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SpaceBlocks: an expert-supervised workflow for cohort-level spatial transcriptomics analysis

SpaceBlocks is a workflow for reproducible, expert-supervised spatial transcriptomics analysis across platforms, identifying new cell types and differentially expressed genes in multiple datasets.

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.

Consensus methods for trees of blobs and level-1 phylogenetic networks

This paper introduces a consensus framework for phylogenetic networks, demonstrating its effectiveness on simulated and real datasets.

A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin

MUTUAL enables cross-modality analysis between transcriptome and chromatin by learning a shared RNA-ATAC space from multiome data without refitting.

Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions

This paper introduces a method to improve RNA-seq transcript quantification by reducing mapping ambiguity through minimal-shared region analysis, showing improved accuracy in isoform detection and abundance estimation.

Peripheral Exercise Transcriptomes Do Not Converge on Glutamatergic or Neuroinflammatory Signatures: A Cross-Platform Meta-Analysis

This study analyzes peripheral transcriptomic responses to exercise and finds no convergence on glutamatergic or neuroinflammatory signatures across tissues.

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

The paper benchmarks variant effect predictors using a leakage-controlled dataset and develops a gradient-boosting consensus model that outperforms existing tools.

scRM: A single-cell foundation model trained on scRNA-seq reads

scRM is a single-cell foundation model trained on raw scRNA-seq reads, showing that raw data pretraining is feasible and cost-effective compared to count-based models.

Predicted condensation-related signatures localize to two C-terminal regions of the prion protein across cervid PRNP variants associated with chronic wasting disease

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

The paper presents the Almond Expression Atlas, a comprehensive transcriptomic resource integrating RNA-seq data to identify tissue-specific genes and improve gene expression analysis in almond.

ToxINsight: An Integrated Web Platform for Sequence, Structure, and Ligand Binding Analysis of Snake Venom Toxins

ToxINsight provides a web platform for analyzing snake venom toxin sequences, structures, ligand interactions, and geographical distributions to aid in antivenom development.

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

MaCADEMIA is a MATLAB toolbox for single-molecule fluorescence image analysis, providing accurate quantification of molecular properties in living cells.

The Quagmire of Immunogenicity-Guided Antibody Design: Labels Limit Progress

The paper evaluates antibody design methods using immunogenicity labels and finds that format-based approaches outperform sequence-based predictors, but label inaccuracies limit progress.

Pycea: a scverse toolkit for single-cell lineage tracing analysis

Pycea provides a toolkit for analyzing single-cell lineage tracing data, integrating with Scanpy and offering visualization and statistical methods for lineage trees.

Transcript quantification using context-aware MAPQ modeling

CALMeR improves transcript quantification by context-aware MAPQ modeling, recovering more spike-in transcripts and better matching known concentrations.

LIMBER: A Hybrid RNA Foundation Model for Predicting and Understanding RNA Structure and Function

LIMBER is a hybrid RNA foundation model that predicts RNA structure and function, showing strong performance in secondary-structure prediction and classification, along with transferability to related tasks.

The Findings Workflow: An agentic, collaborative, provenance-tracked framework for scientific data analysis with Claude Code

The paper introduces the Findings Workflow, a framework that enhances reproducibility and trust in LLM-assisted scientific analysis by structuring the process with provenance tracking and collaborative features.

RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease

The paper evaluates segmentation methods for reconstructing cell-like profiles from spatial transcriptomics data but finds no reliable method under the given constraints.

Computational Repurposing of FDA Approved Drugs Against Cyclin Dependent Kinase (CDK2)

The paper identifies FDA-approved drugs with potential binding activity against CDK2 using computational methods and selects Carteolol as a candidate.

Cross-modal transfer enables zero-shot prediction of drug responses across cell types

GRAFT predicts drug responses across cell types without direct measurements by transferring genetic perturbation data to chemical perturbations.