Olabiyi Obayomi

I am a passionate bioinformatician with a PhD in Microbiology from Ben Gurion University of the Negev. I am skilled in omics data analysis particularly metagenomics, transcriptomics, microbial genomics, programming languages, and microbiology with the desire to develop and apply computational techniques to advance and accelerate biological research. I have over 5 years of experience working in bioinformatics both as a Ph.D. student and a Postdoctoral Researcher. I have developed complex computational pipelines using pipeline tools like Snakemake and provided insights on various next-generation sequencing datasets including but not restricted to metagenomics, transcriptomics, population genetics, and microbial genome assembly.

Texas A&M AgriLife Research, Texas A&M University, Stephenville, Texas June 2021 - present
Postdoctoral Researcher in Bioinformatics
• Actively involved in several metagenomics, transcriptomics, and population genetics projects by assisting PI-s across Texas A&M University system for bioinformatics analysis
• Characterized the microbiome of several environmental samples including water, soil, feces and skin samples of salamander, biochar, Texas beaches, cows, and crops
• Performed RNA-seq and pathway analysis for model plants (Arachis ipaensis) and humans
• Performed RNA-Seq and pathway analysis for non-model plants (Arachis dardanii, little blue stem and Indian grass)
• Compared the transcriptome profiles between plants. Between Arachis ipaensis and Arachis dardanii and between little bluestem and Indian grass.
• Developed a pipeline for the analysis of amplicon (16S, 18S, ITS) sequencing dataset using QIIME2 and PICRUSt 
• Assembled and annotated the genomes of bacteria (E. coli) and virus (fowl pox virus)
• Analyzed RAD-Seq dataset of little blue stem grasses across Texas to understand the genetic basis for their diversity
• Assembled and assigned taxonomy to near full-length 16S rRNA sequences of peanut endophytes
• Mined NCBI database for sequences to be used for primer design in a Texas sea turtles study
• Participating in project conceptualization and grant writing
• Teaching graduate students how to perform statistics using R
• Submitting raw sequences to NCBI
• Writing manuscripts for publication.

Ben Gurion University of the Negev, Bioinformatics Core facility, Beersheba Nov 2019 – June 2021
Postdoctoral Researcher in Bioinformatics
• Applied omics tools for the development of pipelines to analyze Illumina and Oxford nanopore sequencing data to gain biological insights
• Developed a pipeline for RNA-Seq analysis of non-model organisms using NeatSeq_Flow to automate database creation, QC, mapping, assembly, annotation, statistical, clustering and enrichment analysis
• Characterized the microbiome of Wolffia globosa and identified potential cobalamin synthesizing bacteria using 16S amplicon sequences and shotgun metagenomics.
• Characterized the functional and taxonomic diversity of the microbiome of biofilters receiving sand and granular activated carbon treatments using shotgun metagenomics.
• Performed RNA-Seq and pathway analysis for non-model crustaceans (Hippolyte inermis and Cherax quadricarinatus)
• Performed comparative genomics between Z and W chromosomes of Macrobrachium rosenbergii in to identify sex linked genes
• Developed a pipeline for host associated shotgun metagenomics using snakemake
• Developed a pipeline for metatranscriptomics using both read based and assembly approaches 
• Drafted custom scripts in R, Bash, Python and Perl for omics data analysis
• Presented and delivered my analyses results to customers on our bioinformatics core facility computer servers. This involved database management using SQL, MySQL and PHP, scripting with HTML and CSS and HTML report generation using RMarkdown
• Contributed to manuscripts for publication.

Ben Gurion University of the Negev, Zuckerberg Inst. For Water Research, Sde Boker May 2019 – October 2019
Post-doctoral Researcher in Bioinformatics
• Characterized the microbiomes of soil, water and crop samples that were sequenced with Illumina and Oxford Nanopore platforms
• Analyzed and processed data with various bioinformatics tools, including QIIME, SourceTracker, R, and others
• Assisted and mentored fellow students (Masters and PhD) with analyzing their bioinformatics-related data
• Developed a bioinformatics pipeline for the analysis of amplicon sequences generated by Oxford Nanopore
• Developed scripts for detecting pathogens using amplicon sequences
• Wrote and contributed to manuscripts for publication

Ben Gurion University of the Negev Israel
Ph.D. Environmental Microbiology 2019
Cumulative GPA: 96.5
Core Modules: Microbial Pathogens, microbial communities, next-generation sequencing, microbial ecology
Skills and Learning:
• Characterized and tracked the source of microbiomes (bacteria and protists) including pathogens in soil, water and crop samples using both culture- dependent and independent approaches including amplicon (16S and 18S) sequencing
• Analyzed and processed data with various bioinformatics tools, including QIIME, SourceTracker, R Bioconductor packages
• Developed a tool for detection, statistical analysis, and visualization of pathogens in environmental samples using amplicon sequences
• Wrote scripts in Bash, R and Python that used high performance clusters to decrease execution time on tasks
• Wrote and contributed to four manuscripts for publication