbial lineages for targeted cultivation.
• Work with interdisciplinary research teams to validate methods and translate computational findings into biological insights.
• Publish research findings, present at scientific conferences, and contribute software and analytical resources to the scientific community.
• Develop software for organization and handling of metagenomic/metatranscriptomic data and automation of analytical procedures.
• Develop and present updates and reports at group meetings.
• Support the development of user interface for navigation and data comparisons across thousands of genomic/metagenomic samples.

What We Are Looking For

• A recent Ph.D. (within the last 1-2 years) in Computational Biology, Bioinformatics, Microbiology, Molecular Biology, Biochemistry, or a related discipline.
• Strong experience in analysis of microbial genomes and metagenomes, with a proven track record in this area reflected in recent or pending publications.
• Strong programming experience in Python, C/C++, R, or related scientific computing languages.
• Experience with machine learning, statistical modeling, algorithm development, or large-scale data analytics.
• Strong experience with UNIX utilities and filesystems.
• Strong experience with using standard bioinformatics tools and databases.
• Strong knowledge of Biology/Biochemistry and understanding of key and complex biological concepts (e.g., genes, pathways, and microbial phylogeny).
• Strong organizational skills including experience maintaining detailed and accurate records of results and analyzed data.
• Excellent oral and written communication skills including experience presenting at group meetings and conferences, and publishing research findings.
• Demonstrated interpersonal communication skills including experience conducting independent, data-driven research and collaborating with an interdisciplinary research team.

Desired Qualifications

• Experience with high-performance computing and workflow systems (e.g., WDL, Nextflow, and Snakemake) for large-scale genomic analyses.
• Familiarity with command line sequence analysis tools (e.g., Last, Hmmer, Megahit, and MetaSpades).
• Demonstrated ability to accurately and eloquently represent and promote scientific projects to audiences of diverse technical backgrounds.