Large-scale plasma proteomic profiling unveils diagnostic biomarkers and pathways for Alzheimer's disease

Information Science, Artificial Intelligence, Medicine, Medical Laboratory Science, Geriatrics, Neurology, Life Sciences, Cell Biology, Biochemistry, Genetics,
Alzheimer's disease   proteomics   biomarkers   plasma proteins   disease diagnosis   pathway analysis  

1. Research Background and Academic Significance Alzheimer’s Disease (AD) is the most common form of dementia worldwide, accounting for about 60–80% of all dementia cases. The primary affected population is individuals over 65 years old, with characteristic pathological features including the deposition of amyloid-β plaques, neurofibrillary tangles...

Generative Prediction of Causal Gene Sets Responsible for Complex Traits

Information Science, Artificial Intelligence, Life Sciences, Cell Biology, Biochemistry, Bioengineering, Genetics,
gene regulatory networks   complex traits   generative deep learning   variational autoencoder   causal gene sets   phenotypic variation   polygenic diseases  

Generative Deep Learning for Predicting Causal Gene Sets of Complex Traits: PNAS Landmark New Method Explained I. Academic Background and Research Motivation The Dilemma of Complex Traits The relationship between genotype and phenotype has long been one of the core issues in biology and genetics. This challenge is especially prominent in the study ...

Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Genetics, Botany,
plant genomics   deep learning   DNA language model   cross-species prediction   deleterious mutation   gene annotation   angiosperm  

A Milestone in Cross-Species Modeling of Plant Genomes: Creation and Breakthrough Application of the PlantCaduceus DNA Language Model I. Academic Background and Research Motivation In the past two decades, with the rapid development of high-throughput sequencing technology, over 1,000 plant genomes have been published, and this number is expected t...

Amortized Template Matching of Molecular Conformations from Cryoelectron Microscopy Images Using Simulation-Based Inference

Information Science, Artificial Intelligence, Medicine, Medical Imaging, Life Sciences, Cell Biology, Biochemistry, Biophysics,
cryo-EM   biophysics   Bayesian inference   molecular modeling   template matching   deep learning   structural biology  

Accelerating Single-Molecule Structure Identification with Simulation-Based Inference — Research Report on “Amortized Template Matching of Molecular Conformations from Cryoelectron Microscopy Images using Simulation-Based Inference” Research Background and Significance In the fields of molecular biology and structural biology, understanding how bio...

Bias-Aware Training and Evaluation of Link Prediction Algorithms in Network Biology

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Cell Biology, Biochemistry, Bioengineering, Genetics,
link prediction   network biology   bias   protein-protein interaction   graph machine learning   algorithm evaluation  

Revealing “Rich Node” Bias in Link Prediction Algorithms and Countermeasures — An Interpretation of “Bias-aware Training and Evaluation of Link Prediction Algorithms in Network Biology” 1. Academic Background and Motivation Over the past decade, network biology has played an increasingly important role in uncovering associations and functions of bi...

Persistent Pseudopod Splitting is an Effective Chemotaxis Strategy in Shallow Gradients

Information Science, Artificial Intelligence, Life Sciences, Cell Biology, Bioengineering, Immunology, Biophysics,
chemotaxis   pseudopods   reinforcement learning   mechanical intelligence   shallow gradients  

Academic Background Chemotaxis is a critical behavior in which cells or microorganisms move directionally along chemical gradients, playing vital roles in physiological processes such as immune responses, wound healing, and pathogen infections. However, how cells select optimal motility modes (e.g., pseudopod splitting or de novo formation) in comp...

Paving the Way for Social Touch at a Distance: Sonifying Tactile Interactions and Their Underlying Emotions

Information Science, Artificial Intelligence, Medicine, Clinical Psychology, Life Sciences, Bioengineering,
social touch   sonification   emotion recognition   remote interaction   augmented perception  

Academic Background Touch is one of the earliest developed human senses and is crucial for physical and mental well-being. However, with the increasing prevalence of virtual communication, the lack of tactile interaction in remote exchanges may lead to psychological issues such as anxiety and loneliness. Previous studies have shown that touch can e...

DeepRNA-Twist: Language-Model-Guided RNA Torsion Angle Prediction with Attention-Inception Network

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Biophysics,
RNA language model   torsion and pseudo-torsion angles   inception network   deep learning   RNA structure prediction   bioinformatics   long-range dependencies  

1. Academic Background and Research Motivation With the rapid development of life sciences and bioinformatics, research into RNA molecular structure and function has become a hot topic. RNA is not merely a carrier of genetic information, but also plays critical roles in regulation, catalysis, and various physiological processes. The three-dimension...

Chrombus-XMBD: A Graph Convolution Model Predicting 3D-Genome from Chromatin Features

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Cell Biology, Genetics, Biophysics,
3D-genome   graph convolution model   chromatin features   long-range interaction   model generalizability  

Research Background and Disciplinary Significance In eukaryotic cells, the three-dimensional (3D) spatial structure of chromatin plays a crucial role in gene expression regulation. Through complex folding, looping, and local spatial reconfiguration of DNA, different genetic elements (such as promoters and enhancers) are brought into spatial proximi...

Deep scSTAR: Leveraging Deep Learning for the Extraction and Enhancement of Phenotype-Associated Features from Single-Cell RNA Sequencing and Spatial Transcriptomics Data

Information Science, Artificial Intelligence, Medicine, Life Sciences, Cell Biology, Immunology,
Single-cell RNA sequencing   Spatial transcriptomics   Deep learning   Phenotype-associated features   Tumor microenvironment  

In recent years, cutting-edge technologies such as single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have greatly advanced the development of life sciences and clinical medicine. These technologies have revealed cellular heterogeneity and brought novel insights into major fields such as disease, development, and immunity. Howe...