Research

Publications

  • SpaceCell: Clustering spatial scRNA-seq data, M Weerakoon, H Heaton (Under review, Plos Computational Biology),
  • Cellector: A tool to detect foreign genotype cells in scRNAseq data with applications in leukemia and microchimerism, R Behboudi, M Weerakoon, H Heaton (Under review, Nature Communications)
  • Souporcell3: Robust Demultiplexing for High-Donor Single-Cell RNA-seq Datasets, M Weerakoon, H Vu, R Behboudi, H Heaton (Bioinformatics 2026)
  • LCSKPOA: Enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended lcsk++, M Weerakoon, CT Saunders, H Heaton (BMC Bioinformatics 2025)
  • TopoQual polishes circular consensus sequencing data and accurately predicts quality scores, M Weerakoon, S Lee, E Mitchell, H Heaton (BMC Bioinformatics 2025)
  • Impact of AI on publication rates. Weerakoon M, Amarathunga B, Weerasuriya P, Sivasankar P. (arXiv 2026)
  • A Bibliometric Review of Plant Growth-Promoting Rhizobacteria in Drought Tolerance, K Thilina, M Weerakoon, Akila Abesinghe, T Mendis, P Sivashankar (OSF 2025)
  • Interplay between omics, bioinformatics and agriculture: A bibliometric analysis, M Weerakoon, KT Akila Abesinghe, T Mendis, P Sivashankar (OSF 2024)
  • CarM: Hierarchical episodic memory for continual learning S Lee, M Weerakoon, J Choi, M Zhang, D Wang, M Jeon (Proceedings of the 59th ACM/IEEE DAC 2022)

Conference Presentations

  • 2022 Design Automation Conference: Oral presentation: CarM

Poster Presentations

  • 2025 Auburn Research Symposium: Poster presentation: Topoqual
  • 2025 Auburn Graduate Engineering Research Showcase: Poster presentation: LCSKPOA

Peer review

  • Scientific Data: An Imbalanced Dataset with Multiple Feature Representations for Studying Quality Control of Next-Generation Sequencing
  • BMC Genomics: Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
  • PeerJ: A novel and efficient feature extraction algorithm using kmer-derived mutation signal
  • BMC Bioinformatics: SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic molecules

Library Contribution

  • Partial Order Alignment Code in Rust-bio (https://github.com/rust-bio/rust-bio/blob/master/src/alignment/poa.rs)
  • Memory Sanitization of CFDWARP (https://github.com/bernardparent/CFDWARP)

Patents

  • AX Squat analyzer - Minindu Weerakoon, Elona Ibrahim, KR, Provisional.