PUBLICATIONS

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

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3D Chromosome and Genome Structure Modeling

  1. 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
  1. 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.
  1. 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.
  1. 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).
  1. Collins, B.; Oluwadare, O.; Brown, P. (2021) ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction. Genes 2021, 12, 1757.
  1. Hovenga, Van; Oluwadare, O. (2021) CBCR: A Curriculum Based Strategy For Chromosome Reconstruction Int. J. Mol. Sci. 22, no. 8: 4140.
  1. 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.
  1. 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.
  1. 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.
  1. 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)
  1. 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.
  1. 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.
  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.
OFFICE PHONE:
(719) 255-3004
EMAIL:
ooluwada [at] uccs [dot] edu
LAB ADDRESS:
Osborne Center for Science and Engineering A-210
1420 Austin Bluffs Pkwy
Colorado Springs, CO 80918