PUBLICATIONS

SELECT:

All  |  3D Chromosome and Genome Structure Modeling  |  Hi-C data Resolution Enhancement  |  TADs and Chromatin loops detection  |  Splice Site Prediction

SHOWING:

Preprints / Undergoing Peer Review

• Samuel A Olowofila and Oluwatosin E Oluwadare (2024). DiCARN-DNase: Enhancing Cell-to-Cell Hi-C Resolution Using Dilated Cascading ResNet with Self-Attention and DNase-seq Chromatin Accessibility Data. bioRxiv 2024.10.31.621380;  doi: https://doi.org/10.1101/2024.10.31.621380    View Publication    |    GitHub Code
• Pinchuk, Dmitry, H. M. A. Mohit Chowdhury, Abhishek Pandeya, and Oluwatosin Oluwadare (2024). “HiCForecast: Dynamic Network Optical Flow Estimation Algorithm for Spatiotemporal Hi-C Data Forecasting.”
• Menon C, Rohit, and Oluwatosin Oluwadare (2024). “ScHicAtt: Hi-C Super Resolution Using Attention Methods for Single Cell.”
• Chowdhury, H. M. A. Mohit, Mattie Fuller, and Oluwatosin Oluwadare (2024).”Robin: An Advanced Tool for Comparative Loop Caller Analysis Leveraging Large Language Models.”

SHOWING:

All Publications

23. Andrew T. Reckard, Abhishek Pandeya, Jacob M. Voris, Carlos G. Gonzalez Cruz, Oluwatosin Oluwadare & Andrew D. Klocko (2024). A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa. BMC Genomics 25, 1215 (2024). https://doi.org/10.1186/s12864-024-11110-7
    View Publication    |    GitHub Code

22. Houchens, D.; Chowdhury, H.M.A.M.; & Oluwadare, O. (2024). coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data. Genes 2024, 15, 1293.
    View Publication    |    GitHub Code

21. Chowdhury, H. M. A. M., Boult, T., & Oluwadare, O. (2024). Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness. BMC Bioinformatics 25, 123 (2024).View Publication    |    GitHub Code

20. Akpokiro, V., Chowdhury, H. M. A., Olowofila, S., Nusrat, R., & Oluwadare, O. (2023). CNNSplice: Robust Models for Splice Site Prediction Using Convolutional Neural Networks. Computational and Structural Biotechnology Journal. ISSN 2001-0370.
    View Publication    |    GitHub Code    |    Webserver

19. Vadnais, D., & Oluwadare, O. (2023). ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction. Current Issues in Molecular Biology, 45(3), 2549-2560.
    View Publication    |    GitHub Code    |    Webserver

18. Hovenga, V., Kalita, J., & Oluwadare, O. (2023). HiC-GNN: A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks. Computational and Structural Biotechnology Journal, 2023 Jan 1;21:812-36.
    View Publication    |    GitHub Code

17. Hovenga V, Kalita J and Oluwadare O. 3D chromosome structure reconstruction using graph convolutional neural networks [version 1; not peer reviewed]. F1000Research 2022, 11:1419 (poster) (doi: 10.7490/f1000research.1119247.1). 
    View Publication

16. 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, 463 (2022).
    View Publication    |    GitHub Code    |    Webserver

15. Akpokiro, V., Martin, T. & Oluwadare, O.(2022). EnsembleSplice: Ensemble Learning Model for Splice Site Prediction. BMC Bioinformatics 23, 413 (2022).
    View Publication    |    GitHub Code

14. Vadnais, D., Middleton, M. & Oluwadare, O. (2022). ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data. BioData Mining 15, 19 (2022).
    View Publication    |    GitHub Code

13. Hicks, P., & Oluwadare, O. (2022). HiCARN:Resolution Enhancement of Hi-C Data Using Cascading Residual Network. Bioinformatics. [Won 2nd Place at 2022 President’s Academic Showcase at Concordia University Irvine]
    View Publication    |    GitHub Code
    

12. Akpokiro, V., Oluwadare, O., & Kalita, J. (2021, December). DeepSplicer: An Improved Method of Splice Sites Prediction using Deep Learning. In 2021 20th IEEE International Conference on Machine Learning and Applications (ICMLA) (pp. 606-609).
    View Publication    |    GitHub Code

11. Collins, B.; Oluwadare, O.; Brown, P. (2021) ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction. Genes 2021, 12, 1757.
    View Publication    |    GitHub Code

10. Hovenga, Van; Oluwadare, O. (2021) CBCR: A Curriculum Based Strategy For Chromosome Reconstruction Int. J. Mol. Sci. 22, no. 8: 4140.
    View Publication    |    GitHub Code
    

9. Oluwadare, O., Max Highsmith, Douglass Turner, Erez Lieberman-Aiden & Jianlin Cheng. (2020) GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data. BMC Mol and Cell Biol 21, 60.
   View Publication    |    GitHub Code    |    Database
   

8. Highsmith, M. R., Oluwadare, O., & Cheng, J. (2019). Deep Learning For Denoising Hi-C Chromosomal Contact Data. bioRxiv, 69255.
   View Publication
   

7. Oluwadare, Oluwatosin, Max Highsmith, and Jianlin Cheng. An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data. Biological Procedures Online 21.1 (2019):7.
   View Publication

6. Trieu, Tuan, Oluwadare, Oluwatosin, and Jianlin Cheng. Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosome. Scientific reports. 2019 Mar 21;9(1):4971.
   View Publication    |    GitHub Code
   

5. Trieu, Tuan*, Oluwadare, Oluwatosin*, Julia Wopata, and Jianlin Cheng. GenomeFlow: A Comprehensive Graphical Tool for Modeling and Analyzing 3D Genome Structure. Bioinformatics (2018). (* Co-first author)
   View Publication    |    GitHub Code
   

4. Oluwadare, Oluwatosin, Yuxiang Zhang, and Jianlin Cheng. A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data. BMC genomics 19.1 (2018): 161.
   View Publication    |    GitHub Code

3. Oluwadare, Oluwatosin, and Jianlin Cheng. ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. BMC bioinformatics 18.1 (2017): 480.View Publication    |    GitHub Code

2. J. Nowotny, A. Wells, Oluwadare, O., L. Xu, R. Cao, T. Trieu, C. He, J. Cheng. GMOL: an interactive tool for 3D genome structure visualization. Scientific Reports, accepted, 2016.View Publication    |    Code

1. Nowotny, S. Ahmed, L. Xu, Oluwadare, O., H. Chen, N. Hensley, T. Trieu, R. Cao, J. Cheng. Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. BMC Bioinformatics, 16(1):338, 2015.View Publication    |    Code

• 2024, Samuel Olowofila (Presenter) and Oluwatosin Oluwadare, International Conference on Research in Computational Molecular Biology (RECOMB) 2024, “HiC-UNet: A UNet-based Approach for HiC Data Resolution Enhancement” (Conference Poster)
• 2024, Van Hovenga, Jugal Kalita and Oluwatosin Oluwadare(Presenter), International Conference on Research in Computational Molecular Biology (RECOMB) 2024, “HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks” (Conference Poster)
• 2024, H. M. A. Mohit Chowdhury (Presenter), Terrance Boult and Oluwatosin Oluwadare, International Conference on Research in Computational Molecular Biology (RECOMB) 2024, “Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness” (Conference Poster)
• 2023, Hovenga V.(Author), Kalita J.(Author), and Oluwadare O. (Author & Presenter), Pacific Symposium on Biocomputing (PSB) 2023 Conference, “3D chromosome structure reconstruction using graph convolutional neural networks”. [ Conference Poster]
• 2022, “Modeling 3D Human Genome Structure,” Department of Computer Science, University of Texas, El Paso, 2022. (Invited talk).
• 2021, V. A. (Author & Presenter), Oluwadare, O. (Author), Kalita, J.(Author), International Conference on Machine Learning And Applications, “DeepSplicer: An Improved Method of Splice Sites Prediction using Deep Learning,” IEEE, Sensors, ssociation for Machine Learning and Applications (AMLA), Journal of Machine Learning Theory, Applications and Practice, Virtual. (Dec. 13, 2021).
• 2021, Oral Presentation at ROCKY 2021 Bioinformatics Conference. Dec 2 – 4, 2021 | Aspen/Snowmass, CO
• 2019, Keynote speaker at ROCKY 2019 Bioinformatics Conference. Dec 5 – 7, 2019 | Aspen/Snowmass, CO
• 2019, Oluwadare, O. (Author), Zephyr, L. (Author & Presenter), Mountain Lion Research Day – Spring 2019, University of Colorado, Colorado Springs, UCCS. (December 13, 2019).
• 2019, “Modeling 3D Human Genome Structure,” Department of Computer Science, University of Colorado, Colorado Springs, 2019. (Invited talk)
• 2019, “Modeling 3-D Human Genome Structure,” Department of Computer Science, Southeast Missouri State University, 2019. (Invited talk)
• 2016, Poster on “Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data”. in MCBIOS at University of Tennessee, Memphis. Download MCBIOS Abstract and Poster

• Oluwatosin Oluwadare. Data Mining and Machine Learning methods for chromosome conformation data analysis. PhD Dissertation. University of Missouri, Columbia, 2019. [PDF]
• Oluwatosin Oluwadare. Gait Analysis On A Smart Floor For Health Monitoring. Master’s Thesis. University of Texas, Arlington, 2015. [ PDF]

• Jena’ Mazique, an undergraduate student from William Carey University, joined us to work on 3D genome modeling in the Summer 2018, as part of the Computational Neuroscience NSF REU Program. Download the Poster Presentation about genome modeling, Manuscript Report , and a Six page document of the most used terms in Hi-C analysis. Summer 2018

LAB ADDRESS:
Osborne Center for Science and Engineering A-210
1420 Austin Bluffs Pkwy
Colorado Springs, CO 80918