Oluwatosin Oluwadare

Previous Scheduled Teaching

No previous courses scheduled.

Published Intellectual Contributions

Journal Article

• 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
• Olowofila, S., Oluwadare, O., Robinson, P. (2025). DiCARN-DNase: Enhancing Cell-to-Cell Hi-C Resolution Using Dilated Cascading ResNet with Self-Attention and DNase-seq Chromatin Accessibility Data. Other. Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btaf452
• 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.
• Menon, R., Mohit Chowdhury HMA, Oluwadare, O. (2025). ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models.. Other. 27 978-991.
• Pinchuk, D., Chowdhury HMAM, Pandeya, A., Oluwadare, O. (2025). HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting.. Other. 41 (2)
• 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) 1215.
• 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.. Other.
• Houchens, D., Chowdhury HMAM, Oluwadare, O. (2024). coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data.. Other. 15 (10)
• Chowdhury HMAM, Boult, T., Oluwadare, O. (2024). Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness.. BMC Bioinformatics. 25 (1) 123.
• Akpokiro, V., Chowdhury HMAM, Olowofila, S., Nusrat, R., Oluwadare, O. (2023). CNNSplice: Robust models for splice site prediction using convolutional neural networks.. Other. 21 3210-3223.
• Vadnais, D., Oluwadare, O. (2023). ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.. Other. 45 (3) 2549-2560.
• 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) 413.
• Vadnais, D., Middleton, M., Oluwadare, O. (2022). ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.. Other. 15 (1) 19.
• Hicks, P., Oluwadare, O. (2022). HiCARN: resolution enhancement of Hi-C data using cascading residual networks.. Other. 38 (9) 2414-2421.
• Collins, B., Oluwadare, O., Brown, P. (2021). ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction.. Other. 12 (11)
• Hovenga, V., Oluwadare, O. (2021). CBCR: A Curriculum Based Strategy For Chromosome Reconstruction.. International Journal of Molecular Sciences. 22 (8)
• 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., 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) 60.
• 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.
• Trieu, T., Oluwadare, O., Cheng, J. (2019). Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.. Scientific Reports. 9 (1) 4971.
• 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) 480.
• 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 20802.
• 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.

Contracts, Grants and Sponsored Research

Grant - Research

• Oluwadare, O., "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).
• 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).