bioRxiv

Showing 4141 to 4150 of 5016 articles

Circadian and Sleep-Wake Modulation of Functional Connectivity Across Brain Oscillations and States Linked to Cognition in Humans

bioRxiv Jan 1, 2025
Sleep and circadian rhythms both contribute to cognitive performance, but the underlying neuronal network-level changes remain unclear. We quantified the contribution of brain state, sleep-pressure dynamics across the sleep-wake cycle, and circadian ...
View on bioRxiv DOI

SLOGEN: A Structure-based Lead Optimization Model Unifying Fragment Generation and Screening

bioRxiv Jan 1, 2025
Lead optimization plays an important role in preclinical drug discovery. While deep learning has accelerated this process, structure-based approaches that leverage 3D protein-ligand information remain underexplored. Existing models could improve pred...
View on bioRxiv DOI

GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals

bioRxiv Jan 1, 2025
The accuracy of protein structure prediction models such as AlphaFold2 is tightly coupled to the depth and quality of multiple sequence alignments (MSAs), posing a persistent challenge for proteins with few or no identifiable homologs. We present Gho...
View on bioRxiv DOI

ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting

bioRxiv Jan 1, 2025
Despite the maturation of cryogenic electron microscopy (cryoEM) methodologies, generating high-resolution three-dimensional (3-D) reconstructions from micrographs is a time-intensive process involving iterative rounds of subjective data curation and...
View on bioRxiv DOI

DeepEmbCas9: Cas9 coevolution and sgRNA structural information for CRISPR-Cas9 cleavage activity prediction

bioRxiv Jan 1, 2025
The development of CRISPR-Cas9 cleavage activity prediction tools hinges on data produced from high-throughput guide-target lentiviral library screens for different Cas9 variants. However, the majority of such tools remain limited to predictions for ...
View on bioRxiv DOI

Modelling Predictive Coding in the Primary Visual Cortex (V1): Layer 4 Receptive Field Properties in a Balanced Recurrent Spiking Neuronal Network

bioRxiv Jan 1, 2025
Understanding how the cortex encodes sensory input in a biologically efficient and computationally robust manner remains a central question in neuroscience. Predictive coding offers a compelling theoretical framework for such cortical processing, but...
View on bioRxiv DOI

Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation

bioRxiv Jan 1, 2025
Defining the temporal gene regulatory programs that drive human organogenesis is essential for understanding the origins of congenital disease. We combined a time-resolved, single-cell multi-omic atlas of human iPSC-derived cardiac organoids with dee...
View on bioRxiv DOI

Accurately modelling RNase H-mediated antisense oligonucleotide efficacy

bioRxiv Jan 1, 2025
Antisense oligonucleotides (ASOs) are a powerful class of drugs with the potential to treat a wide range of human diseases. However, the prediction of ASO efficacy remains challenging, as large-scale and costly experimental screens are typically requ...
View on bioRxiv DOI

CellTok: Early-Fusion Multimodal Large Language Model for Single-Cell Transcriptomics via Tokenization

bioRxiv Jan 1, 2025
Single-cell transcriptomic data provide a high-resolution view of cellular states and functions, offering critical insights into development, disease, and tissue heterogeneity. Existing foundation models for single-cell analysis typically embed cells...
View on bioRxiv DOI

CHIMERA-DDR: A Machine Learning Framework for Classifying Heterogeneous Mismatch-Repair and Homologous-Recombination Deficiency Patterns in Prostate Cancer

bioRxiv Jan 1, 2025
Current DNA damage repair (DDR) biomarkers employ binary classifications that fail to capture the molecular complexity of tumors with concurrent repair deficiencies. We used genomics analysis to stratify 672 metastatic prostate cancer patients into 1...
View on bioRxiv DOI
Popular Topics
Popular Journals