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).

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

  randomly single-cell single scrna-seq cell-type orthogonal

• Web services and workflow management for biological resources.

  PMID 16351751 · PMC1866383 · BMC bioinformatics · 2005 · 8 claims · 4 setups

  Full-text index only

  Workflow management systems combined with Web Services are a promising ICT approach for automating access to and integration of biomedical data.

  cabri iarc taverna web workflow database

• Integrating and mapping single-cell transcriptomics across the entire gene expression space.

  PMID 42059480 · PMC13130072 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

  Full-text index only

  scGES is a deep learning framework that corrects batch effects across the entire gene expression space by leveraging information from both HVGs and LVGs

  real scrna-seq

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene

• Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.

  PMID 41282419 · PMC12636342 · Computational and structural biotechnology journal · 2025 · 7 claims · 3 setups

  Has reproduction · 83

  POE performs literature-informed dataset retrieval by semantically linking GEO datasets and ENA records through associated PubMed publications

  geo pubmed-linked sbiobert comparative manual faiss

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.

  PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 64

  metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes

  metagenomic prokaryotic reconstructed gut mag genome-scale gem

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

  Full-text index only

  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

  PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

  nsclc epithelial macrophage caf scrna-seq copy gene-set

• Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.

  PMID 41869863 · PMC13170260 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Among ten/eleven evaluated single-cell FMs, scGPT, Geneformer, and CellFM are the top models considering both performance and user accessibility

  scrna-seq unpaired single-cell scgpt batch multi-omic cell-type

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

  Full-text index only

  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.

  PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 6 setups

  Has reproduction · 92

  MCF-7 cell lines and human breast cancer tissues show only minimal similarity in biological processes, though some fundamental functions like cell cycle are conserved.

  mcf-7 breast wgcna-derived top bulk microarray rsem-normalized

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 75

  Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes

  arabidopsis bulk hierarchical gene

• Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

  PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

  peripheral white four gse75360 microarray gene weighted

• Integrative analysis of RUNX1 downstream pathways and target genes.

  PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

  Full-text index only

  Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

  lymphoblastic hela runx1 aml cdna microarray affymetrix

• Single-cell sequencing analysis and machine learning model reveal aberrant TIM-3 expression in microglia during Alzheimer's disease progression.

  PMID 41580850 · PMC12911240 · Journal of translational medicine · 2026 · 7 claims · 8 setups

  Full-text index only

  A TIM-3+ microglial subset drives AD pathogenesis through a dual mechanism: sustained neuroinflammation via TNF-α/NF-κB and IL-6/JAK/STAT3 signaling, and impaired amyloid-β clearance linked to PI3K-AKT and FcγR pathways

  brain overlapping transcriptomic patients single-cell bulk kegg

• Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder.

  PMID 41999209 · PMC13189858 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  DualCellChat, a directed heterogeneous graph autoencoder, reconstructs a complete and accurate CCI network from incomplete single-cell spatial transcriptomics

  visual hypothalamic olfactory breast single-cell cci benchmarking

• Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.

  PMID 41808435 · PMC13012599 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  Souporcell3 can robustly demultiplex pooled scRNA-seq data from up to 64 donors

  pooled scrna-seq doublet genotype-based umap-based