bioRxiv

Showing 4471 to 4480 of 5021 articles

Application of Large Language Models for Annotating Genes into Reactome Pathways

bioRxiv Jan 1, 2025
Reactome is the most comprehensive, open source, open access biological pathway knowledgebase, widely used in the research community. To ensure the highest quality of its content, human pathway data in Reactome is manually curated. However, manual cu...
View on bioRxiv DOI

Deterministic dynamics of distributional multi-agent reinforcement learning

bioRxiv Jan 1, 2025
Understanding how cognition shapes behavior across contexts remains a fundamental challenge for many disciplines. In particular, for the optimism heuristic–i.e., the tendency to overweight positive (relative to negative) information–knowledge remains...
View on bioRxiv DOI

Rethinking Molecular Beauty in the Deep Learning Era

bioRxiv Jan 1, 2025
As (deep) generative chemistry rapidly enters the landscape of drug discovery, evaluating the models and their structural output relevance, tractability, and innovation potential becomes both a scientific and practical challenge. Existing metrics suc...
View on bioRxiv DOI

Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT

bioRxiv Jan 1, 2025
Metagenomes from complex environments such as soil contain vast biodiversity, yet most short reads cannot be taxonomically or functionally annotated because they lack reference genomes, obscuring the true structure and function of microbial communiti...
View on bioRxiv DOI

ROSIE-Enabled Spatial Mapping Reveals Architectural Fragmentation and Immune Reprogramming in Lung Adenocarcinoma Evolution

bioRxiv Jan 1, 2025
The progression of lung adenocarcinoma (LUAD) from precancerous lesions to invasive carcinoma entails extensive remodeling of tissue architecture and immune microenvironments, driven by mechanisms that remain incompletely understood. To investigate t...
View on bioRxiv DOI

De Novo Computational Design of VHH Nanobodies Against LGR5

bioRxiv Jan 1, 2025
VHH discovery traditionally relies on animal immunization or large-scale library screening, methods that are slow, costly, and often ineffective for challenging targets such as GPCRs. We present a fully de novo computational pipeline for epitope-dire...
View on bioRxiv DOI

Sequence-based models for RNA-Protein interactions imputation might be insufficient for novel signal prediction in eCLIP data

bioRxiv Jan 1, 2025
Predicting specific RNA-protein interactions remains a challenging task: despite the existence of numerous methods, a unified approach has yet to emerge. Additional difficulties emerge from the properties of in vivo IP experiments and their systemati...
View on bioRxiv DOI

A foundation model for microbial growth dynamics

bioRxiv Jan 1, 2025
Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific dat...
View on bioRxiv DOI

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

bioRxiv Jan 1, 2025
Imaging-based spatially resolved transcriptomics (imSRT) technologies provide high-throughput molecular-resolution spatial characterization of genes within cells. Conventional analysis methods to identify cell-types and states in imSRT data rely on g...
View on bioRxiv DOI

The human cerebellum encodes temporally sensitive reinforcement learning signals

bioRxiv Jan 1, 2025
In addition to supervised motor learning, the cerebellum also supports nonmotor forms of learning, including reinforcement learning (RL). Recent studies in animal models have identified core RL signals related to reward processing, reward prediction,...
View on bioRxiv DOI
Popular Topics
Popular Journals