Genetics

Molecular unbalances between striosome and matrix compartments characterize the pathogenesis of Huntington’s disease model mouse

The pathogenesis of Huntington’s disease is still incompletely understood, despite the remarkable advances in identifying the molecular effects of the Htt mutation in this disease. When we focus on movement disorders, clinical studies offer us some hints about this issue. Human studies employing positron emission tomography have identified a reduction in phosphodiesterase 10A (PDE10A) as the earli...

Accelerating protein engineering with fitness landscape modeling and reinforcement learning

Protein engineering holds significant promise for designing proteins with customized functions, yet the vast landscape of potential mutations versus limited lab capacity constrains the discovery of optimal sequences. To address this, we present the µProtein framework, which accelerates protein engineering by combining µFormer, a deep learning model for accurate mutational effect prediction, with µ...

ATOMIC: A graph attention neural network for ATOpic dermatitis prediction on human gut MICrobiome

Atopic dermatitis (AD) is a chronic inflammatory skin disease driven by complex interactions among genetic, environmental, and microbial factors; howe...

Deep Evolutionary Fitness Inference for Variant Nomination from Directed Evolution

Iterative screening techniques, such as directed evolution, enable high-throughput affinity maturation to optimize binders to molecular interfaces. Ho...

Deep Learning for genomic prediction accounting for heterosis in crossbreeding systems

Crossbreeding is used in animal breeding to combine desirable traits from different breeds and to exploit hybrid vigor, and many approaches have been ...

Matrix effects influence biochemical signatures and metabolite quantification in dried blood spots

Dried blood spots (DBS) represent a convenient clinical sample material, offering low infection risk, easy transport, and long-term metabolite stabili...

RNALens: Study on 5’ UTR Modeling and Cell-Specificity

Recently, the Transformer architecture has been applied to predict the structure, function, and regulatory activity of biological sequences. Predictin...

Integrating explainable AI with multiomics systems biology and EHR data mining for personalized drug repurposing in Alzheimer’s disease

Alzheimer’s disease (AD) is characterized by region- and patient-specific molecular heterogeneity, which hinders therapeutic design. In this study, we...

UNICORN: Towards Universal Cellular Expression Prediction with a Multi-Task Learning Framework

Sequence-to-function analysis is a challenging task in human genetics, especially in predicting cell-type-specific multi-omic phenotypes from biologic...

Clinical and molecular characterisation of primary refractoriness to atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma

Despite improved outcomes with atezolizumab plus bevacizumab (A+B) in hepatocellular carcinoma (HCC), primary refractoriness (PRef), characterised by ...

WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning

Influenza A virus (IAV) poses a significant threat to animal health globally, with its ability to overcome species barriers and cause pandemics. Rapid...

Advancing Ligand Binding Affinity Prediction with Cartesian Tensor-Based Deep Learning

We present PBCNet2.0, a cartesian tensor-based Siamese Neural Network for protein-ligand relative binding affinity prediction. Trained on 8.6 million ...

Harnessing DNA Foundation Models for Cross-Species Transcription Factor Binding Site Prediction in Plant Genomes

Accurate prediction of transcription factor binding sites (TFBSs) is crucial for understanding gene regulation. While experimental methods like ChIP-s...

DeepPGDB: A Novel Paradigm for AI-Guided Interactive Plant Genomic Database

DeepPGDB (https://www.deeppgdb.chat) is the first AI-driven plant genomics database designed to lower technical barriers in multi-omics research by en...

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Ex...

TU_MyCo-Vision: A Deep Learning Tool for Detection of Cell Morphologies in Fungal Microscopic Images

Morphological switching in response to environmental stimuli is a well-known phenomenon in fungi, leading to diverse morphotypes. Microscopic observat...

GP-ML-DC: An Ensemble Machine Learning-Based Genomic Prediction Approach with Automated Two-Phase Dimensionality Reduction via Divide-and-Conquer Techniques

Traditional machine learning (ML) and deep learning (DL) methods for genome prediction often face challenges due to the imbalance between the limited ...

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis

Bacteria use antagonistic interbacterial weapons such as polymorphic toxin secretion systems (TSS) to compete for niches in the human gut microbiome. ...

CpGeneAge: multi-omics aging clocks associated with Nf-κB signaling pathway in aging

Aging clocks have emerged as the primary tools for measuring biological aging and have been developed for a wide range of single-omic measurements. Ep...

Predicting DNA origami stability in physiological media by machine learning

DNA origami nanostructures offer substantial potential as programmable, biocompatible platforms for drug delivery and diagnostics. However, their stru...