Genetics

RESCUE: An end-to-end multi-agent LLM system for proactive rare-disease patient screening in the EHR

Background: Rare diseases affect a significant portion of the global population, yet patients often endure a lengthy diagnostic odyssey, frequently missing the opportunity for timely whole-exome or whole-genome sequencing (WES/WGS). Existing informatics tools often rely on pre-identified patients or rigid, institution-specific rule sets, failing to address the broader operational question of clini...

Machine-Learning Model Identifies New Diagnostic Criteria for Beckwith-Wiedemann Spectrum

Objective Beckwith-Wiedemann spectrum (BWSp) is an overgrowth and cancer predisposition disorder caused by genetic and epigenetic alterations of chromosome 11p15. The 2018 international consensus produced a clinical scoring system to capture the phenotypic variability of BWSp and guide genetic testing and clinical management, including tumor screening, in patients without molecular confirmation. I...

Integrating Genetic, Environmental, Cognitive, and Temperament Data for ADHD Prediction in Explainable Deep Learning Models

Objective: Attention-deficit/hyperactivity disorder (ADHD) is clinically and etiologically heterogeneous, and diagnostic decisions may benefit from in...

DDTRN: Predicting Bacterial Transcriptional Regulatory Networks Based on Gene Sequences using Dual Descriptor

Accurate computational reconstruction of bacterial transcriptional regulatory network (TRN) from sequence information alone remains a fundamental chal...

Revisiting the base pair maximization approach for RNA secondary structure prediction with SQUARNA

Non-coding RNAs play diverse roles in a wide range of cellular processes, with their spatial structure being pivotal to their function. RNA secondary ...

Tabular Foundation Models Are Competitive Cellular Perturbation Predictors Across Biological Scales

Predicting how cells respond to genetic and chemical perturbations is a central challenge in drug discovery and functional genomics. A growing ecosyst...

In Vitro Detection of Breast Cancer Cell Types Using Machine Learning-Assisted Spectral Fingerprinting of SWCNTs

The early detection of breast cancer currently relies on expensive mammography, followed by pathology that uses biopsied, fixed, and immunohistochemic...

Evolutionary Stratification of Codon Usage Bias In Plants Arises from GC3 Composition and Translational Optimization

Codon usage bias is a fundamental genomic characteristic that prefers non-random preferential use of synonymous codons. It is a major determinant of t...

Decoding the regulatory genetic architecture of endometriosis using AlphaGenome

Background Endometriosis is a complex, estrogen-dependent disease with a strong genetic component. Although genome-wide association studies (GWAS) hav...

Epigenetic signatures of infection within and across generations in the endangered Loggerhead sea turtle

Infection can substantially reduce host fitness and influence population dynamics, yet it is often difficult to detect and quantify in wild animal pop...

GeneBench-Pro: Evaluating Multistage Statistical Reasoning\\in Genomics, Quantitative Biology, and Translational Biomedicine

We introduce GeneBench-Pro, an expanded and improved version of GeneBench that comprises harder problems across a wider breadth of domains. GeneBench-...

Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images

Artificial intelligence is transforming our capability to solve biological challenges. In dimensionality bottleneck regimes exacerbated by high-dimens...

SpheRoPE: Zero-Shot Optimization-Free 360 Panorama Generation with Spherical RoPE

We present a zero-shot, training-free and optimization-free framework for generating 360 panoramic images and videos by directly injecting spherical p...

APRIL-MedSeg: A Modular Medical Image Segmentation Toolbox Embracing Modern Paradigms

We present APRIL-MedSeg, a YAML-driven modular framework for 2D medical image segmentation. It provides a unified and extensible ecosystem that decomp...

Homology-aware cross-validation strategies for generalization assessment in RNA structure prediction

RNA secondary structure prediction is a fundamental challenge in bioinformatics, essential for understanding the functional roles of non-coding RNAs. ...

A Robust Machine Learning Framework for Keloid Biomarker Discovery Beyond Differential Expression

Keloids are fibroproliferative skin disorders arising following dermal injury that extend beyond the original wound margins. Their pathogenesis remain...

Causally measuring aging and rejuvenation through transcriptomic damage

Aging is caused, fully in large part, by the progressive accumulation of damage, yet quantifying age-related damage across tissues and conditions rema...

Retention, not flux: endpoint confounding caps computational prediction of peptide skin penetration, with a delivery-aware reframing

Bioactive peptides are now central to cosmetic and dermatological actives, yet predicting whether a given sequence will reach its site of action in sk...

Learning Fragmentation Physics or Exploiting Sequence Priors? Benchmarking Bias in Deep Learning Models for De Novo Peptide Sequencing

Deep learning models have advanced de novo peptide sequencing, but their predictions may reflect both physics-based spectral evidence and learned pept...

Gene-level complexity explains genome-wide variation in the distribution of fitness effects

The distribution of fitness effects (DFE), describing how harmful, neutral, or beneficial new mutations are, is central to understanding how populatio...