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).

• 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

  Full-text index only

  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

• Strawberry atlas: Fragaria vesca gene expression atlas for strawberry genomics.

  PMID 41664659 · PMC12883160 · PeerJ · 2026 · 8 claims · 8 setups

  Full-text index only

  A consolidated gene expression atlas of F. vesca built from 233 RNA-seq libraries across nine tissue categories, aligned to the v6 T2T reference genome, was constructed.

  vesca bulk rna-seq qpcr

• 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

  Full-text index only

  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

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

  PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

  postmortem million+ pfc each single-nucleus umap pseudobulk

• Multimodal learning reveals plants' hidden sensory integration logic.

  PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

  tomato multimodal transcriptomics metabolomics

• 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

• VIST: variational inference for single cell time series.

  PMID 41535949 · PMC12892444 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  VIST is a VAE-based method that decomposes single-cell gene expression into time-dependent and time-independent latent components

  toy drosophila aorta lung synthetic time-course latent

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• A unified framework for correcting batch effects and integrating multi-omics data.

  PMID 41786846 · PMC13079841 · Scientific reports · 2026 · 7 claims · 6 setups

  Full-text index only

  MoDAmix, a four-stage domain adaptation framework (pre-training, single-omics adversarial adaptation, multi-omics adversarial alignment, semi-supervised class alignment), unifies batch correction across multiple omics layers.

  brain aml same single-cell bulk k-means

• Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

  PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

  pbmcs pbmc cd8+ single-cell cell-type expression

• Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

  PMID 41807578 · PMC13230996 · Molecular systems biology · 2026 · 7 claims · 8 setups

  Full-text index only

  CSI-TME is a computational pipeline that deconvolves bulk tumor RNA-seq into cell-type-specific expression (via CODEFACS), infers transcriptional states per cell type via ICA, and identifies IC pairs from two cell types whose joint activity is associated with survival via Cox regression

  idh-mutant tcga cgga deconvolved scrna-seq bulk independent

• Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

  PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

  hnscc colorectal pan-cancer tcr paired umap convolutional

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

  PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p, Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic CRC sites compared to primary CRC.

  pcrc same mli ngs mirna bioinformatics differential

• Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

  PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

  Full-text index only

  Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

  substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell

• BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.

  PMID 41632825 · PMC12904586 · PLoS computational biology · 2026 · 8 claims · 5 setups

  Full-text index only

  BiCLUM consistently outperforms or matches existing integration methods across multiple RNA+ATAC and RNA+protein datasets in visualization and quantitative benchmarks

  pbmc kidney bmmc bmcite scrna-seq cite-seq

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  CHCT, a two-tier hierarchical classification tool built from methylation data, accurately classifies primary cancer type across 30 cancer types.

  tumor clinical methylation clustered methylation unsupervised anova

• 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