Publications by authors named "Beth Cimini"

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Inflammatory Macrophages Associate With Tissue Injury and Fibrosis in a Mouse Model of Tuberculosis.
Julie Boucau, Jennie Ruelas Castillo, Threnesan Naidoo, Yuming Liu, Shatavisha Dasgupta, Beth A Cimini

J Infect Dis· December 2025

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CellPhePy: A python implementation of the CellPhe toolkit for automated cell phenotyping from microscopy time-lapse videos.
Laura Wiggins, Stuart Lacy, Graeme Park, Joanne Marrison, Ben Powell, Beth Cimini

J Microsc· November 2025

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Alternate dyes for image-based profiling assays.
Suganya Sivagurunathan, Patrick Byrne, Alán F Muñoz, John Arevalo, Anne E Carpenter, Beth A Cimini

SLAS Discov· October 2025

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Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics.
Sameed M Siddiqui, Nicole L Welch, Tien G Nguyen, Amaya Razmi, Tianyi Chang, Beth A Cimini

Nat Biomed Eng· September 2025

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GloBIAS: strengthening the foundations of BioImage Analysis.
Agustin A Corbat, Christa G Walther, Laura R de la Ballina, Nicholas D Condon, Alessandro A Felder, Beth A Cimini

ArXiv· August 2025

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Morphological map of under- and overexpression of genes in human cells.
Srinivas Niranj Chandrasekaran, Eric Alix, John Arevalo, Adriana Borowa, Patrick J Byrne, Beth A Cimini

Nat Methods· August 2025

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Live-cell painting: Image-based profiling in live cells using acridine orange.
Fernanda Garcia-Fossa, Thaís Moraes-Lacerda, Mariana Rodrigues-da-Silva, Barbara Diaz-Rohrer, Shantanu Singh, Beth A Cimini

Mol Biol Cell· July 2025

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Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion.
Matthew Tegtmeyer, Dhara Liyanage, Yu Han, Kathryn B Hebert, Ruifan Pei, Beth A Cimini

Nat Commun· July 2025

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Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling.
Alexandr A Kalinin, Paula Llanos, Theresa Maria Sommer, Giovanni Sestini, Xinhai Hou, Beth Cimini

ArXiv· July 2025

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Evaluating Integrative Strategies for Incorporating Phenotypic Features in Spatial Transcriptomics.
Levin M Moser, Ahmad Kamal Hamid, Esteban Miglietta, Nodar Gogoberidze, Beth A Cimini

ArXiv· July 2025

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Rare missense variants of the leukocyte common antigen related receptor (LAR) display reduced activity in transcellular adhesion and synapse formation.
Mathias Kaas, Nicolas Chofflet, Deniz Bicer, Sune Skeldal, Jinjie Duan, Beth A Cimini

Res Sq· June 2025

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Reproducible image-based profiling with Pycytominer.
Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I Brewer, Jenna Tomkinson, Beth A Cimini

Nat Methods· April 2025

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Enabling global image data sharing in the life sciences.
Peter Bajcsy, Sreenivas Bhattiprolu, Katy Börner, Beth A Cimini, Lucy Collinson

Nat Methods· April 2025

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A genome-wide atlas of human cell morphology.
Meraj Ramezani, Erin Weisbart, Julia Bauman, Avtar Singh, John Yong, Beth A Cimini

Nat Methods· March 2025

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Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.
Jeremiah M Riendeau, Amani A Gillette, Emmanuel Contreras Guzman, Mario Costa Cruz, Aleksander Kralovec, Beth A Cimini

Sci Rep· February 2025

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Rare missense variants of the leukocyte common antigen related receptor (LAR) display reduced activity in transcellular adhesion and synapse formation.
Mathias Kaas, Nicolas Chofflet, Deniz Bicer, Sune Skeldal, Jinjie Duan, Beth A Cimini

bioRxiv· February 2025

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Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes.
Jessica D Ewald, Katherine L Titterton, Alex Bäuerle, Alex Beatson, Daniil A Boiko, Beth A Cimini

bioRxiv· January 2025

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MorphoDiff: Cellular Morphology Painting with Diffusion Models.
Zeinab Navidi, Jun Ma, Esteban A Miglietta, Le Liu, Anne E Carpenter, Beth A Cimini

bioRxiv· December 2024

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Pervasive mislocalization of pathogenic coding variants underlying human disorders.
Jessica Lacoste, Marzieh Haghighi, Shahan Haider, Chloe Reno, Zhen-Yuan Lin, Beth A Cimini

Cell· November 2024

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Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion.
Matthew Tegtmeyer, Dhara Liyanage, Yu Han, Kathryn B Hebert, Ruifan Pei, Beth A Cimini

bioRxiv· November 2024

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Cell Painting Gallery: an open resource for image-based profiling.
Erin Weisbart, Ankur Kumar, John Arevalo, Anne E Carpenter, Beth A Cimini

Nat Methods· October 2024

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The crucial role of bioimage analysts in scientific research and publication.
Beth A Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez

J Cell Sci· October 2024

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A postdoctoral training program in bioimage analysis.
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft

Mol Biol Cell· September 2024

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Live Cell Painting: image-based profiling in live cells using Acridine Orange.
Fernanda Garcia-Fossa, Thaís Moraes-Lacerda, Mariana Rodrigues-da-Silva, Barbara Diaz-Rohrer, Shantanu Singh, Beth A Cimini

bioRxiv· August 2024

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Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.
Jeremiah M Riendeau, Amani A Gillette, Emmanuel Contreras Guzman, Mario Costa Cruz, Aleksander Kralovec, Beth A Cimini

bioRxiv· June 2024

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