Genetics

Deep learning analyses of splicing variants identify the link of PCP4 with amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease, with most sporadic cases lacking clear genetic causes. Abnormal pre-mRNA splicing is a fundamental mechanism in neurodegenerative diseases. For example, TAR DNA-binding protein 43 (TDP-43) loss of function causes widespread RNA mis-splicing events in ALS. Additionally, splicing mutations are major contributors to neurological di...

StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.

StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other molecules. StructMAn maps, aligns, and aggregates data from experimentally resolved and predicted 3D structures of proteins and their homologs for any...

HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and com...

AIoptamer: Artificial Intelligence-Driven Aptamer Optimization Pipeline for Targeted Therapeutics in Healthcare.

Aptamers are short, single-stranded DNA or RNA molecules known for their high specificity and affinity toward target biomolecules, making them powerfu...

CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.

We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the us...

Deep-Learning-Assisted Highly-Accurate COVID-19 Diagnosis on Lung Computed Tomography Images

COVID-19 is a severe and acute viral disease that can cause symptoms consistent with pneumonia in which inflammation is caused in the alveolous regi...

Leveraging infrared spectroscopy for cocoa content prediction: A dual approach with Kohonen neural network and multivariate modeling.

People of all ages enjoy chocolate, and its popularity is attributed to its pleasant taste and aroma, as well as its associated health benefits. Produ...

Beyond Olfaction: New Insights into Human Odorant Binding Proteins

Until today, the exact function of mammalian odorant binding proteins (OBPs) remains a topic of debate. Although their main established function lac...

Willchain: Decentralized, Privacy-Preserving, Self-Executing, Digital Wills

This work presents a novel decentralized protocol for digital estate planning that integrates advances distributed computing, and cryptography. The ...

MPX: Mixed Precision Training for JAX

Mixed-precision training has emerged as an indispensable tool for enhancing the efficiency of neural network training in recent years. Concurrently,...

LANTERN: A Machine Learning Framework for Lipid Nanoparticle Transfection Efficiency Prediction

The discovery of new ionizable lipids for efficient lipid nanoparticle (LNP)-mediated RNA delivery remains a critical bottleneck for RNA-based thera...

How Much Content Do LLMs Generate That Induces Cognitive Bias in Users?

Large language models (LLMs) are increasingly integrated into applications ranging from review summarization to medical diagnosis support, where the...

AI-Based Reconstruction from Inherited Personal Data: Analysis, Feasibility, and Prospects

This article explores the feasibility of creating an "electronic copy" of a deceased researcher by training artificial intelligence (AI) on the data...

Genetic Features for Drug Responses in Cancer -- Investigating an Ensemble-Feature-Selection Approach

Predicting drug responses using genetic and transcriptomic features is crucial for enhancing personalized medicine. In this study, we implemented an...

FreeMorph: Tuning-Free Generalized Image Morphing with Diffusion Model

We present FreeMorph, the first tuning-free method for image morphing that accommodates inputs with different semantics or layouts. Unlike existing ...

Efficient stochastic simulation of gene regulatory networks using hybrid models of transcriptional bursting

Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the t...

Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data.

Single-cell sequencing technology has profoundly revolutionized the field of cancer genomics, enabling researchers to explore gene expression profiles...

spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration.

Spatial multi-omics technologies provide valuable data on gene expression from various omics in the same tissue section while preserving spatial infor...

Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.

Accurate bacterial gene prediction is essential for understanding microbial functions and advancing biotechnology. Traditional methods based on sequen...

Illuminating the Noncoding Genome in Cancer Using Artificial Intelligence.

Understanding the vast noncoding cancer genome requires cutting-edge, high-resolution, and accessible strategies. Artificial intelligence is revolutio...