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BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk.
PLoS Comput Biol
January 2025
Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, United States of America.
While single-cell experiments provide deep cellular resolution within a single sample, some single-cell experiments are inherently more challenging than bulk experiments due to dissociation difficulties, cost, or limited tissue availability. This creates a situation where we have deep cellular profiles of one sample or condition, and bulk profiles across multiple samples and conditions. To bridge this gap, we propose BuDDI (BUlk Deconvolution with Domain Invariance).
View Article and Find Full Text PDFNormalized Protein-Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening.
J Chem Inf Model
January 2025
Department of Chemistry, New York University, New York, New York 10003, United States.
Molecular Docking is a critical task in structure-based virtual screening. Recent advancements have showcased the efficacy of diffusion-based generative models for blind docking tasks. However, these models do not inherently estimate protein-ligand binding strength thus cannot be directly applied to virtual screening tasks.
View Article and Find Full Text PDFVibron Softening of Solid Hydrogen under Nanoconfinement.
Nano Lett
January 2025
Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, P. R. China.
The vibron behavior of hydrogen bears significant importance for understanding the phases of solid hydrogen under high pressure. In this work, we reveal an unusual high-pressure behavior of hydrogen confined within nanopores through a combination of experimental measurements and theoretical calculations. The nanoconfined hydrogen molecules retain an hcp lattice up to 170 GPa, yet significant deviations from the vibrational characteristics of bulk hydrogen are observed in the primary vibrons of both Raman and infrared spectra.
View Article and Find Full Text PDFThe characterization of in regulation of flower size through tuning cell expansion genes.
Front Plant Sci
December 2024
Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang, China.
Flower appearance stands as a key characteristic of flowering plants and is closely linked to their ornamental value. Phytohormone Gibberellin (GA), essential for plant growth and development are widely reported for expansion in flower. DELLA proteins are known to negatively regulate GA signaling and influences plant growth and development through the regulation of cell expansion.
View Article and Find Full Text PDFComplex auditory regularity processing across levels of consciousness in coma: Stage 1 Registered Report.
Brain Commun
December 2024
Department of Clinical Neurosciences, Lausanne University Hospital (CHUV), University of Lausanne, 1011 Lausanne, Switzerland.
A key question for the scientific study of consciousness is whether it is possible to identify specific features in brain activity that are uniquely linked to conscious experience. This question has important implications for the development of markers to detect covert consciousness in unresponsive patients. In this regard, many studies have focused on investigating the neural response to complex auditory regularities.
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