Fatemeh Almodaresi

React-to-Me, a retrieval-augmented chatbot grounding GPT-4o-mini in curated Reactome pathways with hyperlinked citations, earned higher blinded expert ratings than ungrounded GPT-4o-mini (odds ratio 2.01).

PuffAligner is a fast and accurate sequence aligner that balances speed, memory usage, and alignment quality, offering performance comparable to Bowtie2 and STAR.

The paper introduces an updatable and scalable exact sequence-search index based on Mantis, demonstrating its efficiency and scalability over large datasets.

The paper evaluates how alignment and mapping methods affect transcript quantification accuracy and introduces a new method called selective alignment.

The paper introduces an efficient encoding method for color information in de Bruijn graphs, improving compression and scalability for large-scale genomic applications.

Mantis provides a fast, small, and exact sequence search index for large RNA-seq datasets, outperforming existing methods in speed and accuracy.

The paper introduces a space and time-efficient index for the compacted colored de Bruijn graph, balancing speed and space usage for k-mer lookup and pattern matching.

Grouping k-mer color sets into equivalence classes and entropy-compressing them shrinks colored de Bruijn graph color storage up to 20-fold versus VARI, keeping BOSS for topology.