Papers

Malvika Tejura, Yile Chen, Abbye E. McEwen, Ross Stewart, Yuriy Sverchkov, Florent Laval, Ivan Woo, Daniel Zeiberg, Runxi Shen, Shawn Fayer, Jeremy Stone, Nahum Smith, Silvia Casadei, Ziyu R. Wang, Matthew W. Snyder, Benjamin J. Capodanno, Pankhuri Gupta, Mariam Benazouz, Shantanu Jain, Sarah Heidl, Lara Muffley, Shengcheng Dong, Benjamin C. Hitz, Idan Gabdank, Khine Lin, Estelle Y. Da, Sabrina Best, Sally Grindstaff, David Reinhart, Leslie Rodriguez-Salas, Obsa Seid, Allyssa J. Vandi, Cameron Wenman, Melinda K. Wheelock, Sriram Pendyala, Dan Holmes, Alicia Xu, Airi Hosokai, Maxime Tixhon, Chloe Reno, Jessica D. Ewald, Kerstin Spirohn-Fitzgerald, Tanisha Teelucksingh, Tong Hao, Zitong S. Chen, Marzieh Haghighi, Ahmad Kamal Hamid, Esteban A. Miglietta, Erin Weisbart, Georges Coppin, Luke Lambourne, Marinella Gebbia, Atina G. Coté, Warren van Loggerenberg, Kirby M. Fawcett, Robert D. Steiner, Jill M. Johnsen, Andrew B. Stergachis, Lilia M. Iakoucheva, Shantanu Singh, Beth A. Cimini, Frederick P. Roth, Richard G. James, Marc Vidal, Mikko Taipale, Anne E. Carpenter, Michael A. Calderwood, Mark Craven, Vikas Pejaver, Alan F. Rubin, Predrag Radivojac, Douglas M. Fowler, Lea M. Starita

A scalable approach to resolving variants of uncertain significance

bioRxiv (2026).

Meraj Ramezani, Erin Weisbart, Julia Bauman, Avtar Singh, John Yong, Maria Lozada, Gregory P. Way, Sanam L. Kavari, Celeste Diaz, Eddy Leardini, Gunjan Jetley, Jenlu Pagnotta, Marzieh Haghighi, Thiago M. Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A. Cimini, Paul C. Blainey, Anne E. Carpenter, Calvin H. Jan, James T. Neal

A genome-wide atlas of human cell morphology

Nature Methods, 22, 621-633 (2025).

Alexandr A. Kalinin, John Arevalo, Erik Serrano, Loan Vulliard, Hillary Tsang, Michael Bornholdt, Alán F. Muñoz, Suganya Sivagurunathan, Bartek Rajwa, Anne E. Carpenter, Gregory P. Way, Shantanu Singh

A versatile information retrieval framework for evaluating profile strength and similarity

Nature Communications, 16, 5181 (2025).

Matthew Tegtmeyer, Dhara Liyanage, Yu Han, Kathryn B. Hebert, Ruifan Pei, Gregory P. Way, Pearl V. Ryder, Derek Hawes, Callum Tromans-Coia, Beth A. Cimini, Anne E. Carpenter, Shantanu Singh, Ralda Nehme

Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion

Nature Communications, 16, 6332 (2025).

Srinivas Niranj Chandrasekaran, Eric Alix, John Arevalo, Adriana Borowa, Patrick J. Byrne, William G. Charles, Zitong S. Chen, Beth A. Cimini, Boxiong Deng, John G. Doench, Jessica D. Ewald, Briana Fritchman, Colin J. Fuller, Jedidiah Gaetz, Amy Goodale, Marzieh Haghighi, Yu Han, Zahra Hanifehlou, Holger Hennig, Desiree Hernandez, Christina B. Jacob, Tim James, Tomasz Jetka, Alexandr A. Kalinin, Ben Komalo, Maria Kost-Alimova, Tomasz Krawiec, Brittany A. Marion, Glynn Martin, Nicola Jane McCarthy, Lisa Miller, Arne Monsees, Nikita Moshkov, Alán F. Muñoz, Arnaud Ogier, Magdalena Otrocka, Krzysztof Rataj, David E. Root, Francesco Rubbo, Simon Scrace, Douglas W. Selinger, Rebecca A. Senft, Peter Sommer, Amandine Thibaudeau, Sarah Trisorus, Rahul Valiya Veettil, William J. Van Trump, Sui Wang, Michał Warchoł, Erin Weisbart, Amélie Weiss, Michael Wiest, Agata Zaremba, Andrei Zinovyev, Shantanu Singh, Anne E. Carpenter

Morphological map of under- and overexpression of genes in human cells

Nature Methods, 22, 1742-1752 (2025).

Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen J. Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way

Reproducible image-based profiling with Pycytominer

Nature Methods, 22, 677-680 (2025).

Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter

Cell Painting: a decade of discovery and innovation in cellular imaging

Nature Methods, 22, 254-268 (2024).

Jessica Lacoste, Marzieh Haghighi, Shahan Haider, Chloe Reno, Zhen-Yuan Lin, Dmitri Segal, Wesley Wei Qian, Xueting Xiong, Tanisha Teelucksingh, Esteban Miglietta, Hamdah Shafqat-Abbasi, Pearl V. Ryder, Rebecca Senft, Beth A. Cimini, Ryan R. Murray, Chantal Nyirakanani, Tong Hao, Gregory G. McClain, Frederick P. Roth, Michael A. Calderwood, David E. Hill, Marc Vidal, S. Stephen Yi, Nidhi Sahni, Jian Peng, Anne-Claude Gingras, Shantanu Singh, Anne E. Carpenter, Mikko Taipale

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Cell, 187, 6725-6741.e13 (2024).