Tasfia Zahin

EquiRep accurately detects tandem repeats from error-prone sequences by refining unit estimation and reconstructing repeat units through a weighted graph approach.

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.

This paper introduces an alignment-free maximum likelihood method for phylogenetic tree construction and shows it is competitive with existing alignment-free tools.

TERRACE improves circRNA assembly accuracy by using a splice graph and dynamic programming, outperforming existing methods in sensitivity and precision.