9 papers · ranked by Valyu relevance
Yiming Xue, Xiaojian Liu, Weimin Zhu, Shengfan Wang + 2 more
While protein-RNA interactions are fundamental to post-transcriptional processes, achieving a holistic understanding of their regulatory logic remains challenging. Current computational models often treat binding affinity, interface mapping, and RNA design as isolated tasks, thereby failing to provide a unified…
Ilaria Cassotti, Vito Fiume, Paolo Gandellini, Clelia Tiziana Storlazzi
Small cell lung cancer is one of the most aggressive malignancies, characterized by rapid tumor growth, early metastatic spread and extremely poor survival. Although most patients initially respond to platinum-based chemotherapy, relapse is almost inevitable and treatment options at recurrence remain limited. The…
Shangru Jia, Artem Lysenko, Keith A Boroevich, Alok Sharma + 1 more
Prognostic stratification in multiple myeloma (MM) relies on staging systems fixed at diagnosis, discarding temporal information accumulated during treatment. We developed a dynamic multimodal framework that predicts residual overall survival from observation windows of 1-18 months post-diagnosis. The model integrates…
Yoshita Sriramkumar, Rhea Wali, Kasturi Mitra
The quiescent adult stem cells are activated to maintain tissue integrity. Mitochondria have emerged as critical regulators of stem/progenitor cells. Scattered literature suggests existence of a high-potency stemness state with characteristic mitochondrial structure-function properties that may ‘prime’ stem cell…
Raphael Mostov, Greyson Lewis, Gabriel Sturm, Wallace F. Marshall
This paper addresses the increasing need for comprehensive mathematical descriptions of cell organization by examining the algebraic structure of mitochondrial network dynamics. Mitochondria are cellular structures involved in metabolism that take the form of a network of membrane-based tubes that undergo continuous…
Dianzhuo Wang, Qian Xu, Arjun Banerjee, Rishi Jain + 7 more
Inferring biological function from experimental data is central to understanding emerging pathogens and developing effective countermeasures, yet interpreting these data remains slow and expert-intensive. AI agents could help accelerate this process by reasoning across sequence, structural, and biophysical evidence. We…
Alexander Adrian-Hamazaki, Paul Pavlidis
It is widely accepted in genomics that coexpression of RNA transcripts suggests a commonality of function. This intuition is explicitly leveraged in machine learning methods that predict gene function, where it is often combined with other features such as protein interactions and sequence similarity. For example…
William JF Rieger, Sebastian Häussermann, Luca Herrmann, Zecheng Li + 8 more
Enzymes frequently exhibit promiscuous activity beyond their native roles, providing starting-points for new functions. Finding these promiscuous enzymes, especially for non-native chemical transformations, is challenging but highly valuable, as they promise novel, sustainable solutions for chemistry and biotechnology.…
Tyler Kennedy, Damilola Oje, Kylie Howerter, Susan Reese + 9 more
The species-specific anatomy of nervous systems suggests that circuit architecture is largely encoded by genetic blueprints. In C. elegans, PVD nociceptive neurons synapse with PVC and AVA interneurons to drive escape responses to noxious stimuli. We used fluorescent markers for PVD synapses with PVC and AVA in a…