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).

• Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

  PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

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  SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

  pbmc bone skin embryos scrna-seq scnmt-seq asap-seq

• CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

  PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

  bmmc pbmc foetal cis-regulatory enhancer-promoter scalability

• Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

  PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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  HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

  tcga-luad best brain advanced bulk kaplan-meier pearson

• sCellST predicts single-cell gene expression from H& E images.

  PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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  sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

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• GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.

  PMID 41769841 · PMC12970594 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Incomplete/inaccurate gene annotations, especially missing or truncated 3' UTRs, cause reads to map to non-genic regions and genes to be under-quantified or missing from scRNA-seq expression matrices in non-model species

  genomes whole-organism xenia octopus peak scrna-seq

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna

• PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.

  PMID 41673899 · PMC12998178 · Genome biology · 2026 · 7 claims · 8 setups

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  PreTSA dramatically reduces computational time and memory versus GAM (Monocle, TSCAN) and PseudotimeDE for identifying temporally variable genes (TVGs) while producing highly similar results

  simulated null pbmc pancreas pseudotime tvg false-positive