Oluwatosin Oluwadare

Previous Scheduled Teaching

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

Contracts, Grants and 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).