Leukemia

RNAStabFormer: Region-Aware Multi-Task Hybrid Learning for RNA Stability Prediction from Pulse-Chase Transcriptomics

RNA stability is a central layer of post-transcriptional gene regulation, yet large-scale stability labels derived from pulse-chase transcriptomics depend strongly on quantification region, time-window definition, and replicate quality control. We present RNAStabFormer, a controlled learning framework for predicting human RNA stability proxies from transcript sequence. Its core model, RAMHT, combi...

Predicting Motor Recovery After Stroke: Utility and Limits of Corticospinal Tract Biomarkers

Background: Corticospinal tract (CST) damage is a major cause of post-stroke motor deficits. However, it remains unclear which estimates of CST damage best predict motor recovery, especially regarding different aspects of motor control. While conventional CST-lesion metrics offer superior feasibility, data-driven machine learning (ML) approaches may better capture patients propensity for task-spec...

MOSAIC: Methylation-Oriented Site Analysis and Information Classifier for Robust Epigenomic Classification of Acute Leukemia in Clinical Cohorts with Variable Tumor Purity

DNA methylation-based classification offers a rapid diagnostic complement to conventional molecular workflows in acute leukemia. Existing classifiers ...

Looking beyond stereotyped neuron structures reveals links between beading and morphological rearrangements in aging phenotypes.

Understanding how neuronal morphology changes during aging and acute stress is essential for elucidating mechanisms of neurodegeneration. The highly b...

DART: A design-aware microfluidic chip paradigm for real-time live-cell image analysis

High-throughput microfluidic live-cell imaging generates rich single-cell data. Yet semi-automated procedures for locating regions of interest (RoIs),...

A Transformer-derived transcriptomic score associates with ex-vivo drug response in AML

Background Drug-tolerant persister (DTP) cell states have been implicated in relapse across multiple cancers, including acute myeloid leukaemia (AML) ...

The Importance of Phase in Neural Representations: An Internal Oppenheim-Lim Test of Image Classifiers

Oppenheim and Lim (1981) showed that natural images stay recognizable when reconstructed from their Fourier phase alone, while the magnitude carries l...

Explainable AI identifies H3K18ac as a new marker of active enhancers

Enhancers are non-coding regions of DNA that regulate gene transcription, yet the mechanisms underlying enhancer activity remain incompletely understo...

Calibrated Uncertainty Quantification for Patient-Level AML Drug Sensitivity Prediction Using Split Conformal Prediction

Accurate prediction of ex vivo drug sensitivity in acute myeloid leukemia (AML) patients from transcriptomic data is a critical challenge for precisio...

TMO: ASYMMETRIC CROSS-MODAL ATTENTION FOR LEARNINGCELL-STATE-DEPENDENT REGULATORY LAGS FROM SINGLE-CELL MULTIOMIC DATA

Abstract Background: Single-cell multi-omics technologies simultaneously measure chromatin accessibility (ATAC) and gene expression (RNA), providing a...

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individ...

Physics-Informed Neural Networks for Chemotherapy Pharmacokinetics: Benchmarking the Clinical Estimator and Exposing Parameter Identifiability

Physics-Informed Neural Networks (PINNs) are an attractive tool for partial-observation problems in biology, where the governing dynamics are known bu...

Transcriptomic Architecture of Type 2 Diabetes in Human Pancreatic Islets:An Integrative Meta-Analysis and Machine Learning Framework for Biomarker Discovery

Background. Type 2 diabetes mellitus (T2D) is defined by progressive pancreatic {beta}-cell dysfunction whose molecular underpinnings remain incomplet...

Seeing Below the Limit of Detection: A Censored-Poisson Bayesian Latent-Growth Change-Point Detector (the Span Detector) for Serial ctDNA in HR+/HER2- Metastatic Breast Cancer

Circulating-tumour DNA (ctDNA) carries evidence of drug resistance months before imaging shows it, but the earliest evidence lives below the assay's l...

Patient-Level Diagnosis of Acute Myeloid Leukemia via Deep Learning Analysis of Bone Marrow Smear

Bone marrow smear review remains important for acute myeloid leukemia (AML) assessment, but manual single-cell interpretation is labor-intensive and p...

Recipient cell identity governs intracellular transport and membrane interactions of extracellular vesicles across species

Extracellular vesicles (EVs) function as a natural communication system, enabling transfer of biomolecules between cells. Although EVs are produced by...

The machine-learning classifier ALLCatchR2 identifies 20 T-ALL subtypes across cohorts and age groups

T-cell acute lymphoblastic leukemia (T-ALL) comprises molecularly diverse subtypes, but robust cross-cohort validations and operational gene-expressio...

Hierarchical refinements of cis-regulatory inputs improve scalable gene expression prediction

Deciphering the relationships between cis-regulatory elements (CREs) and target gene expression has long been a challenging problem in molecular biolo...

Eyewire II - A connectomic resource for resolving cell types and circuits of the mouse retina

Comprehensive wiring diagrams from electron microscopy (EM) are a powerful tool to understand the inner workings of the brain. The retina is an easily...

Boundary-Specific Failure Modes and Safety Trade-offs of Large Language Models in ChronicKidney Disease Renoprotective Therapy Review:A Stratified Synthetic Benchmark

Background.Renoprotective therapies - SGLT2 inhibitors, finerenone, and renin-angiotensin system inhibitors (RASi) - remain underutilisedin chronic ki...