Genetics

intDesc-AbMut: Describing and understanding how antibody mutations impact their environmental interactions1

Previously, we proposed a double-point mutation (DPM) strategy involving the simultaneous substitution of two amino acids to optimize antibodies. By selecting mutants based on the criterion that favorable interactions between mutated residues and their local environments are preserved or enhanced, improvements in antibody affinity were achieved. Nonetheless, manual extraction of these interactions...

MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery

Rare disease variant interpretation requires navigating multiple genomic databases with strict input formats and synthesizing heterogeneous evidence, creating barriers for non-experts and cognitive burdens even for specialists. MARRVEL exemplifies this challenge by requiring precise queries (e.g., HGVS notation) and returning complex, difficult-to-synthesize outputs. To address this input-output a...

Inferring virtual cell environments using multi-agent reinforcement learning

Single cells interact continuously to form a cell environment that drives key biological processes. Cells and cell environments are highly dynamic acr...

Computational redesign of a thermostable T7 RNA polymerase

T7 RNA polymerase (T7 RNAP) is a foundational enzyme for biotechnology, but its utility for many potential applications is limited by low thermal stab...

SARS-CoV-2 Variant-Dependent Alterations in Nasopharyngeal Microbiota and Host Inflammatory Response

The SARS-CoV-2 pandemic saw multiple outbreaks occur over short periods. This was linked to the virus’s high infectivity and rapid mutation rate, whic...

CDR Conformation Aware Antibody Sequence Design with ConformAb

Antibody lead optimization methods seek to enhance a lead candidate’s therapeutic properties through targeted sequence mutation. However, the mutation...

Integrative transcriptomic analysis identifies miR-642a-5p as a regulator of POFUT1 expression in colon cancer

Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide, underscoring the urgent need for novel biomarkers and therapeutic targ...

A Minimal Plasma Proteome-Based Biomarker Panel for Accurate Prostate Cancer Diagnosis

Early and accurate diagnosis of prostate cancer (PRC) remains a major clinical challenge, particularly with existing biomarker panels relying on invas...

Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning

Amino acid mutations may lead to significant changes in the binding affinity of protein complexes, thereby causing a series of cellular dysfunctions. ...

Automated Annotation of Plant Gene Regions Using Supervised Machine Learning

Rapid sequencing now enables analysis across many species, including plants, but repeat-rich, redundant plant genomes still hinder precise annotation....

Fine-Tuning Protein Language Models Enhances the Identification and Interpretation of the Transcription Factors

Transcription factors (TFs) are pivotal regulators of gene expression and play essential roles in diverse cellular activities. The three-dimensional o...

scDNAm-GPT Captures Genome-wide CpG Dependencies in Single-cell DNA methylomes to Revolutionize Epigenetic Analysis

Single-cell DNA methylomes are challenging to interpret because of sparse CpG coverage and the complexity of genome-wide sequences. We present scDNAm-...

PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation

Single-cell foundation models (FMs) pretrained on massive unlabeled scRNA-seq data show strong potential in predicting transcriptional responses to un...

Predicting strain-specific metabolic capabilities in the Genus Pseudomonas using a Flux-to-AI approach unravels hidden cell envelope properties

Bacteria from the Pseudomonas genus are omnipresent in air, soil, and water. They have been widely studied for their broad metabolic versatility and p...

Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics

CRISPR-associated transposons (CAST) use guide RNAs to direct their transposition and are being harnessed as tools for programmable genome engineering...

MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences

MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes by binding to target messenger RNAs (mRNAs), causing them to degrade or suppressing t...

RNAcentral in 2026: Genes and literature integration

RNAcentral was founded in 2014 to serve as a comprehensive database of non-coding RNA sequences. It began by providing a single unified interface to m...

Genolator: A Multimodal Large Language Model Fusing Natural Language, Genomic, and Structural Tokens for Protein Function Interpretation

Decoding the genetic code to unveil its genome functionality is a monumental task which would greatly advance the understanding of disease mechanisms ...

Iterative immunogen optimization to focus immune responses on a conserved, subdominant viral epitope

Designing effective vaccination strategies against genetically diverse viruses, such as HIV or influenza, is hindered by the ability of these pathogen...

Heimdall: A Modular Framework for Tokenization in Single-Cell Foundation Models

Foundation models trained on single-cell RNA-sequencing (scRNA-seq) data have rapidly become powerful tools for single-cell analysis. Their performanc...