Genetics

Multimodal gene embeddings for drug-target prediction and lineage reconstruction

Understanding how gene function emerges across molecular, cellular, and pharmacologic contexts remains a central challenge in systems biology and drug discovery. Conventional computational models typically operate within a single modality, such as expression, ontology, or interaction networks, limiting their ability to capture the multidimensional nature of gene function. Here, we present NEWT (Ne...

Spatially Resolved Reaction-Diffusion Modeling Reveals Effects of Intracellular Spatial Heterogeneity on Yeast Galactose Network Dynamics

Eukaryotic cells are spatially organized into functionally-distinct compartments. This three-dimensional(3D) organization generates intracellular heterogeneities that can modulate regulatory dynamics. Despite this knowledge of subcellular organization, most quantitative gene-regulation models still assume a well-mixed environment in which molecules can react regardless of their spatial positions. ...

Trisomy 21 impairs synchronized activity and connectivity in developing human Down syndrome cortical excitatory neuron networks

Down syndrome (DS) is the most common genetic cause of intellectual disability, affecting one in 700 live births worldwide, and is caused by trisomy o...

Generating Biologically Relevant Subtypes of Autism Spectrum Disorder with differential responses to Acute Oxytocin Administration in a Randomized Trial using Random Forest Models and K-means Clustering

Autism Spectrum Disorder (ASD) is a heterogenous condition that has no biologically relevant subtypes yet. Here, we utilized a multidimensional approa...

CausalCellInfer: Resolving cell-type-specific disease mechanisms from biobank-scale GWAS

Integrating the cellular resolution of single-cell RNA sequencing (scRNA-seq) with the phenotypic depth of population-scale biobanks is essential for ...

Analysis of Age-Specific Dysregulation of miRNAs in Lung Cancer Via Machine learning: Biomarker Identification and Therapeutic Implications in Patients Aged 60 and Above.

Lung cancer is the leading cause of cancer-related mortality worldwide, predominantly affects older individuals, with non-small cell lung cancer (NSCL...

evoCancerGPT: Generating Zero-Shot Single-Cell and Single-Sample Cancer Progression Through Transfer Learning

Cancer evolution is driven by complex changes in gene expression as cells transition and change states during tumorigenesis. Single-cell RNA sequencin...

Machine learning-guided design of artificial microRNAs for targeted gene silencing

Artificial microRNAs (amiRNAs) offer a powerful strategy for targeted gene silencing, but their rational design is limited by complex sequence-structu...

IndicFairFace: Balanced Indian Face Dataset for Auditing and Mitigating Geographical Bias in Vision-Language Models

Vision-Language Models (VLMs) are known to inherit and amplify societal biases from their web-scale training data with Indian being particularly misre...

LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference

Summary: A bioinformatics tool is presented for estimating recent effective population size by using a neural network to automatically compute linkage...

Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures

Multiplexed protein imaging enables spatially resolved analysis of molecular organization in tissues, but existing spatial proteomics platforms remain...

Parameter-free representations outperform single-cell foundation models on downstream benchmarks

Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale f...

Designing RNAs with Language Models

RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains comput...

A custom phenotypic profile for Fanconi anemia: Addressing gaps in existing disease annotations

Fanconi anemia (FA) is a rare genetic disorder of impaired DNA repair characterized by progressive bone marrow failure, congenital malformations, and ...

Generative AI Guided Design of High-Affinity T cell Receptors

Developing T cell receptors (TCRs) with sufficiently high affinity for tumor antigens (TAs) remains a fundamental challenge in TCR-T immunotherapy. Ex...

Deep learning-based non-invasive profiling of tumor transcriptomes from cell-free DNA for precision oncology

Circulating tumor DNA (ctDNA) profiling from liquid biopsies is increasingly adopted as a minimally invasive solution for clinical cancer diagnostic a...

A spectral framework for measuring diversity in multiple sequence alignments

Machine learning (ML) methods for proteins and RNAs rely on multiple sequence alignments (MSAs) and related datasets such as experimental mutagenesis ...

Network-based integration of gene expression and DNA methylation identifies prognostic biomarkers for early-stage pancreatic cancer

Pancreatic ductal adenocarcinoma remains one of the most lethal malignancies, largely due to the absence of reliable early stage biomarkers. Here, we ...

A machine learning approach to identify key Epigenetic Transcripts for Ageing research in human blood (Epitage)

DNA methylation is an established biomarker of human ageing, and analysing CpGs grouped by transcript as functional units may reveal new insights into...

C^2ROPE: Causal Continuous Rotary Positional Encoding for 3D Large Multimodal-Models Reasoning

Recent advances in 3D Large Multimodal Models (LMMs) built on Large Language Models (LLMs) have established the alignment of 3D visual features with L...