Irtesam Mahmud Khan

TENNIS predicts unannotated isoforms and refines existing annotations using an evolution-based model of alternative splicing, validated by deep long-read RNA-seq.

Amaranth improves single-cell transcript assembly by discriminatively modeling UMI and internal reads, outperforming existing assemblers on Smart-seq3 datasets.

The paper introduces CircPlex, a method to accurately reconstruct circRNAs from complex rolling circular long reads by addressing repeat pattern complexities, improving detection sensitivity and uncovering novel isoforms.

Telos improves transcript assembly by accurately detecting TSSs and TESs and ranking transcripts, outperforming existing methods across multiple RNA-seq datasets.