Discover, rate, and discuss biology preprints.

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.

The paper uses spatial and single-cell transcriptomics with mitochondrial lineage tracing to uncover fate switching and premetastatic niche formation in osteosarcoma.

The paper introduces RNA3D-Decoy, a benchmark dataset of AI-generated RNA structure models, to evaluate quality assessment methods for RNA structure prediction.

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

This study evaluates cross-cohort generalization of mammography diagnostic models using different image representations and domain-adversarial learning, finding that MedSigLIP embeddings provide the best transferability.

CryoCodex improves cryo-EM map quality by jointly enhancing density, estimating local quality, and masking molecules, outperforming existing methods on experimental maps.

FilAdh is a framework for analyzing focal adhesions and actin stress fibers, achieving high accuracy in segmentation, reconstruction, and classification while revealing measurement biases under degradations.

HyperCom infers cell-resolved cell-cell communication using hypergraphs from single-cell transcriptomics data, providing a continuous sender-receiver score for ligand-receptor pairs.

D-plus improves introgression detection by addressing rate heterogeneity and ghost lineages, re-analyzing Jaltomata data to challenge prior interpretations.

This study integrates proteomics and functional data using topological analysis to reveal how opposite inotropic drugs affect engineered cardiac tissue.

Mastodon is a software platform for analyzing large-scale lineage-tracing microscopy datasets, enabling manual and automated cell tracking and lineage analysis in complex 3D geometries.

The paper identifies and characterizes m6A-related gene families in Marchantia polymorpha, revealing conservation, diversification, and expression dynamics across developmental stages and stress conditions.

AntiCapt uses fine-tuned nucleotide language models to predict and design anticancer aptamers, achieving high accuracy in distinguishing them from non-aptamers.

The paper investigates the molecular mechanisms of comedogenesis in human acne using single-cell transcriptomics, identifying a microcomedone-like cell population and supporting the comedone switch hypothesis.

This paper introduces a Bayesian framework for laboratory risk management that quantifies biosafety risk using a log-risk scale and incorporates WHO Risk Group classifications and incident escalation models.

The paper introduces Super Bloom, a Bloom filter variant for streaming k-mer queries, which improves cache efficiency and reduces false positives.

This study evaluates AlphaGenome's ability to decode regulatory mechanisms in ALS, finding it fails to accurately recover variant effects and assign regulatory signals to correct genes.

The paper introduces iDMS, a neural network that predicts optimal separation and compensation voltages for DMS, improving glycosphingolipid analysis.