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INTERN
Skills
  • PHP; HTML; Python, Perl programming language; Shell scripting.
  • OPERATING SYSTEMS: Unix /Linux; Windows Operating Systems.
  • PIPELINE DEVELOPMENT: Nextflow, Docker.
  • VERSION CONTROL: git
  • NGS Analysis: RNAseq (Illumina miseq), DNAseq (Illumina hiseq, PacBio RS)
  • DATABASE: Design; Implementation and Administration of MySQL; NoSQL [FastBit, MongoDB].
  • TOOLS: Statistics (R, Matlab); Genomic Assembly, Transcriptomic Assembly Variant Analysis, Variant Annotation tools (Tuxedo suite, BWA, CLC Genomics Workbench, Samtools, GATK, VEP, SNPEff, Annovar, Blast, David); De novo assemblers and error detection tools (SOAPdenovo, Velvet, Trinity, PBJelly, PBcR pipeline, Celera assembler); Visualization software (Cytospace, Seqmonk, IGV, UCSC Browser); Microsoft Office (Word, Powerpoint, Excel).
Experience
06/2016 to 08/2016
Intern ROCHE DIAGNOSTICS CORP － Pleasanton, CA
  • 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 Assistant UNIVERSITY 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 Assistant CBCB 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).
Publications
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 PUBLICATION *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
May 2018
PhD: Bioinformatics and Systems Biology UNIVERSITY OF DELAWARE － Newark, DE Bioinformatics and Systems Biology 3.98/4.0
December 2014
Masters of Science: Bioinformatics and Computational Biology REDEEMER'S UNIVERSITY － Ogun Nigeria Bioinformatics and Computational Biology 4.0/4.0 Improving Eukaryotic Genome Assembly through Application of Single Molecule Real-Time Sequencing Data.
August 2009
Bachelor of Science: Biochemistry Biochemistry 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.
Skills
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
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Resume Overview

Companies Worked For:

  • ROCHE DIAGNOSTICS CORP
  • UNIVERSITY OF DELAWARE Schmidt Lab
  • CBCB Bioinformatics Core

School Attended

  • UNIVERSITY OF DELAWARE
  • REDEEMER'S UNIVERSITY

Job Titles Held:

  • Intern
  • Bioinformatics Graduate Research Assistant

Degrees

  • PhD : Bioinformatics and Systems Biology
    Masters of Science : Bioinformatics and Computational Biology
    Bachelor of Science : Biochemistry

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