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Caspase 3 and Caspase 7 Promote Cytoprotective Autophagy and the DNA Damage Response during Non-Lethal Stress Conditions in Human Breast Cancer Cells. Samarasekera, G.; Go, N. E.; Choutka, C.; Xu, J.; Takemon, Y.; Chan, J.; Chan, M.; Perera, S.; Aparicio, S.; Morin, G. B.; Marra, M. A.; Chittaranjan, S.; Gorski, S. M. PLoS biology 2025, 23 (2), e3003034.

Geospatially Informed Representation of Spatial Genomics Data with SpatialFeatureExperiment. Moses, L.; Huseynov, A.; Rich, J. M.; Pachter, L. bioRxiv 2025.

Hepatic Stellate Cells Control Liver Zonation, Size and Functions via R-spondin 3. Sugimoto, A.; Saito, Y.; Wang, G.; Sun, Q.; Yin, C.; Lee, K. H.; Geng, Y.; Rajbhandari, P.; Hernandez, C.; Steffani, M.; Qie, J.; Savage, T.; Goyal, D. M.; Ray, K. C.; Neelakantan, T. V.; Yin, D.; Melms, J.; Lehrich, B. M.; Yasaka, T. M.; Liu, S.; Oertel, M.; Lan, T.; Guillot, A.; Peiseler, M.; Filliol, A.; Kanzaki, H.; Fujiwara, N.; Ravi, S.; Izar, B.; Brosch, M.; Hampe, J.; Remotti, H.; Argemi, J.; Sun, Z.; Kendall, T. J.; Hoshida, Y.; Tacke, F.; Fallowfield, J. A.; Blockley-Powell, S. K.; Haeusler, R. A.; Steinman, J. B.; Pajvani, U. B.; Monga, S. P.; Bataller, R.; Masoodi, M.; Arpaia, N.; Lee, Y. A.; Stockwell, B. R.; Augustin, H. G.; Schwabe, R. F. Nature 2025.

Hierarchical Refinement: Optimal Transport to Infinity and Beyond. Halmos, P.; Gold, J.; Liu, X.; Raphael, B. J. arXiv 2025.

Inferring Active Mutational Processes in Cancer using Single-Cell Sequencing and Evolutionary Constraints. Satas, G.; Myers, M. A.; McPherson, A.; Shah, S. P. bioRxiv 2025.

Joint Imputation and Deconvolution of Gene Expression across Spatial Transcriptomics Platforms. Zheng, H.; Sarkar, H.; Raphael, B. J. bioRxiv 2025.

Resolving Discrepancies between Chimeric and Multiplicative Measures of Higher-Order Epistasis. Chitra, U.; Arnold, B.; Raphael, B. J. Nature Communications 2025, 16 (1), 1711.

The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. Schmidt, H.; Raphael, B. J. bioRxiv 2025.

Transcriptomic Plasticity is a Hallmark of Metastatic Pancreatic Cancer. Jimenez-Sanchez, A.; Persad, S.; Hayashi, A.; Umeda, S.; Sharma, R.; Xie, Y.; Mehta, A.; Park, W.; Masilionis, I.; Chu, T.; Zhu, F.; Hong, J.; Chaligne, R.; O'Reilly, E. M.; Mazutis, L.; Nawy, T.; Pe'er, I.; Iacobuzio-Donahue, C. A.; Pe'er, D. bioRxiv 2025.