Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX.

  PMID 41723123 · PMC13035843 · Nature communications · 2026 · 8 claims · 6 setups

  Full-text index only

  CAMEX outperforms state-of-the-art integration methods on cross-species scRNA-seq benchmarking datasets ranging from one to eleven species

  liver ovary pancreas testis scrna-seq type

• ASTROREPOMICS: A curated transcriptomic database for reproductive biology in space.

  PMID 41940322 · PMC13049440 · iScience · 2026 · 8 claims · 6 setups

  Full-text index only

  ASTROREPOMICS integrates 17 rigorously normalized and batch-corrected transcriptomic datasets spanning multiple species and reproductive tissues

  pooled mus rattus pca-based combat differential

• Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.

  PMID 41869863 · PMC13170260 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Among ten/eleven evaluated single-cell FMs, scGPT, Geneformer, and CellFM are the top models considering both performance and user accessibility

  scrna-seq unpaired single-cell scgpt batch multi-omic cell-type

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene

• Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets.

  PMID 41971949 · PMC13068006 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Full-text index only

  spVIPES decomposes unpaired scRNA-seq datasets with nonmatching features into shared and private latent representations using a Product of Experts framework

  simulated zebrafish kidney peripheral simulated cross-species scrna-seq

• Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.

  PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups

  Has reproduction · 84

  Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.

  solanum bulk term novo

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial