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).

• A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.

  PMID 41884004 · PMC13010111 · iScience · 2026 · 8 claims · 8 setups

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  Malignant cells cluster predominantly by tumor of origin, while non-malignant cells from the same tumors cluster by cell type independent of patient

  malignant non-malignant ovarian normal scrna-seq alternative paired

• Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

  PMID 41862467 · PMC13168514 · Nature communications · 2026 · 8 claims · 8 setups

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  UCASpatial is a novel deconvolution algorithm that uses Shannon entropy-based gene weighting combined with weighted non-negative least squares to estimate cell-type composition from spatial transcriptomics data

  simulated colorectal hippocampus ear simulated runtime spatial

• Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

  PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

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  snRNA-seq census of 227,680 nuclei across 48 cell types reveals altered cellular states and compositional rewiring of the distal lung in ILD

  frozen lung flash-frozen spatial single-nucleus scrna-seq 10x

• Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data.

  PMID 41944570 · PMC13055433 · Statistics in medicine · 2026 · 8 claims · 3 setups

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  cosmoDA extends the a-b power interaction model by adding a linear covariate effect on the location vector, enabling differential abundance testing on compositional data with feature interactions.

  simulated cell-type microbial simulated single-cell 16s

• Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.

  PMID 41925227 · PMC13099265 · The ISME journal · 2026 · 8 claims · 8 setups

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  Built a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes) using culturomics and PacBio HiFi metagenomics

  giant panda panda-derived pbac pacbio illumina 16s

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

  Has reproduction · 78

  INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

  testis young testicular invade-seq histology sperm

• Atlas-guided discovery of transcription factors for T cell programming.

  PMID 41639465 · PMC13017511 · Nature · 2026 · 8 claims · 8 setups

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  A multi-omics atlas (Taiji pipeline) integrating RNA-seq and ATAC-seq across nine CD8+ T cell states can predict TF activity and identify state-selective versus multi-state TFs

  cd8+ lcmv p14 c57bl rna-seq pearson crispr

• Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

  PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups

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  PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit

  tumor paired single-cell bulk multiplex