bulk RNA-seq

Systematic promoter perturbation reveals limitations of AlphaGenome gene expression predictions

This study evaluates AlphaGenome's ability to predict gene expression changes after promoter perturbations, finding discrepancies between CAGE and RNA-sequencing predictions.

Evaluation effects can rival reported concordance gains in cross-cancer survival prediction

This paper evaluates how much improvement in cross-cancer survival prediction is due to model selection methods versus actual concordance gains, finding evaluation effects can be as significant as reported gains.

From Fill to Freeze: Redesigning homeRNA to Enable Robust Sampling and Scalable Downstream Processing Workflows for Remote Blood Transcriptomics

This paper validates the redesigned homeRNA platform's robustness to remote study stresses, showing it maintains RNA quality under varied conditions and storage times.

Stoichiometric Encoding of Amplification Kinetics Enables High-Level Multiplexing in Single-Channel TaqMan Real-Time PCR

This paper introduces a method to increase multiplexing in TaqMan qPCR by encoding target-specific information into amplification curves and decoding them with a transformer model, achieving 8-plex detection with high accuracy.

Transportability of mouse gene knockout models to human complex phenotypes

The paper assesses the transportability of mouse gene knockout models to human complex phenotypes using GPAT framework, finding evidence for 12 phenotypes but limited for others.

TensorPLS: an R package for exploring molecular and temporal patterns in longitudinal omics data using PLS-DA

TensorPLS is an R package for analyzing longitudinal omics data using PLS-DA, handling missing data and providing temporal insights through VIP scores and cross-validation.

Rho: A Purpose-Driven Workspace for Human-AI Collaborative Analysis

Rho is a collaborative analysis environment that organizes materials by scientific purpose to support human-AI judgment in bioinformatics.

When perfect is a warning: explanations expose shortcuts that accuracy hides in cancer gene-expression classifiers

The paper shows cancer classifiers can achieve perfect accuracy by learning data source shortcuts rather than biological features, and introduces a method to detect and mitigate this issue.

RELAY: Relational In-Context Learning for Cellular Perturbation Prediction

RELAY predicts cellular responses to perturbations by learning relational patterns from measured data, outperforming existing methods on unseen variable values and combinations.

BioResearchBench: 50 Long Horizon Biological Research Tasks

BioResearchBench evaluates AI models on 50 biology research tasks, revealing low success rates and highlighting challenges in data analysis, interpretation, and experimental design.

The Reasoning Paradox in Scientific Sandboxes: Why Extended Reasoning Fails in Autonomous Bioinformatics and How to Fix It.

This paper identifies two failure modes in extended reasoning models within bioinformatics tasks and introduces DTDR to improve accuracy and reduce errors.

SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication

SEngEAR is a web platform for annotating senescent cells, visualizing communication networks, and comparing senescence signatures across datasets and contexts.

DECAPPING PROTEIN 5 regulates the circadian clock in Arabidopsis

This study identifies DCP5 as a key regulator of circadian RNA stability in Arabidopsis by modulating the decay of high-amplitude clock-controlled genes.

Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions

The paper benchmarks sparse-to-transcriptome reconstruction models using high-expression profiles from mouse adrenal cells under sex and sex-steroid conditions, finding that gene-wise metrics and strong baselines are critical for evaluation.

Unravelling genomic and environmental contributions to nitrogen-use efficiency in tropical maize through Bayesian causal forests

This paper uses Bayesian causal forests to estimate the causal effect of nitrogen levels on maize traits, finding that environmental factors largely drive trait variation while genomic background influences baseline levels.

A spin glass representation of hierarchical gene regulation and the partial resolution of frustration

This paper develops a multicellular Ising model to study frustration in gene regulatory networks and shows how intercellular communication affects frustration resolution.

A human induced pluripotent stem cell-based high-throughput screening platform for teratogenicity hazard identification

Four-model hiPSC screen in 384-well imaging reached 83% accuracy (88% sensitivity, 75% specificity) on 130 scored compounds from a 146-compound reference set, scalable to hundreds of compounds monthly.

Algorithmic Geometry Shapes the Biological Meaning of Thalamocortical Structural Covariance

The paper compares five algorithms for deriving structural covariance networks in the thalamocortical system and finds they emphasize different neurobiological aspects based on their mathematical properties.

iGEX: an interactive Gene EXpression exploration platform for the analysis of transcriptomic and proteomic datasets

iGEX provides an interactive platform for exploring transcriptomic and proteomic datasets, enabling comparison of expression patterns across experiments and public resources.

Evolutionary conservation and divergence of regional fructose-responsive gene regulation in the intestine

This study examines how fructose-responsive gene regulation varies across intestinal regions in mice and fruit flies, finding conserved pathways and divergent metabolic responses.

Citizen science gamers enable automated flow cytometry gating through machine learning

The paper develops flowMagic, a machine learning tool for automated flow cytometry gating trained on expert data and citizen science gaming annotations, achieving high accuracy in cell population identification.

Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

The paper evaluates sparse autoencoder features on various embeddings, finding that reproducibility does not guarantee meaningfulness, and proposes reporting features with concept coverage and purity.

Transcriptomic similarity guides source selection beyond tissue lineage

The paper shows that transcriptomic similarity can rank candidate sources for response prediction better than random, but does not resolve aggregation or transfer uncertainty.

Circulating hematopoietic stem and progenitor cells in myeloproliferative neoplasms

This study profiles circulating hematopoietic stem and progenitor cells in MPN patients, identifying transcriptional signatures and quantitative readouts to distinguish MF from other MPNs and predict progression.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

Benchmarking Large Language Models for Transcriptomic Data Analysis and Visualization: Multi-Model Workflow Evaluation

This study benchmarks large language models for automated transcriptomic data analysis and visualization workflows, finding that prompt specificity improves code quality but performance varies with preprocessing and environment.

CBX3 Deletion Overcomes Ferroptosis Resistance in Colorectal Cancer by Targeting IFNγ/SLC7A11/SLC3A2 Axis

This study shows that CBX3 deletion increases ROS and lipid ROS levels in CRC cells, sensitizing them to ferroptosis by disrupting the IFNγ/SLC7A11/SLC3A2 axis.

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.

Primary Human Macrophages Exhibit Functional CYP3A4 Activity with Marked Expression-Function Discordance and Cocaine-Induced Catalytic Activation

This study shows human macrophages have functional CYP3A4 activity, with expression and function discordance, and cocaine increases CYP3A4 activity across donors.

Host brain infection induces RNAi epimutation in Mucor circinelloides and enhances blood-brain barrier invasion

The paper shows brain infection induces RNAi epimutations in Mucor circinelloides that enhance blood-brain barrier invasion.