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

March 14, 2025

Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C. Melms, Sebastian Niezen, Toni M. Delorey, Adam L. Essene, Olga R. Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S. Andrews, Carly G.K. Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, […]

Transcriptional profile of the rat cardiovascular system at single cell resolution

January 28, 2025

Alessandro Arduini†, Stephen J. Fleming†, Ling Xiao†, Amelia W. Hall, Amer-Denis Akkad, Mark D. Chaffin, Kayla J. Bendinelli, Nathan R. Tucker, Irinna Papangeli, Helene Mantineo, Patricio Flores-Bringas, Mehrtash Babadi, Christian M. Stegmann, Guillermo García-Cardeña, Mark E. Lindsay, Carla Klattenhoff, and Patrick T. Ellinor (†: These authors contributed equally). Cell Reports 44(1):115091, (2025). BioRxiv Preprint, Posted […]

Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning

April 4, 2024

Yang Xu, Stephen J. Fleming, Matthew Tegtmeyer, Steven A. McCarroll & Mehrtash Babadi. Cell Systems 16(4):101245. April 16, 2025. BioRxiv Preprint, Posted March 16, 2024. Collaboration with McCarroll Lab

CellBender removes technical artifacts from single-cell RNA sequencing data

August 17, 2023

Stephen Fleming and Mehrtash Babadi. Nature Methods 20, 1285–1286 (2023).

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

August 7, 2023

Stephen J. Fleming, Mark D. Chaffin, Alessandro Arduini, Amer-Denis Akkad, Eric Banks, John C. Marioni, Anthony A. Philippakis, Patrick T. Ellinor, and Mehrtash Babadi. Nature Methods 20, 1323–1335 (2023).

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

June 22, 2022

Mark Chaffin, Irinna Papangeli, Bridget Simonson, Amer-Denis Akkad, Matthew C. Hill, Alessandro Arduini, Stephen J. Fleming, Michelle Melanson, Sikander Hayat, Maria Kost-Alimova, Ondine Atwa, Jiangchuan Ye, Kenneth C. Bedi Jr, Matthias Nahrendorf, Virendar K. Kaushik, Christian M. Stegmann, Kenneth B. Margulies, Nathan R. Tucker & Patrick T. Ellinor. Nature 608, 174–180 (2022) Collaboration with Ellinor […]

Deep learning enables genetic analysis of the human thoracic aorta

November 26, 2021

James P. Pirruccello, Mark D. Chaffin, Elizabeth L. Chou, Stephen J. Fleming, Honghuang Lin, Mahan Nekoui, Shaan Khurshid, Samuel F. Friedman, Alexander G. Bick, Alessandro Arduini, Lu-Chen Weng, Seung Hoan Choi, Amer-Denis Akkad, Puneet Batra, Nathan R. Tucker, Amelia W. Hall, Carolina Roselli, Emelia J. Benjamin, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Christian M. Stegmann, […]

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

April 29, 2021

Toni M. 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, Devan Phillips, Jana Biermann, Zohar Bloom-Ackermann, Nikolaos Barkas, Andrea Ganna, James Gomez, Johannes C. Melms, Igor Katsyv, […]

Transcriptional and Cellular Diversity of the Human Heart

August 4, 2020

Nathan R. Tucker, Mark Chaffin, Stephen J. Fleming, Amelia W. Hall, Victoria A. Parsons, Kenneth C. Bedi Jr, Amer-Denis Akkad, Caroline N. Herndon, Alessandro Arduini, Irinna Papangeli, Carolina Roselli, François Aguet, Seung Hoan Choi, Kristin G. Ardlie, Mehrtash Babadi, Kenneth B. Margulies, Christian M. Stegmann and Patrick T. Ellinor. Circulation 142(5), 466-482 (2020). Collaboration with […]