Genetics

A Resolution-Agnostic Geometric Transformer for Chromosome Modeling Using Inertial Frame

Chromosomes are the carriers of genetic information. Further understanding their 3D structure can help reveal gene-regulatory mechanisms and cellular functions. However, high-resolution 3D structures are often missing due to the high cost and inherent noise of experimental screening. A standard pipeline for reconstructing the chromosome 3D structure first applies the single-cell Hi-C high-throughp...

A spatial multi-omic portrait of survival outcome for clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the leading cause of kidney cancer-related death, but how the tumor microenvironment shapes patient survival is not completely understood. Here, we describe the characterization of ccRCC tumor ecosystems from 498 patients using imaging mass cytometry with a focus on tumor, myeloid, and T cell landscapes. Data from more than 3 million single cells is analy...

Pan-cancer tumour classification and risk stratification from whole-genome somatic variants via dual-task representation learning

Tumour typing from whole-genome sequencing is increasingly accurate, yet molecular subtyping from somatic variants remains challenging because of tumo...

Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased manner

Zinc finger (ZF) proteins (ZFPs) constitute the largest family of transcription factors in mammals; however, their regulatory mechanism remains largel...

AOI: Turning Failed Trajectories into Training Signals for Autonomous Cloud Diagnosis

Large language model (LLM) agents offer a promising data-driven approach to automating Site Reliability Engineering (SRE), yet their enterprise deploy...

Aging Out of the Blue: Estimating and Calibrating Region-specific Epigenetic Clocks for a Blue Zone via SuperLearner

Epigenetic clocks estimate biological age from DNA methylation patterns at CpG sites, providing robust predictions of mortality and morbidity risk. "B...

Exposomics for childhood asthma

Identification of early interventions to reduce/eliminate asthma - the most common chronic disease among children - could significantly reduce burden ...

Conversational Artificial Intelligence Agents-Enabled Dissection of RTK-RAS and MAPK Pathway Dependencies in Gemcitabine-Treated Pancreatic Ductal Adenocarcinoma (PDAC)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by profound molecular heterogeneity and inconsistent responses to ge...

A comprehensive benchmark of publicly available image foundation models for their usability to predict gene expression from whole slide images

Recent advances in large-scale self-supervised learning have led to the emergence of foundation models capable of extracting transferable visual repre...

An autonomous system for multi-objective continuous evolution at scale

Natural evolution is high-dimensional; organisms adapt to many pressures at once, across substrates, environments, and genetic backgrounds. Yet most d...

h5adify: neuro-symbolic metadata harmonizationenables scalable AnnData integration with locallarge language models

Background: The rapid growth of public single-cell and spatial transcriptomics repositories has shifted the main bottleneck for atlas-scale integratio...

Exploration of the screening and regulatory mechanisms of biomarkers related to ac4C modification in laryngeal squamous cell carcinoma patients based on single-cell analysis and machine learning

Background: N4-acetylcytidine (ac4C) modification plays a critical role in cancer development. Exploring ac4C modification in laryngeal squamous cell ...

NN-Assisted Image Analysis for Quantifying Intracellular Trypanosoma cruzi Infection

Trypanosoma cruzi infection remains a central, yet methodologically challenging step in Chagas disease research and early-stage drug discovery. Curren...

Large-Scale Dataset and Benchmark for Skin Tone Classification in the Wild

Deep learning models often inherit biases from their training data. While fairness across gender and ethnicity is well-studied, fine-grained skin tone...

Temporal dynamics of radiotherapy and chemotherapy response in lower-grade gliomas using causal machine learning

Lower-grade gliomas (World Health Organization [WHO] grades 2-3) exhibit variable treatment responses, yet clinical decisions remain guided by populat...

Interpretable Fine-tuned Large Language Models Facilitate Making Genetic Test Decisions for Rare Diseases

Clinical decision making often relies on expert judgment guided by established guidelines, which can be challenging to standardize and abstract to imp...

High Diversity Gene Libraries Facilitate Machine Learning Guided Exploration of Fluorescent Protein Sequence Space

While protein language models (PLMs) have shown great promise for protein design, their performance is fundamentally constrained by the diversity and ...

DNA fragment length analysis using machine learning assisted vibrational spectroscopy

DNA length analysis is essential for genomic workflows including next-generation sequencing and fragmentomics based diagnostics. Conventional approach...

Genomic language models improve cross-species gene expression prediction and accurately capture regulatory variant effects in Brachypodium mutant lines

Predicting gene expression from cis-regulatory DNA sequences at the promoter and terminator regions is a central challenge in plant genomics. This cap...

Detecting Extrachromosomal DNA from Routine Histopathology

Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, tumour heterogeneity and poor clinical outcomes [1-3], yet its detection rel...