Previous publications
Spatial multiomics of acute myocardial infarction reveals immune cell infiltration through the endocardium
Florian Wünnemann, Florian Sicklinger, Kresimir Bestak, Jose Nimo, Tobias Thiemann, Junedh M Amrute, Mathias Nordbeck, Niklas Hartmann, Miguel A Ibarra-Arellano, Jovan Tanevski, Margot Chazotte, Clara Heine, Norbert Frey, Kory J Lavine, Fabian Coscia, Julio Saez-Rodriguez, Florian Leuschner, Denis Schapiro
Nat Cardiovasc Res. 2025 Oct;4(10):1345-1362. doi: 10.1038/s44161-025-00717-y. Epub 2025 Oct 3.
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L Muhlich, Joshua Hess, Allison L Creason, Ajit J Nirmal, Gregory J Baker, Maulik K Nariya, Jia-Ren Lin, Zoltan Maliga, Connor A Jacobson, Matthew W Hodgman, Juha Ruokonen, Samouil L Farhi, Domenic Abbondanza, Eliot T McKinley, Daniel Persson, Courtney Betts, Shamilene Sivagnanam, Aviv Regev, Jeremy Goecks, Robert J Coffey, Lisa M Coussens, Sandro Santagata, Peter K Sorger
Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25.
histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
Denis Schapiro, Hartland W Jackson, Swetha Raghuraman, Jana R Fischer, Vito R T Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller
Nat Methods. 2017 Sep;14(9):873-876. doi: 10.1038/nmeth.4391. Epub 2017 Aug 7.
Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases
Somnath Tagore, Lindsay Caprio, Amit Dipak Amin, Kresimir Bestak, Karan Luthria, Edridge D'Souza, Irving Barrera, Johannes C Melms, Sharon Wu, Sinan Abuzaid, Yiping Wang, Viktoria Jakubikova, Peter Koch, D Zack Brodtman, Banpreet Bawa, Sachin K Deshmukh, Leon Ebel, Miguel A Ibarra-Arellano, Abhinav Jaiswal, Carino Gurjao, Jana Biermann, Neha Shaikh, Priyanka Ramaradj, Yohanna Georgis, Galina G Lagos, Matthew I Ehrlich , Patricia Ho, Zachary H Walsh, Meri Rogava , Michelle Garlin Politis, Devanik Biswas, Azzurra Cottarelli, Nikhil Rizvi, Catherine A Shu, Benjamin Herzberg, Niroshana Anandasabapathy, George Sledge, Emmanuel Zorn, Peter Canoll, Jeffrey N Bruce, Naiyer A Rizv, Alison M Taylor, Anjali Saqi, Hanina Hibshoosh, Gary K Schwartz, Brian S Henick, Fei Chen, Denis Schapiro, Parin Shah, Benjamin Izar
Nat Med. 2025 Apr;31(4):1351-1363. doi: 10.1038/s41591-025-03530-z. Epub 2025 Feb 27.
In silico tissue generation and power analysis for spatial omics
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu , Sanja Vickovic, Aviv Regev
Nat Methods. 2023 Mar;20(3):424-431. doi: 10.1038/s41592-023-01766-6. Epub 2023 Mar 2.
micronuclAI enables automated quantification of micronuclei for assessment of chromosomal instability
Miguel A Ibarra-Arellano, Lindsay A Caprio, Aroj Hada, Niklas Stotzem, Luke L Cai, Shivem B Shah, Zachary H Walsh, Johannes C Melms, Florian Wünneman, Kresimir Bestak, Ibrahim Mansaray, Benjamin Izar, Denis Schapiro
Commun Biol. 2025 Mar 4;8(1):361. doi: 10.1038/s42003-025-07796-4.
MITI minimum information guidelines for highly multiplexed tissue images
Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A Burlingame; Human Tumor Atlas Network; Young H Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L Drewes, Dana Pe'er, David A Gutman, Markus D Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T Roland, John M Herndon, Michael P Snyder, Michael Angelo, Garry Nolan, Jason R Swedlow, Nikolaus Schultz, Daniel T Merrick, Sarah A Mazzili, Ethan Cerami, Scott J Rodig, Sandro Santagata, Peter K Sorger
Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4.
