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TideCluster: clustering and classification of tandem repeats for comparative and pangenomic analysis

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

scPolyA enables efficient, interactive and agent-guided alternative polyadenylation analysis in single-cell and spatial transcriptomes

scPolyA provides a framework for analyzing alternative polyadenylation in single-cell and spatial transcriptomes, revealing APA patterns in cancer tissues.

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.

AOPTK: Open-Source Software for AI-Assisted Toxicological Literature Analysis

AOPTK automates toxicological literature analysis using AI, achieving high accuracy in identifying chemical-biological effect relationships.

mFrag: Integrating External DNA Methylation References Improves Lung Cancer Early Detection by Fragmentomics

mFrag improves lung cancer early detection using fragmentomics by integrating DNA methylation data and combining two models to enhance prediction accuracy.

BEHAV3D-Explorer enables natural language-assisted profiling of 3D cellular dynamics

BEHAV3D-Explorer provides a user-friendly platform for analyzing 3D live-cell imaging data using natural language guidance to select analysis strategies and configure workflows.

BioMeme: biological response memory for virtual cells

BioMeme predicts cell responses to new perturbations by recalling measured experiments, outperforming neural models in accuracy and speed.

Ok-k-mer: Selecting k-mer length ensembles for calculating genomic distance

Ok-k-mer selects optimal k-mer length ensembles to improve genomic distance estimation by maximizing correlation with phylogenetic branch distances.

Integrated genotyping, annotation and epigenetic characterization of transposable elements with GraffiTE

GraffiTE v1.1 is a Nextflow pipeline that genotypes structural variants, annotates polymorphic mobile elements, and maps epigenetic data to transposable elements using pangenome graphs, revealing hypomethylated elements and age-related demethylation.

PyTorch Frustratometer: An Ultra-fast, Parallelized Tool for Proteome-Scale Local Energetic Frustration Analysis

The paper introduces a PyTorch-based tool for fast proteome-scale local frustration analysis, achieving 70-13,000x speedup over the original FrustratometeR.

Extracting and Updating Compact Colored k-mer Indexes

This paper introduces efficient methods to update colored k-mer indexes without rebuilding them from scratch, enabling dynamic maintenance of large genomic collections.

Glycine-Proline driven flexibility and interface-dependent conservation of six-residue {Omega}-loops in protein complexes

The paper analyzes six-residue Omega-loops in protein complexes, showing their structural constraints, sequence conservation patterns, and functional significance through sequence design and mutation mapping.

MELD: Mutation Effect Learning through Differential embeddings

MELD predicts SNV functional effects by directly training on wild-type versus mutant differences, outperforming post-hoc in-silico mutagenesis methods with fewer parameters.

RabbitCD-HIT: Distributed High-Sensitivity Greedy Incremental Clustering for Billion-Scale Protein Sequences in Hours

RabbitCD-HIT clusters billion-scale protein sequences efficiently, achieving faster performance than CD-HIT on large datasets.

StableProt: Structure-Aware Deep Learning for Protein Thermostability (Tm) and Environmental Adaptation (OGT) Prediction

StableProt predicts protein thermostability and organismal optimal growth temperature using a structure-aware deep learning framework, achieving high accuracy and robustness across temperature regimes.

Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics

This paper introduces SSAF-T, a segmentation-free framework for cell-type inference in spatial transcriptomics that avoids cell segmentation and enables accurate cell-type-guided segmentation.

Label-free flow operators and stability operators from single-cell time courses: what local dynamical operators can and cannot identify

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

DisCell: Separating Spillover from Niche Response in Spatial Transcriptomics

DisCell identifies and separates spillover from niche responses in spatial transcriptomics data, confirming a previously reported finding about esophageal cancer cells.

Learning interpretable compositional features associated with continuous covariates

This paper introduces IsoVita, a framework for learning interpretable compositional features from continuous covariates, showing improved detection of temporal isoform variation in human brain RNA-seq data.

TestNet-PA: Sampling-Zero-Aware Inference of Microbial Presence-Absence Networks

TestNet-PA addresses sampling zeros in microbial presence-absence networks by modeling them as structural or sampling zeros, improving FDR control and sensitivity compared to Fisher's exact test.