Denye Ogeh
21 Gumcester Way, Godmanchester
Summary
An experienced software developer and database administrator, with a research-oriented and analytical mindset, gained through 6+ years experience in transforming seemingly tough human problems into straight-forward automated solutions. Strong technical background in applying current and innovative technologies for processing big data, identifying and reporting hidden patterns for good decision making, managing complex projects and training people.
Overview
16
16
years of professional experience
Work History
Senior Bioinformatician/Developer
EMBL-EBI
08.2022 - 07.2023
- Developed model for genebuild meta database
- Tested model on terabytes of publicly available sequence data
- Refined legacy data checks to more robust and concise MySQL data quality checks
- Migrated code-base from PERL to Python
- Redeveloped legacy pipelines to NextFlow workflows
- Enhanced functionality of Ensembl annotation pipeline to allow for automated gene annotation
- Led Ensembl gene annotation efforts within African Biogenome Project (ABP)
- Coordinated Ensembl gene rapid release cycle
- Managed machine learning initiative to identify repeat sequences in highly-repetitive genomic sequences.
- Tested and provided feedback on Repeatmodeler, leading to development of Repeatmodeler 2.0.
- Annotation of high-quality eukaryotic genomes using automated workflows
Bioinformatician/Developer Programmer
EMBL-EBI
08.2017 - 07.2022
- Designed relational database model to process transcriptomic and genomic sequence data
- Developed and implemented algorithm to fetch, process, analyze and store quality metrics off publicly available transcriptomic and genomic sequence data
- Developed automated repeat classification pipeline, using data from internally curated genomic sequence database, thus improving the efficiency of the automated gene annotation by 20%
- Use of GitHub, JIRA, Confluence, and Kanban boards to collaborate and track project development
- Ran production pipelines on a large compute cluster to download, process and integrate data from various public sequence archives
- Produced high-quality, evidence-based gene sets for eukaryotic species including protein-coding genes,
- Produced tissue-specific RNA-seq alignments and transcript models, noncoding RNA genes and pseudogenes
- Documented data and processes used in gene annotation
- Contributed to Ensembl code-base including design and implementation of new annotation pipelines and software
Software Developer
First Data Limited
07.2007 - 12.2011
- Discussed issues with team members to provide resolution and apply best practices.
- Updated old code-bases to modern development standards, thus improving functionality by 20%.
- Designed intuitive graphical user interfaces to improve user experience.
- Led version control efforts for organization, employing public and open source repositories.
- Tested and deployed scalable and highly available software products.
- Created proofs of concept for innovative new solutions.
- Documented software development methodologies in technical manuals to be used by IT personnel in future projects.
- Participated in software field testing to verify performance of developed projects.
- Collaborated on stages of systems development lifecycle from requirement gathering to production releases.
Education
Ph.D. - Bioinformatics
University of Leicester
Leicester, UK07.2018
Master of Science - Bioinformatics
University of Leicester
Leicester, UK01.2013
Bachelor of Science - Computer Science
Bowen University
Iwo, Nigeria07.2006
Skills
- Data analysis, Genome Annotation, Computational Genomics, Next-Generation Sequencing
- Programming: Python, Perl, Java, C, Visual StudioNet, ASPNet, PHP, HTML, XML, JavaScript, CSS, JQuery, R, Bash
- Relational databases: MySQL, Oracle
- High Performance Computing (HPC) cluster, Linux
- WorkFlow management: NextFlow
- Cloud computing: AWS, Google Cloud
- Jira, Git, Version control, Confluence
- Supervision and Leadership
- Dependable and Responsible
- Critical Thinking
- Organization and Time Management: Scrum
PROFESSIONAL QUALIFICATIONS
- Oracle Certified Database Professional
- Microsoft Certified Technical Specialist (JAVA web based applications)
- Professional Scrum Master I
References
Available on request
Publications
Harrison,P.W. et al. (2023) Ensembl 2024. Nucleic Acids Research, 2023, 1–9 https://doi.org/10.1093/nar/gkad1049
Martin,F.J. et al. (2023) Ensembl 2023. Nucleic Acids Res, 2023, doi:10.1093/nar/gkac958
Karawita,A.C. et al. (2023) The swan genome and transcriptome, it is not all black and white. Genome Biol. 2023 Jan 23;24(1):13.doi: 10.1186/s13059-022-02838-0
Cunningham,F. et al. (2022) Ensembl 2022. Nucleic Acids Res, 2022, doi:10.1093/nar/gkab1049.De Silva,N.H. et al. (2022) The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. Nucleic Acids Res, 2022, Nucleic Acids Res, 01 Jan 2022, 50(D1):D765-D770
Zhu,F. et al. (2021) Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nature Communications, 11 Oct 2021, 12(1):5932. https://doi.org/10.1038/s41467-021-26272-1
Howe,K.L. et al. (2021) Ensembl 2021. Nucleic Acids Res, 2021, Jan 8;49(D1):D884-D891. doi: 10.1093/nar/gkaa942.
Yates,A.D. et al. (2020) Ensembl 2020. Nucleic Acids Res, 2020 Jan 8;48(D1):D682-D688. doi: 10.1093/nar/gkz966.
Cunningham,F. et al. (2019) Ensembl 2019. Nucleic Acids Res, 2019, doi:10.1093/nar/gky1113.
Zerbino,D.R. et al. (2018) Ensembl 2018. Nucleic Acids Res, 2018, Nucleic Acids Res, 2018. doi:10.1093/nar/gkx1098.
Ogeh,D.N. and Badge,R.M (2017) A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. Bioinformatics, Volume 33, Issue 5, March 2017, Pages 650–653, https://doi.org/10.1093/bioinformatics/btw687
Oluwagbemi,O.O, et al. (2016) Computational and mathematical modelling: Applicability to infectious disease control in Africa. Asian Journal of Scientific Research, 2016. DOI: 10.3923/ajsr.2016.88.105
Timeline
Senior Bioinformatician/Developer
EMBL-EBI
08.2022 - 07.2023
Bioinformatician/Developer Programmer
EMBL-EBI
08.2017 - 07.2022
Software Developer
First Data Limited
07.2007 - 12.2011
Ph.D. - Bioinformatics
University of Leicester
Master of Science - Bioinformatics
University of Leicester
Bachelor of Science - Computer Science
Bowen University
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