Genedex integrates gene signatures from Alzheimer's disease studies to contextualize gene expression across pathology, cell types, and brain regions, revealing new insights into disease mechanisms.

bioRxiv · Oct 27, 2026 · PreprintNeuroscience

African Green Monkey Cerebrospinal Fluid miRNome Captures Conserved miRNAs Relevant to Human Neurodegenerative Disease

Sara Dzigurski, Rashid Al-Abri, Xiaoting Li, Monica R. Grasty, Alice Cristina Rodrigues, Michael R. Weed, John D. Elsworth, Matthew S. Lawrence, Yujing Jan Heng, Cristina Stewart Bittencourt Bogsan, Pourya Naderi Yeganeh, Yoshihide Hayashizaki, Frank John Slack, Gamze Gürsoy, Andrew D. Miranker, Bianca R. P. Brown

The paper characterizes the miRNome of African green monkey cerebrospinal fluid, identifying conserved miRNAs relevant to human neurodegenerative diseases and highlighting species-specific variations.

bioRxiv · Aug 17, 2026 · PreprintGenomics

MicroRNA correlates of resilience to Alzheimer's disease identify candidate therapeutic targets for neuroprotection

Pourya Naderi Yeganeh, Latika Matai, Quadri Adewale, Isabel Castanho, Alice Rodrigues, Maria Mavrikaki, Ioannis S. Vlachos, Frank John Slack, Winston Hide

This study identifies miRNA signatures associated with resilience to Alzheimer's disease, revealing potential therapeutic targets for neuroprotection.

bioRxiv · Aug 10, 2026 · PreprintNeuroscience

A microRNA atlas of the human prefrontal cortex across the adult lifespan

Irais E. Valenzuela-Arzeta, Pourya Naderi Yeganeh, Anupama Rai, Jane Banahan, Artemis Iatrou, Leinal Sejour, Madison M. Uyemura, Isaac H. Solomon, Nikolaos P. Daskalakis, Ioannis Vlachos, Winston Hide, Frank John Slack, Maria Mavrikaki

The paper creates a miRNA atlas of the human prefrontal cortex across aging, identifying age-related miRNA changes and highlighting miR-34a-5p as a key upregulated miRNA in older individuals.

bioRxiv · May 28, 2026 · PreprintNeuroscience

Aging-related Transcriptomic Changes with Spatial Resolution in the Human Prefrontal Cortex

Anupama Rai, Artemis Iatrou, Irais E. Valenzuela-Arzeta, Alexandra L. Bartlett, Jane Banahan, Vedant Desai, Lorena Pantano, Isabel Castanho, Pourya Naderi Yeganeh, Athanasios Ploumakis, Shuoshuo Wang, Antonella Arruda de amaral, Nikolaos Kalavros, Sheethal Umesh Nagalakshmi, Peter Tsvetkov, , Maria Mavrikaki

The paper performs spatial transcriptomics on the human prefrontal cortex across the lifespan to identify aging-related changes in different cortical layers.

bioRxiv · Jan 12, 2026 · PreprintNeuroscience

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

Yered H. Pita-Juárez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C. Melms, Sebastian Niezen, Toni Marie Delorey, Adam L. Essene, Olga Rachel Brook, Deepti B. Pant, Disha Skelton-Badlani, Pourya Naderi Yeganeh, Pinzhu Huang, Liuliu Pan, TYLER D. HETHER, Tallulah S. Andrews, , Ioannis S. Vlachos

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

Genome biology · Mar 14, 2025Peer-reviewedGenomics

Molecular hallmarks of excitatory and inhibitory neuronal resilience and resistance to Alzheimer's disease

Isabel Castanho, Pourya Naderi Yeganeh, Carles A. Boix, Sarah L. Morgan, Hansruedi Mathys, Dmitry Prokopenko, Bartholomew White, Larisa M. Soto, Giulia Pegoraro, Saloni A. Shah, Athanasios Ploumakis, Nikolaos Kalavros, David A. A Bennett, Christoph Lange, Doo Yeon Kim, , Winston Hide

This study identifies molecular and cellular signatures of cognitive resilience in Alzheimer's disease by integrating multi-omics data from brain tissues.

bioRxiv · Jan 13, 2025 · PreprintNeuroscience

PanomiR: A systems biology framework for analysis of multi-pathway targeting by miRNAs

Pourya Naderi Yeganeh, Alan Yue Yang Teo, Dimitra Karagkouni, Yered H. Pita-Juárez, Sarah L. Morgan, Frank John Slack, Ioannis S. Vlachos, Winston A Hide

PanomiR identifies miRNAs regulating groups of interacting pathways by analyzing pathway activity and miRNA-mRNA interactions in gene expression data.

Briefings in Bioinformatics · Sep 22, 2023Peer-reviewedSystems Biology

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Toni Marie Delorey, Carly G.K. Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Stephen J. Fleming, Ayshwarya Subramanian, Daniel T. Montoro, Karthik A. Jagadeesh, Kushal K. Dey, Pritha Sen, Michal Slyper, Yered H. Pita-Juárez, , Alexandra–Chloé Villani

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

bioRxiv · Feb 25, 2021 · PreprintGenomics