Biology subjects

Verandani, K.

Publications and source records attributed to Verandani, K..

3 recordsLinked to original sources

bioRxiv2025

GeneF: A High-Performance Processing-in-Memory Accelerator for Efficient DNA Alignment

In this paper, we explore the compute and memory characteristics of the FM-index and identify data movement as a significant contributor to overall energy consumption in genomic processing. We propose GeneF, a Processing-in-Memory (PIM) accelerator designed specifically for DNA alignment tasks, leveraging 3D-stacked memory to enhance memory bandwidth and computing parallelism. Our architecture features a custom RISC-V-based processing element (PE) array, a lightweight messaging mechanism to mitigate remote access latency, and specialized prefetchers for improved efficiency. Experimental results demonstrate that GeneF achieves substantial speedups--1820x for counting and 1728x for determining stages--over traditional CPU implementations and offers remarkable energy efficiency, consuming only 25% of the energy compared to conventional CPU-DDR3 systems. The findings highlight the potential of PIM architectures in minimizing data movement and enhancing performance for genomic workloads, paving the way for more energy-efficient computing solutions in the field of bioinformatics.

bioinformatics↗

bioRxiv2025

A Semantic Framework for Predicting Herbal-Drug Biotransformation Conflicts via Biomedical Literature Mining

The widespread use of herbal supplements alongside conventional medicines increases the risk of unpredictable interactions affecting drug absorption and metabolism. This study introduces a comprehensive semantic framework that synthesizes knowledge from biomedical ontologies, curated databases, and full-text literature to model potential biotransformation conflicts between natural compounds and pharmaceutical agents. Leveraging advanced relation extraction systems and graph-based inference techniques, we constructed an enriched knowledge graph capable of highlighting mechanistic pathways involving enzymes, transporters, and drug constituents. Case studies with compounds like green tea and kratom demonstrate the frameworks potential to surface both known and previously underexplored interactions. The proposed system offers a scalable, hypothesis-generating platform for early-stage pharmacokinetic safety analysis in the context of natural product co-administration.

bioinformatics↗

bioRxiv2025

A Novel Infrared-Based Non-Invasive Brain Stimulation Approach for Neurological Disorders

Non-invasive neuromodulation techniques are gaining attention as alternatives to traditional deep brain stimulation for treating neurological disorders. This study explores the use of short-wave infrared light to stimulate deep-brain regions without surgical intervention. By leveraging advanced photon modeling and optical simulations, the proposed system optimizes light penetration for effective neural activation. Experimental evaluations demonstrate its feasibility in delivering targeted stimulation while maintaining safety and efficiency. These findings highlight the potential of infrared-based neuromodulation for future clinical applications in neurotherapy and cognitive enhancement.

neuroscience↗