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).

• Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

  PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

  Has reproduction · 100

  S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

  gastric colorectal additional breast xenium visium histology

• SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.

  PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Has reproduction · 74

  SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.

  pairs nanostring st-sc osmfish_zeisel st-sc 5-fold spatially

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 8 setups

  Has reproduction · 42

  CanCellCap, a multi-domain learning framework integrating domain adversarial learning and Mixture of Experts, identifies cancer cells across all tissues, cancers, and sequencing platforms by extracting tissue-common and tissue-specific gene expression patterns.

  testing datasets tisch2 prostate scrna-seq simulated spatial

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups

  Has reproduction · 50

  A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation

  pre-treatment domingo geo bulk bulk external spatial

• PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.

  PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 4 setups

  Has reproduction · 40

  Adding PD-1 blockade to neoadjuvant chemotherapy (NAPC) increases tumor infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells, whereas NAC alone increases only CD20+ B cells.

  cd45+ ffpe nsclc scrna-seq single-cell multiplex geo

• Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

  PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups

  Has reproduction · 75

  CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 ffpe end-stage single-cell single-nucleus integrative

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.

  PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA

  model dipicolinic hek293t 28s crosslinking nmr crosslink

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage