Improved and automated our target enrichment analysis workflow using Nextflow and SGE (Sun Grid Engine).
Reduced server clutter by implementing custom bash/perl scripts for metrics and cleanup of temporary directories.
Created shareable and successful deployable packages of our pipeline for our external clients using Docker and integrated the Nextflow pipeline with Docker.
Contributed in meetings and gave presentations on projects progress for the group.
01/2015 to Current
Bioinformatics Graduate Research AssistantUNIVERSITY OF DELAWARE Schmidt Lab － Newark, DE
Developing a Perl and/or Nextflow Variant Analysis Pipeline for DNAseq and RNAseq data from either the Fastq files or alignment files (SAM/BAM format) with TopHat2, HISAT2, STAR, BWA, BowTie2, Picard tools and GATK.
Created a local hybrid database application and toolkit for storing and connecting transcriptome NGS metadata, gene expression profiling and variant analysis results from different various bioinformatics tools (TransAtlasDB - https://modupeore.github.io/TransAtlasDB/).
Developed web-user interface for transcriptome gene-expression MySQL and NoSQL database using HTML and PHP.
Designed the database solution for storage of large amount of transcriptome analysis (RNAseq) metadata and variant information using open source RDBMS and NoSQL platform and created the webpages to interact with both databases seamlessly.
Designed a lossless relational database (MySQL) for storage and manipulation of gene expression data, variant detection and annotation analysis from RNAseq assemblies.
Developed pipeline workflows for transcriptome variant detection and annotation analysis.
01/2012 to 12/2014
Bioinformatics Graduate Research AssistantCBCB Bioinformatics Core
Provided solutions and informative insights in designing workflows for the assembly of large genomes.
Developed novel pipeline workflows for genome assembly of large eukaryotic genomes using SMRT sequencing and next-generation sequencing data.
Performed comparative genomics and variant detection analysis on High Throughput Sequencing data using various reference genome alignment tools.
Evaluated genome assembly alignment and variants using different reference assemblers and variant detection tools.
Involved in core bioinformatics research and support/services to end users at CBCB (Center for Bioinformatics and Computational Biology).
GHC Scholar at the Grace Hopper Women in Computing Conference at Orlando, FL. October 2017
Participant in the CRA-Women 2017 Workshop at Washington, DC. April 2017
Helper for Data Carpentry Workshop at University of Delaware. March 2017
Vice President of the Bioinformatics Student Association (BiSA), UD. 2016 - 2017
Participant in the CRA-Women 2016 Workshop at San Diego, CA. April 2016
Participant in the CRA-Women 2015 Workshop at San Francisco, CA. April 2015
Helper for Software Carpentry Workshop at University of Delaware September 2014
Participant in the CRA-Women 2014 Workshop at Santa Clara, CA. April 2014
Treasurer of the Bioinformatics Student Association (BiSA), UD. 2012 - 2013
Teaching Assistant for RNA-SEQ Data Analysis Workshop. CBCB, UD May 2012
Participant in the NSF: High Performance Computing in Life/Medical Science
Workshop at the Virginia Bioinformatics Institute (VBI) at Virginia Tech. July 2012
*Modupe Adetunji and Carl Schmidt. TransAtlasDB: An informatics system for Transcriptome Analysis Data. Plants and Animal Genome XXV (PAG 2017), San Diego, California, USA, January 14-18, 2017.
*Modupe Adetunji and Carl Schmidt. An Integrated Database connecting Expression data, Meta-Data and Variants. Plants and Animal Genome XXIV (PAG 2016), San Diego, California, USA, January 9-13, 2016.
*Barthold JS, Pugarelli J, MacDonald ML, Ren J, Adetunji MO, Polson SW, Mateson A, Wang Y, Sol-Church K, McCahan SM, Akins RE, Devoto M, Robbins AK. Polygenic inheritance of cryptorchidism susceptibility in the LE/orl rat. Molecular Human Reproduction. 2015. doi: 10.1093/molehr/gav060.
*Modupe Adetunji, Chris Ashwell, Max Rothschild, Susan Lamont, Mike Persia, Carl Schmidt. Characterization of Transcriptome Associated SNPs in the Chicken. Plants and Animal Genome XXIII (PAG 2015), San Diego, California, USA, January 10-14, 2015.
Education and Training
PhD: Bioinformatics and Systems BiologyUNIVERSITY OF DELAWARE － Newark, DEBioinformatics and Systems Biology 3.98/4.0
Masters of Science: Bioinformatics and Computational BiologyREDEEMER'S UNIVERSITY － OgunNigeriaBioinformatics and Computational Biology 4.0/4.0 Improving Eukaryotic Genome Assembly through Application of Single Molecule Real-Time Sequencing Data.
Bachelor of Science: BiochemistryBiochemistry 4.2/5.0 Dean's Honors List Senior Thesis: The Effect of Artemisinin-based Antimalarial Drug, Anate® on Specific Enzyme Activities in the Erythrocytes and Hepatocytes of Rats.
bash, Biology, clients, VERSION CONTROL, DATABASE, databases, designing, HTML, PHP, Linux, Matlab, meetings, Excel, Microsoft Office, Windows Operating Systems, Powerpoint, Word, MongoDB, MySQL, next, NoSQL, novel, OPERATING SYSTEMS, Perl, Perl programming, presentations, progress, Python, RDBMS, Real-Time, relational database, research, scripts, Shell scripting, Statistics, Sun, Tuxedo, Unix, user interface, Workbench, workflow