Genetics

Mapping Risk and Conservation Potential Across the Indo-Pacific with Reefshark Genomescapes

Overfishing has severely depleted marine populations worldwide, including within protected areas. Illegal and unreported fishing are major contributors to this decline. Large-bodied apex predators such as sharks are among the most affected, with overfishing causing dramatic species declines and ecosystem destabilization due to trophic downgrading. Key barriers to effective marine conservation and ...

Machine Learning Enables Viral Genome-Agnostic Classification of RNA Virus Infections from Host Transcriptomes

Targeted PCR diagnosis of RNA viruses is sequence dependent, meaning that the accuracy of the assay depends on the identity of the viral sequence. However, sequence-targeted assays can miss novel or divergent viruses. We test whether the host transcriptome alone can classify RNA virus infections without using viral sequences. Using publicly available data on Huh7 and Calu-3 cells experimentally in...

Single-and double-strand circulating DNA fragmentomics for enhanced cancer detection performance

In early detection of cancer, the use of circulating cell-free DNA (cirDNA) obtained from blood samples is notable for its minimally invasive nature. ...

rpcFold: Residual Parallel Convolutional neural network to decipher RNA folding from RNA sequence

Precise secondary structure information offers deeper insights into the functionality of many RNA molecules. Earlier approaches, which primarily relie...

Disease-specific tau polymorphs define unique protein interaction networks across proteinopathies

Tau protein aggregates exhibit distinct conformations across tauopathies, but their disease-specific protein interactions remain poorly understood. He...

Revive-Flow: A Foundation Model for Blood DNAm Aging

Epigenetic clocks can predict biological age but cannot prescribe the interventions needed to reverse it. Here, we introduce REjuVenatIon Via Epigenet...

Edit Distance Embedding with Genomic Large Language Model

Edit distance is a fundamental metric in genomic sequence analysis, yet it is computationally expensive to calculate. A practical approach for large-s...

Sampling Protein Language Models for Functional Protein Design

Protein language models have emerged as powerful tools for learning rich protein representations, improving performance in tasks like structure predic...

Generation of a global freshwater algal taxonomic database by application of PCR-free rbcL gene detection and machine-learning-based taxonomic classification to public metagenome datasets

While it has become increasingly evident that microalgae are critical components of aquatic ecosystems, comprehensive taxonomic analysis of the microa...

Augmented prediction of multi-species protein–RNA interactions using evolutionary conservation of RNA-binding proteins

RNA-binding proteins (RBPs) play critical roles in gene expression regulation. Recent studies have begun to detail the RNA recognition mechanisms of d...

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model

In eukaryotes, most genes produce multiple transcript isoforms that diversify the transcriptome and proteome, serving as a key mechanism of functional...

STARNet enables spatially resolved inference of gene regulatory networks from spatial multi-omics data

Biological tissues are composed of distinct microenvironments that spatially orchestrate gene expression and cell identity. However, the regulatory pr...

AI methods and biologically informed data curation enable accurate RNA m5C prediction

5-methylcytosine (m5C) RNA modifications influence nearly every aspect of RNA metabolism, but their transcriptome wide detection is limited by costly,...

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

Base editors create precise nucleotide changes in DNA, but their off-target activity remains challenging to quantify. Here, we develop and deploy a di...

A Transformer based method for the Cap Analysis of Gene Expression and Gene Expression Tag associated 5’ cap site prediction in RNA

5’ RNA capping is one of the major post-transcriptional modifications for the mobility and stability of RNA molecules. Measuring 5’ caps of RNAs can h...

Recovery of human upper airway epithelium after smoking cessation is driven by a slow-cycling stem cell population and immune surveillance

The upper airway epithelium in humans is maintained in homeostasis by a resident population of basal stem cells. In the presence of tobacco smoke thes...

MicroNucML: A machine learning approach for micronuclei segmentation and the refinement of nuclei-micronuclei relationships

Micronuclei (MN) are structures containing small fragments of DNA, arising from mitotic errors or failed DNA repair attempts. Therefore, MN serve as m...

Discovery and performance of DNA methylation panels for cancer detection and classification in blood

Examining DNA in a liquid biopsy for non-invasive cancer detection relies on identifying dilute signal in a high background. This study aims to identi...

YeastSAM: A Deep Learning Model for Accurate Segmentation of Budding Yeast Cells

An essential step for quantitative image analysis is cell segmentation, which is the process of defining the outline of individual cells in microscopy...

SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction

Accurate RNA splicing is essential for gene expression and protein function, yet the mechanisms governing splice site recognition remain incompletely ...