9 papers · ranked by Valyu relevance
Maryam Majeed, Mara C.P. Rue, Aixin Zhang, Sabrina Cheng + 14 more
Parallel visual streams segregate information into pathways specialized for distinct computations, but how this segregation is achieved by anatomical segregation of primary visual cortex output remains unclear. This problem is complicated because individual neurons frequently send broadcasting projections to multiple…
Jiuzhou Lu, Erica Kholinne, Kangqi Yang, Yudong Yang + 4 more
Chronic Monteggia lesions are difficult to treat when longstanding radial head dislocation results in severe radial head deformity. In such cases, corrective ulnar osteotomy with or without annular ligament repair may not achieve stable or congruent radiocapitellar reduction. This technical note describes a combined…
Polina Bombina, Kevin R. Coombes
Comparative studies of trajectory inference (TI) methods evaluate complete computational pipelines, making it impossible to isolate how much distortion is introduced specifically by the dimensionality reduction (DR) step. To our knowledge, no study has directly and systematically evaluated how well DR methods alone…
Alexei Iakhiaev
Tissue Factor (TF) is a tightly regulated transmembrane protein that maintains its encrypted state on the cell surface with an unknown conformation. Generation of TF conformational ensembles by the co-folding method using alphafold3 and boltz2 software revealed two mechanisms of TF self-regulation and corresponding…
Kunyu Wang, Jon Paul Janet, Alessandro Tibo
Three-dimensional molecular generative models have emerged that produce de novo molecules both unconditionally and conditionally, e.g., within protein pockets. However, steering those models in a specific region of the chemical space that satisfies a set of desired properties remains challenging. In this study, we…
Alp Tartici, Mihajlo Stojkovic, Anru Tian, Michael C. Jewett + 2 more
Protein engineering has important implications in the bioeconomy, enabling applications in materials, medicine, and energy. A key challenge is designing protein sequences that have a specific form and function. Protein inverse folding seeks to address this challenge by identifying amino acid sequences compatible with a…
Joshua Justison, Gustavo A. Ballen, Carlos Acosta-Cortés, Roberto Ceja + 2 more
Phylogenetic networks extend the traditional tree model to capture reticulate evolutionary processes such as gene flow and hybridization. Among available inference tools, SNaQ is a widely used quartet-based method that offers a computationally efficient, statistically grounded approach to network estimation, but is…
Jackie Rao, Muntadher Jihad, Giulia Biffi, Paul D.W. Kirk
Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor…
Kapali Suri, Anshul Yadav, Abhishek Tripathi, N. Arul Murugan
Protein-ligand pose prediction is central to structure-based drug discovery, yet the relative performance of physics-based and AI-driven methods under realistic cross-docking conditions remains insufficiently characterized. Here, we compare physics-based docking methods (AutoDock4, AutoDock Vina, and DOCK 6) with…