4 papers
Il Memming Park, Jonathan W. Pillow
Letting sensory codes optimize any posterior-based loss makes information maximization (infomax) one special case; blowfly large monopolar cell responses match p = 1/2 Lp reconstruction-error codes better than infomax.
bioRxiv · Sep 21, 2026 · PreprintNeuroscience✦ In-depth digest
Abhinav Adduri, Dhruv Gautam, Beatrice Bevilacqua, Mohsen Naghipourfar, Alishba Imran, Rohan Shah, Noam Teyssier, Rishi Verma, Christopher Carpenter, Basak Eraslan, Francis Chalissery, Rajesh Ilango, Vishvak Subramanyam, Chiara Ricci-Tam, Sanjay Nagaraj, , Yusuf Roohani
State, a set-based transformer trained on over 100 million perturbed cells, predicts perturbation responses in new cellular contexts better than mean, linear and deep learning baselines.
Cell · Aug 31, 2026Peer-reviewedSystems Biology✦ In-depth digest
Jason Earl Chan, Chun‐Hao Pan, Jonathan Rub, Gary Guzman, Klavdija Bastl, Emma Brown, Zeda Zhang, Hannah C. Styers, Griffin G. Hartmann, Zhuxuan Li, Xueqian Zhuang, Scott W. Lowe, Doron Betel, Yan Yan, Tuomas Tammela
In vivo lineage tracing and targeted ablation in autochthonous mouse lung adenocarcinoma establish the Slc4a11+ high-plasticity cell state as a bidirectional transition hub driving tumor progression and therapy resistance.
Nature · Jan 21, 2026Peer-reviewedCancer Biology✦ In-depth digest
Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing, Aimée Bastidas-Ponce, Perla Cota, Marta Tarquis-Medina, Shrey Parikh, Ilan Gold, , Fabian Joachim Theis
moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.
Nature · Jan 22, 2025Peer-reviewedBioinformatics✦ In-depth digest