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Recent selected publications

Elmalam N and Assaf Zaritsky§. Cell-context dependent in silico organelle localization in label-free microscopy images. bioRxiv. DOI: https://doi.org/10.1101/2024.11.10.622841

Hollander S, Guo Y, Haguy Wolfenson§, Assaf Zaritsky§. Spatiotemporal analysis of F-actin polymerization with micropillar arrays reveals synchronization between adhesion sites. Molecular Biology of the Cell (MBoC) 2024. DOI: https://doi.org/10.1091/mbc.E24-06-0276

Erlich I, Saravelos S, Hickman C, Ben-Meir A, Har-Vardi I, Grifo JA, Kahraman S, Zaritsky A. Decoupling implantation prediction and embryo ranking in machine learning: the impact of clinical data and discarded embryos. Advanced Intelligent Systems (2024). DOI: https://doi.org/10.1101/2021.10.07.21264503

Rotem O, Schwartz T, Maor R, Tauber Y, Tsarfati Shapiro M, Meseguer M, Gilboa D, Seidman D.S., Zaritsky A. Visual interpretability of image-based classification models by generative latent space disentanglement applied to in vitro fertilization. Nature Communications 2024. DOI: https://doi.org/10.1038/s41467-024-51136-9

Rotem O & Assaf Zaritsky. Visual interpretability of bioimaging deep learning models. Nature Methods 2024. DOI: https://doi.org/10.1038/s41592-024-02322-6

Alon Shpigler*, Naor Kolet*, Shahar Golan, Erin Weisbart, Assaf Zaritsky. Anomaly detection for high-content image-based phenotypic cell profiling. bioRxiv. DOI: https://doi.org/10.1101/2024.06.01.595856 

Yuval Tamir, Yuval Bussi, Claudia Owczarek, Luciana Luque, Giuseppe Torrisi, Leor Ariel Rose, Orit Kliper-Gross, Linus Schumacher, Maddy Parsons, Leeat Keren, Assaf Zaritsky. Data-modeling the interplay between single cell shape, single cell protein expression, and tissue state. bioRxiv. DOI: https://doi.org/10.1101/2024.05.29.595857

Elmalam Nitsan*, Ben Nedava Lion*, Zaritsky A. In silico labeling in cell biology: potential and limitations. Current Opinion in Cell Biology 2024. DOI: https://doi.org/10.1016/j.ceb.2024.102378.

Ben David S*, Ho K.Y.L.*, Tanentzapf G§, Zaritsky A§. Formation of recurring transient Ca2+-based intercellular communities during Drosophila hematopoiesis. Proceedings of the National Academy of Sciences 2024. DOI: https://doi.org/10.1073/pnas.2318155121

Shakarchy A*, Zarfati G*, Hazak A, Mealem R, Huk K, Avinoam O§, Zaritsky A§. Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion. Molecular Systems Biology 2024. DOI: https://doi.org/10.1038/s44320-024-00010-3

Nahum A, Koren Y, Ergaz B, Natan S, Miller G, Tamir Y, Goren S, Kolel A, Jagadeeshan S, Elkabets M, Lesman A,  Zaritsky A. Inference of long-range cell-cell force transmission from ECM remodeling fluctuations. Communications Biology 2023. DOI: https://doi.org/10.1038/s42003-023-05179-1

Tzukerman N*, Rotem O*, Tsarfati Shapiro M, Maor R, Meseguer M, Gilboa D, Seidman D.S., Zaritsky A. Using Unlabeled Information of Embryo Siblings from the Same Cohort Cycle to Enhance In Vitro Fertilization Implantation Prediction. Advanced Science 2023. DOI: https://doi.org/10.1002/advs.202207711

Zamir A, Li G, Chase K, Moskovitch R, Sun B§, Zaritsky A§. Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer. Cell Systems 2022. DOI: https://doi.org/10.1016/j.cels.2022.07.002

Andrews B§, Chang J-B§, Collinson L§, Li D§, Lundberg E§, Mahamid J§, Manley S§, Mhlanga M§, Nakano A§, Schöneberg J§, Van Valen D§, Wu TC§, Zaritsky A§. Imaging cell biology. Nature Cell Biology 2022. DOI: https://doi.org/10.1038/s41556-022-00960-6 (Viewpoint)

Zaritsky A.*§, Andrew R. Jamieson*, Erik S. Welf*, Andres Nevarez*, Justin Cillay, Ugur Eskiocak, Brandi L. Cantarel, Gaudenz Danuser§. Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma. Cell Systems 2021. DOI: https://doi.org/10.1016/j.cels.2021.05.003. The article was featured on the cover and the project was highlighted by The Scientist as "Image of the Day" in 2018 and 2019.

Driscoll MK§ and Zaritsky A§. Data science in cell imaging. Journal of Cell Science 2021. DOI: https://doi.org/10.1242/jcs.254292

Riegman M, Sagie L, Galed C, Levin T, Steinberg N, Dixon SJ, Wiesner U, Bradbury MS, Niethammer P, Zaritsky A§, Overholtzer M§. Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture. Nature Cell Biology 2020. DOI: https://doi.org/10.1038/s41556-020-0565-1 

Full publications list:

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 Assaf Zaritsky lab of computational cell dynamics, applying data science to microscopy cell images since 2018

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