Genetics

Latest AI and machine learning research in genetics for healthcare professionals.

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Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

Macromolecular complexes in the genetically minimized bacterium, JCVI-syn3A, support gene expression...

Qimai: a multi-agent framework for zero-shot DNA-protein interaction prediction

Accurate prediction of DNA-protein interactions, a fundamental task in genomics, is limited by the p...

A validated set of neural gene reporter mice and chemical tracers tools for mapping knee innervating neurons

Joint pain is an increasing concern for our aging population, as current therapies to slow joint dis...

Structural constraints acting on the SARS-CoV-2 spike protein reveal limited space for viral adaptation

The SARS-CoV-2 pandemic resulted in an unprecedented scientific response. The enormous scale of glob...

PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings

High-fidelity scoring of RNA 3D structures remains a major challenge in RNA structure prediction and...

TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

High-throughput chromosome conformation capture sequencing (Hi-C) is a key technology for studying t...

Single-cell RNA sequencing and large-scale bulk combination with machine learning reveal gastric cancer-related macrophage heterogeneity

The tumor microenvironment (TME) significantly impacts cancer progression and overall patient surviv...

Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence

Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genet...

Deep Learning Bridges Histology and Transcriptomics to Predict Molecular Subtypes and Outcomes in Muscle-Invasive Bladder Cancer

Muscle-Invasive Bladder Cancer (MIBC) is a heterogeneous disease with distinct molecular subtypes in...

Simulation and empirical evaluation of biologically-informed neural network performance

Biologically-informed neural networks (BiNNs) offer interpretable deep learning models for biologica...

Control of gene output by intron RNA structure

Intron removal through pre-mRNA splicing is a central step in gene expression across Eukarya. The pr...

Multi-Dimensional Spatiotemporal Attention Neural Network for Next Generation Sequencing Basecalling

Next-generation sequencing (NGS) remains the most used sequencing technique in the field of genomics...

From Circles to Signals: Representation Learning on Ultra-Long Extrachromosomal Circular DNA

Extrachromosomal circular DNA (eccDNA) is a covalently closed circular DNA molecule that plays an im...

A deep learning framework for building INDEL mutation rate maps

Germline short insertions and deletions (INDELs) are pervasive genetic variants that shape genome ev...

Morphology-Guided Deep Learning for Nanoparticle Agglomeration Diagnostic Assays

Affordable, accurate, and rapid point-of-care diagnostic tests remain elusive due to inherent trade-...

USP-ddG: A Unified Structural Paradigm with Data Efficacy and Mixture-of-Experts for Predicting Mutational Effects on Protein-Protein Interactions

Accurately estimating changes in binding free energy (ΔΔG) is essential for understanding protein-pr...

An Enhanced Variant-Aware Deep Learning Model for Individual Gene Expression Prediction

Accurate prediction of gene expression from individual whole-genome sequences is critical for unders...

A machine learning framework for supervised treatment response prediction from tumor transcriptomics: A large-scale pan-cancer study

Precision oncology aims to guide treatment decisions using biomarkers. While DNA-based panels are in...

Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

Female genital tumors (FGTs), including ovarian, endometrial, and cervical cancers, pose a major glo...

Covary: A translation-aware framework for alignment-free phylogenetics using machine learning

In large-scale phylogenetic analysis, incorporating translation awareness is critical to account for...

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