Genetics

Decoding Prokaryotic Whole Genomes with a Product-Contextualized Large Language Model

Genomes encode the instructions for life, yet their full interpretation requires models capable of capturing long-range context and functional meaning at scale. Existing genome language models (gLMs) are limited by short context windows, high computational cost, and poor interpretability. We present GenSyntax, a product-contextualized large language model (LLM) trained on 49,250 annotated prokaryo...

Dysregulated Microglial Synaptic Engulfment in Diffuse Midline Glioma

Diffuse midline glioma (DMG) is a near-universally lethal form of pediatric high-grade glioma, driven by neuronal activity-regulated paracrine signaling and synaptic integration of malignant cells into neural circuits. In turn, DMG increases neuronal excitability, augmenting neuron-to-glioma signaling. In the healthy brain, microglia, the resident immune cells of the central nervous system (CNS), ...

A Computational Pipeline for Glioblastoma Vaccine Development: Integrating Novel Omics-Driven OIP5 Target Discovery to Create a Deep Learning-Based Immunogenicity Framework for Personalized Immunotherapy

This work introduces a modular, open-source computational pipeline for glioblastoma (GBM) vaccine design that integrates omics-based OIP5 target disco...

Acropora millepora’s microbiome is predicted by algal symbionts, host genetics, and environment

The coral microbiome is a critical component of coral health and resilience, yet it is unclear what factors drive coral microbiome composition, especi...

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain

Cereal grains are fundamental to global food security and bioenergy production, yet the genetic and molecular bases of grain metabolic diversity remai...

Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation

Plasmids are central to modern biotechnology, especially therapeutic development, yet their propagation in Escherichia coli remains difficult to predi...

OTRec: deep learning recommender for prospective druggable disease–target associations

OTRec is a deep learning recommender system that prospectively predicts druggable disease– target associations. Unlike methods that rely on manually a...

TRIO-AI: Hybrid temporal graph, ODE, and VAE modeling for high-resolution cellular trajectory inference in liver injury

Resolving dynamic cellular transitions at single-cell resolution is essential for understanding complex biological processes in development, disease, ...

LoMuS: Low-Rank Adaptation with Multimodal Representations Improves Protein Stability Prediction

Protein folding stability is a key determinant for understanding protein dynamics, including molecular function, pathogenicity, and/or protein enginee...

PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA

DNA language models are emerging as powerful tools for representing genomic sequences, with recent progress driven by self-supervised learning. Howeve...

Design principles of neuromorphic computing using genetic circuits

Cells have evolved to sense a wide range of input combinations and integrate those signals through signaling pathways to produce context-specific resp...

Evaluation of a structure-based method for ab initio gene detection using deep learning

In this work, a novel method for the detection of exons within genomic DNA sequences was implemented and evaluated. This is a structure-based approach...

Enigma: An Efficient Model for Deciphering Regulatory Genomics

Genomic sequence-to-function models have emerged as powerful tools for deciphering cis-regulatory grammar to advance our understanding of disease biol...

AlphaRING-X: accurate interpretation of missense variant deleteriousness based on protein structural stability

Accurate interpretation of missense variants remains a significant challenge hindering genomic diagnosis. While state-of-the-art machine learning and ...

Identification of SASP-associated biomarkers and regulatory mechanisms in diabetic foot ulcers based on transcriptomics and experimental validation

Diabetic foot ulcers (DFU) constitute a major complication arising from diabetes mellitus. Emerging research findings have underscored the pivotal con...

Social isolation upregulates takeout expression in female Drosophila melanogaster to promote sucrose feeding

Drosophila melanogaster provides a model system to examine how environmental stress interacts with sex to induce changes in brain function and behavio...

Comparative Analysis of Feature Selection Methods for Single-Cell RNA Sequencing Data

Feature selection is a critical preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis, directly impacting downstream clustering and bi...

Sequence-based models for RNA-Protein interactions imputation might be insufficient for novel signal prediction in eCLIP data

Predicting specific RNA-protein interactions remains a challenging task: despite the existence of numerous methods, a unified approach has yet to emer...

Islands of Signal and Transcriptomic Sequencing: A Foundation Model for Mutation and Lineage Prediction based on DNA Methylation and RNA-seq

DNA methylation and RNA-seq provide complementary views of oncogenic state, but their high dimensionality complicates robust modeling. We develop a pa...

Genetic Influences on Neural Responses in Placebo Analgesia Circuitry

Placebo analgesia is a well-established medical phenomenon with overlapping neural representations between humans and rodents, but the genetic contrib...