Negin Rahimzadeh

Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis

FORGE is a configurable Nextflow pipeline for snMultiome analysis that integrates snRNA-seq and snATAC-seq data through latent-variable models and enables regulatory network inference and differential testing.

An Integrated Single-Nucleus Atlas Resolves Cell-Type-Specific Programs and Molecular Subtypes in Alzheimer's Disease

The paper constructs a single-nucleus transcriptomic atlas of Alzheimer's disease and identifies cell-type-specific molecular subtypes and therapeutic targets using a new framework.

Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease

This study uses single-nucleus multi-omics to identify shared and distinct regulatory pathways in Pick's and Alzheimer's disease, revealing disease-specific enhancers and TF binding patterns.

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease

This study uses spatial transcriptomics and single-nucleus RNA-seq to compare genetic and sporadic Alzheimer's Disease, finding similar spatial and cell-type specific changes between sporadic AD and AD in Down Syndrome.

High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

This paper introduces hdWGCNA, a framework for analyzing co-expression networks in high-dimensional transcriptomics data, demonstrating its application in identifying disease-relevant modules in single-cell datasets.

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

The paper curates a dataset of physical molecular interactions between SARS-CoV-2, SARS-CoV-1, and other Coronaviridae proteins, providing a resource for studying virus-host interactions.