Ali Sharifi‐Zarchi

ARYANA-BS: Context-Aware Alignment of Bisulfite-Sequencing Reads

ARYANA-BS improves bisulfite sequencing read alignment by considering DNA methylation patterns, achieving high accuracy and efficiency.

Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning

This study introduces ExoGRU, a machine learning model that predicts small RNA secretion from sequence, identifies key RNA-binding proteins, and develops exoCLIP to map RNA interactomes in extracellular vesicles.

InterOpt: Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes

The paper introduces a mathematical framework for improving qPCR gene expression normalization by optimizing weighted aggregation of reference genes using scale-invariant functions.

Alignment of Single-Molecule Sequencing Reads by Enhancing the Accuracy and Efficiency of Locality-Sensitive Hashing

The paper improves the accuracy and efficiency of MinHash for aligning single-molecule sequencing reads by using a single hash function and allowing one sequencing error in seed sequences, outperforming existing aligners on E. coli and human genomes.

Identification of hub genes and pathways in nonalcoholic steatohepatitis by integrated bioinformatics analysis

The paper identifies hub genes and key pathways in nonalcoholic steatohepatitis using integrated bioinformatics analysis of gene expression data.

StrongestPath: a Cytoscape application for protein-protein interaction analysis

StrongestPath identifies the highest confidence interaction cascades between proteins using PPI networks and provides pathway analysis tools within Cytoscape.

DNA-RNA hybrid (R-loop): from a unified picture of the mammalian telomere to the genome-wide

The paper develops a method to detect and isolate stable DNA-RNA triplexes in complex genomes and defines terminal R-loop complexes in mouse and human genomes.

BNrich: A Bayesian network approach to the pathway enrichment analysis

BNrich improves pathway enrichment analysis by incorporating Bayesian networks and gene expression data to prioritize impacted pathways.

Enhanced Waddington Landscape Model with Cell-CellCommunication Can Explain Molecular Mechanisms ofSelf-Organization

The paper introduces an enhanced Waddington landscape model incorporating cell-cell communication to explain self-organization in human ESCs during in vitro gastrulation.

A Novel Workflow for Health Survey Analysis: Results on the Yazd Health Study (YaHS)

The paper introduces a novel workflow for health survey analysis and validates it on the Yazd Health Study dataset, revealing both aligned and novel findings.

Pin1 Regulatory miRNAs as Novel Candidates for Alzheimer’s Disease Treatment

The paper identifies miRNAs that regulate Pin1, a key player in Alzheimer's disease pathology, through genome-wide analysis and experimental validation.