The paper characterizes immune microenvironment dysregulation in multiple myeloma using single-cell data and links it to disease progression and patient outcomes.

Nature Cancer · Jan 9, 2026Peer-reviewedGenomics

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

snPATHO-seq: unlocking the pathology archives

Taopeng Wang, Kate Harvey, Javier Escudero Morlanes, Beata Kiedik, Ghamdan Al‐Eryani, Alissa Greenwald, Nikolaos Kalavros, Felipe Segato Dezem, Yuling Ma, Yered H. Pita-Juárez, Kellie Wise, Cyril Dégletagne, Anna Elz, Azi Hadadianpour, John B. Johanneson, , Luciano Gastón Martelotto

This study introduces a method to generate high-quality single-nucleus transcriptomic data from FFPE samples using recent single-cell genomic technology.

bioRxiv · Dec 7, 2023 · PreprintMolecular Biology

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