Professional Experience
- Converted legacy Snakemake pipelines to Nextflow to leverage advanced portability and provenance capabilities for metagenomics and amplicon sequencing
- Developed pipelines and workflows for low biomass metagenomics analysis using nanopore and illumina sequences
- Designed, developed, maintained, validated and running standard processing pipelines for sequence data (amplicon sequencing and metagenomics) from space biology experiments
Technologies: Nextflow, Snakemake, Python, R, Kraken2, DADA2, Docker, Singularity, Conda, SLURM, AWS, nanopore/illumina sequencing, megahit, metabat, CheckM, GitHub
- Led and provided technical contributions on multiple microbial genomics and metagenomics projects
- Designed and analyzed omics studies to enable discovery and improve product performance
- Hunted potential microbial contaminants in microbial isolate stocks using 16S rRNA amplicon sequencing
- Refactored microbial prevalence analysis pipeline codebase and converted it to a Nextflow pipeline
- Performed metabolite and antibiotic-resistant gene analyses for product development
Technologies: Nextflow, Snakemake, Make, Python, R, Bash, AWS Batch/S3/EC2/ECS, BLAST, QIIME 2, HMMER, NCBI, JGI/IMG, EBI, Diamond
- Analyzed and derived insights on metagenomics, transcriptomics, genome assembly, and population genetics projects
- Developed pipelines for amplicon sequencing (16S, 18S, ITS) analysis using QIIME2 and usearch
- Assembled and assigned taxonomy to near full-length 16S rRNA sequences
- Identified antibiotic resistance genes in soil samples using next-generation sequencing
Technologies: Snakemake, Make, Python, R, MySQL, BLAST, Conda, SLURM, GitHub, Docker, GATK, Stacks, machine learning
- Developed pipelines for non-model organisms RNA-seq analysis, host-associated shotgun metagenomics and metatranscriptomics
- Characterized microbiome samples using 16S amplicon sequences and shotgun metagenomics
- Performed RNA-seq and pathway enrichment analysis for non-model organisms
- Performed comparative genomics between Z and W chromosomes to identify sex-linked genes
- Database management, website building and report generation
Technologies: Snakemake, Make, NeatSeq-Flow, Python, R, Perl, MySQL, BLAST, PHP, HTML, CSS, Trinity, Trinonate, Mauve, SGE, metaErg, MEGAN, Machine learning
Publications & Research
Democratizing Microbial Omics Analyses: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows
American Society for Microbiology (ASM) Microbe 2025
AM Saravia-Butler, JM Kelliher, A Torres, OA Obayomi, LM Sanders, et al.
Occurrence and Distribution of Antibiotics and Corresponding Antibiotic Resistance Genes in Different Soil Types Irrigated with Treated Wastewater
Science of the Total Environment 782, 146835 • 2021
MM Seyoum, O Obayomi, N Bernstein, CF Williams, O Gillor
65 citations
Soil Texture and Properties Rather Than Irrigation Water Type Shape the Diversity and Composition of Soil Microbial Communities
Applied Soil Ecology 161, 103834 • 2021
O Obayomi, MM Seyoum, L Ghazaryan, CC Tebbe, J Murase, N Bernstein, et al.
63 citations
Importance of Soil Texture to the Fate of Pathogens Introduced by Irrigation with Treated Wastewater
Science of The Total Environment 653, 886-896 • 2019
O Obayomi, N Bernstein, M Edelstein, A Vonshak, L Ghazayarn, et al.
43 citations
The Combined Effects of Treated Wastewater Irrigation and Plastic Mulch Cover on Soil and Crop Microbial Communities
Biology and Fertility of Soils 56 (5), 729-742 • 2020
O Obayomi, M Edelstein, J Safi, M Mihiret, L Ghazaryan, A Vonshak, et al.
33 citations
Response of Soil Microbial Communities, Inorganic and Organic Soil Carbon Pools in Arid Saline Soils to Alternative Land Use Practices
Ecological Indicators 150, 110227 • 2023
AC Somenahally, J McLawrence, VN Chaganti, GK Ganjegunte, et al.
33 citations
The Fate of Pathogens in Treated Wastewater-Soil-Crops Continuum and the Effect of Physical Barriers
Science of the Total Environment 681, 339-349 • 2019
O Obayomi, L Ghazaryan, M Ben-Hur, M Edelstein, A Vonshak, J Safi, et al.
21 citations
The Dissemination of Antibiotics and Their Corresponding Resistance Genes in Treated Effluent-Soil-Crops Continuum, and the Effect of Barriers
Science of the Total Environment 807, 151525 • 2022
MM Seyoum, O Obayomi, N Bernstein, CF Williams, O Gillor
16 citations
RNA-Seq in Nonmodel Organisms
Deep Sequencing Data Analysis, 143-167 • 2021
V Chalifa-Caspi
17 citations
Dairy Manure-Derived Biochar in Soil Enhances Nutrient Metabolism and Soil Fertility, Altering the Soil Prokaryote Community
Agronomy 13 (6), 1512 • 2023
O Obayomi, CB Taggart, S Zeng, K Sefcik, B Willis, JP Muir, E Kan, et al.
6 citations
Exploring the Application of Signaling Compounds and Soil Amendments to Modulate Plant–Microbe Interactions
Plant and Soil 501 (1), 267-288 • 2024
S Priya, AC Somenahally, O Obayomi, TJ Gentry, TC Sarker, JA Brady, et al.
8 citations
Engineering a Biofilters Microbiome with Activated Carbon and Bioaugmentation to Improve Stormwater Micropollutant Removal
Environmental Technology & Innovation 103338 • 2023
I LeviRam, A Gross, A Lintern, O Obayomi, V Chalifa-Caspi, O Gillor, et al.
8 citations
Wood- and Manure-Derived Biochars Reduce Antibiotic Residues and Shift Antibiotic Resistance Genes and Microbial Communities
Agronomy 14 (9), 2100 • 2024
G Choi, JA Brady, O Obayomi, E Green, C Leija, K Sefcik, DA Gonzalez, et al.
3 citations
