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).

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

  PMID 41571662 · PMC12923738 · Nature communications · 2026 · 8 claims · 8 setups

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  Fin and limb regeneration share conserved proximal and distal blastema territory markers, DNA damage repair activation, hif1a-mediated hypoxia response, and sequential pro-/anti-inflammatory gene programs.

  polypterus axolotl zebrafish regenerating single-nucleus spatial single-cell

• Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.

  PMID 41980775 · PMC13198004 · Cell reports methods · 2026 · 7 claims · 4 setups

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  Common DGE analysis methods (Wilcoxon test, unweighted t-test, pseudo-bulk aggregation, SCTransform-style parametrization) rely on unnecessary simplifications and assumptions that are inconsistent with experimental data and cause false findings

  e18 simulated scrna-seq sprna-seq scrna-seq simulation count

• transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

  PMID 41645434 · PMC12930851 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  transFusion is a comprehensive, web-based platform for integrated analysis of scRNA-seq and 10x Visium spatial transcriptomics data requiring no parameter configuration

  breast scrna-seq 10x cellphonedb

• Single-Cell and Spatial Transcriptomics Reveal That TXNIP and BIRC3 Contribute to Human Prostate Tumor Progression.

  PMID 41972735 · PMC13072731 · Cells · 2026 · 6 claims · 8 setups

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  TXNIP and BIRC3 are established as spatially restricted tumor-niche genes associated with metabolic stress and inflammatory survival pathways

  prostate tcga-prad integration single-cell spatial pseudotime

• Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

  PMID 41760664 · PMC13066420 · Nature communications · 2026 · 8 claims · 8 setups

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  CellRefiner is a physical/particle-based model (subcellular element method) that integrates scRNA-seq and spatial transcriptomics data to reconstruct single-cell resolution spatial data

  hypothalamic embryo hippocampus visual merfish seqfish slide-seqv2

• Identification of cycling regulatory T cell precursors as conductors of immune escape during breast carcinoma progression.

  PMID 41997138 · PMC13213619 · Cancer cell · 2026 · 8 claims · 8 setups

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  A novel proliferative Treg precursor state, cycling Treg (cycTreg: FOXP3^int, MKI67^hi, IKZF2/4^int-hi), is absent in normal breast, low in DCIS, and strongly expanded in IBC

  normal mammary dcis tumor-draining scrna-seq spatial multiplex

• Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma.

  PMID 42010788 · PMC13102037 · Oncoimmunology · 2026 · 7 claims · 7 setups

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  DLBCL tissues are organized into six recurrent, spatially defined cellular ecosystems (Cell-Eco) with distinct immune compositions, transcriptional programs, and neighborhood architectures.

  dlbcl cd45+ spots scrna-seq spatial scrna-seq cell-type

• DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

  PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

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  DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

  heart cortex visual brain spatial cell-type

• Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

  PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

  skin combined annotated scrna-seq single-cell spatial cell2location

• Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

  PMID 36450262 · PMC9792173 · Cell reports · 2022 · 8 claims · 6 setups

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  IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

  cd44+ splenocytes spleen tcr scrna-seq flow spatial

• Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

  PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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  The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

  first-trimester decidual spots dnk 10x h&e type

• MultiSP deciphers tissue structure and multicellular communication from spatial multi-omics data.

  PMID 41650976 · PMC13174227 · Cell genomics · 2026 · 7 claims · 5 setups

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  MultiSP outperforms existing spatial and single-cell multi-omics integration methods in detecting biologically accurate spatial domains across multiple spatial multi-omics technologies and tissue types

  lymph embryo brain postnatal spatial misar-seq chromvar

• Single cell multiomics revealed fibrotic trajectories of endometrial cells and interaction with the pro-fibrotic macrophages in intrauterine adhesion.

  PMID 41947225 · PMC13188631 · Genome medicine · 2026 · 8 claims · 8 setups

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  Human IUA endometrium contains a novel ACTA2+KRT8+ myofibrotic-epithelial subpopulation and an ACTA2+CD31+ myofibrotic-endothelial subpopulation, in addition to myofibroblasts

  endometrial iua scrna-seq snatac-seq spatial

• Identification of a new population of Tnn(+) progenitors to form tendon enthesis fibrocartilage.

  PMID 42009636 · PMC13096267 · Bone research · 2026 · 8 claims · 8 setups

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  A novel Tnn+ progenitor cell population resides in the tendon enthesis and serves as a cellular origin of fibrocartilage lineages

  tendon developing spatial single-cell visium single-cell stamp

• 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

• Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

  PMID 41882353 · PMC13216075 · Nature · 2026 · 8 claims · 8 setups

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  GluN1 and GluN2B NMDAR subunits are ectopically expressed in cancer cells of human TNBC tumours

  breast tnbc 4t1-nmdar orthotopic bulk spatial immunofluorescence

• SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

  PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

  gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish

• scSurv: a deep generative model for single-cell survival analysis.

  PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

  simulated tcga melanoma renal scrna-seq bulk single-cell

• Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

  PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups

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  CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC

  intestinal colorectal single-cell serum bulk single-cell spatial