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TADs and Chromatin loops detection

  1. Chowdhury, H. M. A. M., Fuller, M., & Oluwadare, O.(2026). Robin: An Advanced Tool for Comparative Loop Caller Analysis Leveraging Large Language Models. NAR Genomics and Bioinformatics, Volume 8, Issue 1, March 2026, lqag009, https://doi.org/10.1093/nargab/lqag009 
EmbedTAD
  1. Chowdhury, H. M. A. M., & Oluwadare, O.(2025). EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data. Communications Biology.
  1. 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.
  1. 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).
  1. 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).
  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, 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.
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