Saber Hafezqorani

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

ntEmbd is a deep learning tool for nucleotide sequence embedding, demonstrating utility in RNA classification and adapter sequence identification.

RNA-Bloom2 is a reference-free transcriptome assembler for long-read data, showing competitive performance with reference-based methods and lower resource usage.

Meta-NanoSim simulates and characterizes nanopore metagenomic data to improve microbial abundance estimation and guide algorithm development.

Trans-NanoSim simulates nanopore RNA-seq reads using features learned from real data, enabling cost-effective development of analytical tools.

RBPSponge identifies lncRNAs that act as sponges for RBPs by analyzing RBP binding sites and CLIP peaks on lncRNAs.