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Oluwatosin Oluwadare

Associate Professor

University of North Texas

Department of Computer Science and Engineering

Email: Oluwatosin.Oluwadare@unt.edu

Education

  • PhD, University of Missouri - Columbia, 2019
    Major: Computer Science
  • MS, University of Texas at Arlington, 2015
    Major: Computer Science
    Dissertation: Gait Analysis on a Smart Floor for Health Monitoring

Professional Positions

    Academic - Post-Secondary

  • Tenure-Track Assistant Professor, University of Colorado, Colorado Springs. University of Colorado, Colorado Springs. (2019 - 2025).
  • Graduate Teaching Assistant, University of Missouri, Columbia. University of Missouri, Columbia. (2018 - 2019).
  • Graduate Research Assistant, University of Missouri, Columbia. University of Missouri, Columbia. (2015 - 2019).
  • Graduate Research Assistant, University of Texas at Arlington. University of Texas at Arlington. (2014 - 2015).
  • Graduate Teaching Assistant, University of Texas at Arlington. University of Texas at Arlington. (2014 - 2014).

Professional Memberships

  • International Society of Computational Biology. (2021 - Present).

Teaching

Teaching Experience

    University of North Texas

  • CSCE 3201 - Applied Artificial Intelligence, 2 courses.
  • CSCE 5218 - Deep Learning, 1 course.
  • CSCE 5934 - Directed Study, 2 courses.
  • CSCE 6940 - Individual Research, 3 courses.
  • CSCE 6950 - Doctoral Dissertation, 1 course.

Teaching at Other Institutions

  • University of Colorado Colorado Springs, CS 4435/5435 Data Mining, Fall 2024.
  • University of Colorado Colorado Springs, CS 4850/5850 Bioinformatics & Computational Biology, Spring 2024.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Spring 2024.
  • University of Colorado Colorado Springs, CS 2020 Introduction to Statistics for Data Analytics, Spring 2024.
  • University of Colorado Colorado Springs, CS 1120 Computational Thinking with Beginning Programming, Fall 2023.
  • University of Colorado Colorado Springs, CS 4435/5435 Data Mining, Fall 2023.
  • University of Colorado Colorado Springs, INOV 1010 The Innovation Process, Fall 2023.
  • University of Colorado Colorado Springs, CS 1120 Computational Thinking with Beginning Programming, Summer 2023.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Spring 2023.
  • University of Colorado Colorado Springs, CS 2020 Introduction to Statistics for Data Analytics, Spring 2023.
  • University of Colorado Colorado Springs, CS 4435/5435 Data Mining, Fall 2022.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Fall 2022.
  • University of Colorado Colorado Springs, CS 1120 Computational Thinking with Beginning Programming, Summer 2022.
  • University of Colorado Colorado Springs, CS 1120 Computational Thinking with Beginning Programming, Fall 2021.
  • University of Colorado Colorado Springs, CS 4435/5435 Data Mining, Fall 2021.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Fall 2021.
  • University of Colorado Colorado Springs, CS 1120 Computational Thinking with Beginning Programming, Spring 2021.
  • University of Colorado Colorado Springs, CS 4850/5850 Bioinformatics & Computational Biology, Fall 2020.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Fall 2020.
  • University of Colorado Colorado Springs, CS 5435 Data Mining, Spring 2020.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Spring 2020.
  • University of Colorado Colorado Springs, ENTP 1000 Introduction to Entrepreneurship, Fall 2019.

Non-Credit Instruction

  • Workshop, 8 participants. (November 17, 2025).
  • Guest Lecture, Anuradha and Vikas Sinha Department of Data Science, (September 10, 2025).

Directed Student Learning

  • Dissertation Committee Member, "BRIDGING LUNG CANCER BIOLOGY AND BIOSENSOR DATA USING AGENT-BASED MATHEMATICAL MODELS," Information Science. (November 2025).
  • Dissertation Committee Member, "COMPUTATIONAL METHODS FOR PROTEIN AND PEPTIDE IDENTIFICATION AND QUANTIFICATION IN PROTEOMICS," Computer Science and Engineering. (September 2025).

Awards and Honors

  • National Institutes of Health Maximizing Investigators’ Research Award (MIRA) Early-Career Award, National Institutes of Health. (2023).
  • $1 Million Dollar Club Inductee, University of Colorado, Colorado Springs. (2024).
  • College of Engineering and Applied Sciences (EAS) Outstanding Researcher of the Year Award, University of Colorado, Colorado Springs. (2024).
  • Distinguished Alumnus Award, Federal University of Technology, Akure (FUTA), Nigeria. (2024).
  • Missouri Building Entrepreneurial Capacity Program (MOBEC) Grant Award for Prototyping, Missouri. (2016).
  • Microsoft Imagine Cup USA Finalist, Microsoft. (2015).
  • First Bank of Nigeria Award for Best Graduating Students, First Bank of Nigeria. (2012).
  • University Academic Performance Prize (2011/2012), Federal University of Technology Akure (FUTA). (2012).
  • University Merit Award (2010/2011 and 2011/2012 Academic Session), Federal University of Technology, Akure (FUTA). (2010).

Research

Published Intellectual Contributions

    Conference Proceeding

  • Akpokiro, V., Oluwadare, O., Kalita, J. (2021). DeepSplicer: An Improved Method of Splice Sites Prediction using Deep Learning. 2021 20th IEEE International Conference on Machine Learning and Applications (ICMLA). 606-609. IEEE. https://doi.org/10.1109/icmla52953.2021.00101

    • Journal Article

  • Chowdhury, H.M., Fuller, M., Oluwadare, O. (2026). Robin: an advanced tool for comparative loop caller result analysis leveraging large language models. Other. 8 (1) Oxford University Press (OUP). https://doi.org/10.1093/nargab/lqag009
  • Menon, R., Mohit Chowdhury, H., Oluwadare, O. (2025). ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models. Other. 27 978-991. Elsevier BV. https://doi.org/10.1016/j.csbj.2025.02.031
  • Chowdhury, H.M., Oluwadare, O. (2025). EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data. Other. 9 (1) Springer Science and Business Media LLC. https://doi.org/10.1038/s42003-025-09224-z
  • Olowofila, S., Oluwadare, O. (2025). DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data.. Other. 41 (9)
  • Chandrashekar MKB, Menon, R., Olowofila, S., Oluwadare, O. (2025). Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.. Other. 41 (Supplement_1) i475-i483.
  • Pinchuk, D., Chowdhury, H.M., Pandeya, A., Oluwadare, O., Alkan, C. (2025). HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting. Other. 41 (2) Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btaf030
  • Reckard, A.T., Pandeya, A., Voris, J.M., Gonzalez Cruz, C.G., Oluwadare, O., Klocko, A.D. (2024). A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa. BMC Genomics. 25 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12864-024-11110-7
  • Houchens, D., Chowdhury, H.M., Oluwadare, O. (2024). coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data. Other. 15 (10) 1293. MDPI AG. https://doi.org/10.3390/genes15101293
  • Chowdhury, H.M., Boult, T., Oluwadare, O. (2024). Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness. BMC Bioinformatics. 25 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12859-024-05713-w
  • Akpokiro, V., Chowdhury, H.M., Olowofila, S., Nusrat, R., Oluwadare, O. (2023). CNNSplice: Robust models for splice site prediction using convolutional neural networks. Other. 21 3210-3223. American Association for the Advancement of Science (AAAS). https://doi.org/10.1016/j.csbj.2023.05.031
  • Vadnais, D., Oluwadare, O. (2023). ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction. Other. 45 (3) 2549-2560. MDPI AG. https://doi.org/10.3390/cimb45030167
  • Hovenga, V., Kalita, J., Oluwadare, O. (2022). HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks.. Other. 21 812-836.
  • Higgins, S., Akpokiro, V., Westcott, A., Oluwadare, O. (2022). TADMaster: a comprehensive web-based tool for the analysis of topologically associated domains.. BMC Bioinformatics. 23 (1) 463.
  • Akpokiro, V., Martin, T., Oluwadare, O. (2022). EnsembleSplice: ensemble deep learning model for splice site prediction. BMC Bioinformatics. 23 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12859-022-04971-w
  • Hicks, P., Oluwadare, O., Robinson, P. (2022). HiCARN: resolution enhancement of Hi-C data using cascading residual networks. Other. 38 (9) 2414-2421. Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btac156
  • Collins, B., Oluwadare, O., Brown, P. (2021). ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction. Other. 12 (11) 1757. MDPI AG. https://doi.org/10.3390/genes12111757
  • Hovenga, V., Oluwadare, O. (2021). CBCR: A Curriculum Based Strategy For Chromosome Reconstruction. International Journal of Molecular Sciences. 22 (8) 4140. MDPI AG. https://doi.org/10.3390/ijms22084140
  • Oluwadare, O., Highsmith, M., Turner, D., Lieberman Aiden, E., Cheng, J. (2020). GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data. Other. 21 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12860-020-00304-y
  • Oluwadare, O., Highsmith, M., Turner, D., Lieberman Aiden, E., Cheng, J. (2020). Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.. Other. 21 (1) 62.
  • Oluwadare, O., Highsmith, M., Cheng, J. (2019). An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data. Other. 21 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12575-019-0094-0
  • Trieu, T., Oluwadare, O., Wopata, J., Cheng, J. (2019). GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.. Other. 35 (8) 1416-1418.
  • Oluwadare, O., Zhang, Y., Cheng, J. (2018). A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data. BMC Genomics. 19 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12864-018-4546-8
  • Oluwadare, O., Cheng, J. (2017). ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. BMC Bioinformatics. 18 (1) Springer Science and Business Media LLC. https://doi.org/10.1186/s12859-017-1931-2
  • Nowotny, J., Wells, A., Oluwadare, O., Xu, L., Cao, R., Trieu, T., He, C., Cheng, J. (2016). GMOL: An Interactive Tool for 3D Genome Structure Visualization. Scientific Reports. 6 (1) Springer Science and Business Media LLC. https://doi.org/10.1038/srep20802
  • Nowotny, J., Ahmed, S., Xu, L., Oluwadare, O., Chen, H., Hensley, N., Trieu, T., Cao, R., Cheng, J. (2015). Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.. BMC Bioinformatics. 16 338.

    • Research/Creativity Activity Cited by Other Scholars

  • Olowofila, S., Oluwadare, O. (2024). DiCARN-DNase: Enhancing Cell-to-Cell Hi-C Resolution Using Dilated Cascading ResNet with Self-Attention and DNase-seq Chromatin Accessibility Data. openRxiv. https://doi.org/10.1101/2024.10.31.621380
  • Menon, R., Chowdhury, H.M., Oluwadare, O. (2024). ScHiCAtt: Enhancing Single-Cell Hi-C Resolution Using Attention-Based Models. openRxiv. https://doi.org/10.1101/2024.12.16.628505
  • Vadnais, D., Middleton, M., Oluwadare, O. (2021). ParticleChromo3D: A Particle Swarm Optimization Algorithm for Chromosome and Genome 3D Structure Prediction from Hi-C Data. openRxiv. https://doi.org/10.1101/2021.02.11.430871
  • Highsmith, M., Oluwadare, O., Cheng, J. (2019). Deep Learning For Denoising Hi-C Chromosomal Contact Data. openRxiv. https://doi.org/10.1101/692558

    • posted-content

  • Thapa, S., Tamargo, M., Oluwadare, O. ASPECT: Alternative Splicing Event Classification with Transformers. openRxiv. https://doi.org/10.64898/2026.02.04.700904
  • Mohit Chowdhury, H.M., Oluwadare, O. HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture Analysis. openRxiv. https://doi.org/10.64898/2026.02.06.704438
  • Reckard, A.T., Pandeya, A., Voris, J.M., Gonzalez Cruz, C.G., Oluwadare, O., Klocko, A.D. (2024). A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa. openRxiv. https://doi.org/10.1101/2024.06.07.597955
  • Hovenga, V., Kalita, J., Oluwadare, O. (2022). 3D chromosome structure reconstruction using graph convolutional neural networks. F1000 Research Ltd. https://doi.org/10.7490/f1000research.1119247.1
  • Van Hovenga, Oluwadare, O., Kalita, J. (2021). HiC-GNN: A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks. openRxiv. https://doi.org/10.1101/2021.11.29.470405
  • Trieu, T., Oluwadare, O., Cheng, J. (2019). Hierarchical Reconstruction of High-Resolution 3D Models of Human Chromosomes. openRxiv. https://doi.org/10.1101/415810

Presentations Given

    Keynote/Plenary Address

  • Oluwadare, O. (Author & Presenter), Rocky Mountain Bioinformatics Conference, 3D Chromosome and Genome Structure Modeling, ISCB, Aspen, United States of America. (2019 - 2019).

    • Oral Presentation

  • Oluwadare, O. (Author & Presenter), Intelligent Systems for Molecular Biology, Unicorn: Enhancing Single-Cell Hi-C Data with Blind Super-Resolution for 3D Genome Structure Reconstruction, nternational Society for Computational Biology (ISCB), Liverpool, United Kingdom. (2025 - 2025).

Media Contributions

    Internet

  • "Developers look to create disability apps," Marketplace News.. (July 22, 2015).

    • Newspaper

  • "Oluwadare Receives Prestigious NIH NIGMS Maximizing Investigators’ Research Award," UCCS Communique. (September 14, 2023).
  • "A self-learning algorithm may help predict how genetic disease occurs," UCCS Communique. (June 8, 2023).
  • "App helps visually impaired connect," UT Arlington News. (August 5, 2015).

    • Radio

  • "A Tech Challenge To Empower People With Disabilities.," KERA NEWS. (July 21, 2015).

    • TV

  • "MU PhD. Student launches app to help visually impaired," KOMU-TV News. (December 5, 2017).

Contracts, Grants, Sponsored Research

    Grant - Research

  • Oluwadare, O. (Principal), "Can one size fit all? - High-Resolution 3D Genome Spatial Organization Inference with Generalizable Models," sponsored by National Institute of Health, Federal, $1007407 Funded. (2025 - 2028).
  • Oluwadare, O. (Principal), "Can one size fit all? – High-Resolution 3D Genome Spatial Organization Inference with Generalizable Models," sponsored by National Institute of Health, Federal, $1611219 Funded. (2023 - 2028).
  • Macias, V.M. (Principal), Baxter-Slye, J.L. (Co-Principal), Junker, J. (Co-Principal), Oluwadare, O. (Co-Principal), "Artificial Intelligence and the Classical Entomologist: Designing interdisciplinary pedagogy to revive an essential, but dying art-(Start date January 16th 2025)," sponsored by Learning Institutes, University of North Texas, $5000 Funded. (2025 - 2026).
  • Oluwadare, O.E. (Co-Principal), "CyberRangerForge: A University of Colorado System Virtual Institute for Cyber Range and Research based Advanced Training of ROTC Cadets for Next Generation Cyber Operations," sponsored by Griffiss Institute, Private, $1500000 Funded. (2023 - 2025).
  • Oluwadare, O. (Principal), ""CRII:III:Development of deep learning methods for high-resolution 3D genomestructure spatial reconstruction," sponsored by National Science Foundation, Federal, $175000 Funded. (2022 - 2025).
  • Oluwadare, O. (Co-Principal), "REU Site: Deep Learning: Theory, Concepts and Applications," sponsored by National Science Foundation, Federal, $404980 Funded. (2021 - 2024).

Service

University Service

  • Grant Proposal Reviewer, Internal, Center for Computational Life Sciences (CCLS). (August 2025 - January 5, 2026).
  • Committee Member, Promotion and Tenure Committee (PTC). (September 2025 - September 30, 2025).

Professional Service

  • Reviewer, Journal Article, IEEE Transactions on Computational Biology and Bioinformatics (TCBB). Washington, DC. (November 5, 2025 - January 16, 2026).
  • Reviewer, Journal Article, Oxford Bioinformatics Journal. Oxford, (September 19, 2025 - January 8, 2026).
  • Mentor, CRA UR2PhD Program. Denton, TX. (August 2025 - December 2025).
  • Reviewer, Journal Article, NAR Genomics and Bioinformatics. Oxford, (December 1, 2025 - December 30, 2025).
  • Reviewer, Journal Article, BMC Bioinformatics Journal. London, (September 8, 2025 - December 30, 2025).
  • Reviewer, Journal Article, Nucleic Acids Research Journal. Oxford, (September 5, 2025 - December 28, 2025).
  • Committee Member, Pacific Symposium on Biocomputing 2026. Waimea, HI. (August 7, 2025 - December 21, 2025).
  • Editor, Journal Editor, Plant Communications. Cambridge, MA. (November 12, 2025 - November 26, 2025).
  • Reviewer, Grant Proposal, National Science Center, Poland. Kraków, (October 2, 2025 - October 23, 2025).
  • Reviewer, Journal Article, Molecular Plant. Shanghai, (September 11, 2025 - September 29, 2025).
  • Committee Member, IEEE International Conference on Bioinformatics & Biomedicine 2025. Wuhan, (August 25, 2025 - September 25, 2025).
  • Guest Speaker, Data Science Talk Series at UNT. Denton, TX. (September 10, 2025).
  • Reviewer, Journal Article, Briefings in Bioinformatics. Oxford, (August 2025 - August 2025).