Publications
- Souporcell3: Robust Demultiplexing for High-Donor Single-Cell RNA-seq Datasets Minindu Weerakoon, Hai Vu, Reza Behboudi, Haynes 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
- 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.