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).

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

  PMID 41493197 · PMC13110159 · Plant biotechnology journal · 2026 · 8 claims · 5 setups

  Full-text index only

  An optimised Visium spatial transcriptomics protocol (two-step OCT embedding combined with OCT-Immersion First cryopreservation) preserves high-integrity RNA from fragile plant tissues such as SAM

  maize integrated spatial integrity dimensional

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

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

  Full-text index only

  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

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

  PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups

  Has reproduction · 81

  SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains

  pan-cancer pc9 451lu a375 bulk scrna-seq computational

• Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.

  PMID 41806374 · PMC13148403 · G3 (Bethesda, Md.) · 2026 · 8 claims · 5 setups

  Full-text index only

  Only ultra-long long-reads (N50 > 50 kb) are capable of accurately calling structural variants of any size in D. melanogaster euchromatin

  inbred downsampled aligned putative ont illumina novo

• A comparative analysis of blastoid models through single-cell transcriptomics.

  PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 60

  EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

  blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov