Genetics

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

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Comparative Single-Cell Transcriptomics Uncovers Shared and Distinct Molecular Signatures in Cystic Fibrosis and Primary Ciliary Dyskinesia

Cystic Fibrosis (CF) and Primary Ciliary Dyskinesia (PCD) are both inherited respiratory disorders t...

TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

Therapeutic progress in glioma, one of the most lethal human cancers, has been limited by molecular ...

Zygosity-Aware DNA Language Modeling Improves Ancestry and Gene Expression Prediction

DNA language models (DNA-LMs) are transforming how genomic sequence information is represented and i...

Puget predicts gene expression across cell types using sequence and 3D chromatin organization data

Gene expression is governed by both linear DNA sequence and three-dimensional (3D) chromatin archite...

Multi-cohort, cross-species urinary proteomics reveals signatures of LRRK2 dysfunction in Parkinson’s disease

Pathogenic mutations in Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Pa...

Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape

Mechanistic understanding of how gene activity is regulated has focussed on the roles of transcripti...

Incorporating Large Language Model-Derived Information into Hypothesis Testing for Genomics

We propose strategies for incorporating the information in large language models (LLMs) into statist...

Billion-Scale Deciphering of Human Gene Regulatory Grammar

Predicting how DNA sequence specifies gene expression remains a core challenge across regulatory gen...

Unified modeling of cellular responses to diverse perturbation types

Predicting cellular responses to perturbations is essential for understanding gene regulation and ad...

TSProm: Deciphering the Genomic Context of Tissue Specificity

Characterizing tissue-specific (TSp) gene expression is crucial for understanding development and di...

GeneCAD: Plant Genome Annotation with a DNA Foundation Model

Accurate genome annotation remains a bottleneck in plants, where polyploidy and repeat-rich sequence...

Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data

Chromatin accessibility profiling is an important tool for understanding gene regulation and cellula...

Overcoming Extrapolation Challenges of Deep Learning by Incorporating Physics in Protein Sequence-Function Modeling

Understanding protein sequence-to-function relationship is crucial to assist studies of genetic dise...

Deep learning challenge to generate apo RNA conformations with cryptic binding site

RNA plays vital roles in diverse biological processes, thus drawing much attention as potential ther...

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Programmable control of gene expression in specific cell types is essential for both basic discovery...

Deviation Error: assessing predictions for replicate measurements in genomics and beyond

A quantitative measurement can have variation, referred to here as measurement variation, which is a...

Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Despite substantial progress in genomic foundation models, accurately predicting inter-individual va...

Molecular Evolution under Macro-Perturbation Barrier and the Fixation Process of Polyploidization

The Neutral Theory in molecular evolution mainly addresses the allele frequency change of individual...

Scoring gene importance by interpreting single-cell foundation models

Determining a gene’s functional significance within a cellular context has long been a challenge, as...

Predicting and Designing Red Fluorescent Protein Variants Using Sequence-to-Function Machine Learning Models

Fluorescent proteins (FPs) are widely used reporters for visualizing cellular structures and process...

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