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).

• Cell-type annotation with accurate unseen cell-type identification using multiple references.

  PMID 37379341 · PMC10335708 · PLoS computational biology · 2023 · 8 claims · 4 setups

  Has reproduction · 68

  mtANN integrates multiple reference datasets and eight gene selection methods via ensemble learning (multiple deep classification models + majority voting) to improve cell-type annotation accuracy

  pbmc pancreas covid-19 scrna-seq

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 4 setups

  Has reproduction · 67

  Removal of batch effects in reference scRNA-seq datasets (via Harmony-Symphony) benefits the task of cell composition deconvolution

  pbmc derived tcga-lihc scrna-seq simulated bulk

• Rare variant analyses provide insights into the genetic architecture of endometriosis.

  PMID 41736152 · PMC13001359 · Human genomics · 2026 · 7 claims · 8 setups

  Full-text index only

  Gene-based burden testing of rare LoF and deleterious missense variants identifies SOGA1 as significantly associated with endometriosis after Bonferroni correction

  unrelated finngen biobank soga1 exome gene-based protein-protein

• PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

  PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

  Full-text index only

  PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

  pah scrna-seq pah-former candidate scrna-seq transfer perturbation

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

  Has reproduction · 95

  Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

  kidney live blood snrna-seq snatac-seq bulk

• Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

  PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

  renal kidney pbmc heart scrna-seq snrna-seq snatac-seq

• 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

• Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

  PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

  Full-text index only

  cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

  discoideum single-cell scrna-seq dissecting

• 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

• Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

  PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

  brain hippocampus neuronal bulk trade gene

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

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

  Full-text index only

  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

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

  PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

  Has reproduction · 75

  rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

  saccharomyces model ribose-seq emriboseq rhii-hyden-seq

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

  Full-text index only

  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data.

  PMID 41549280 · PMC12838065 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  TSniffer is a novel tool that uses a rolling window Fisher's exact test approach to identify RNA editing sites (TsRegions) de novo in RNA-seq data without relying on editing databases or two-sample differential comparison.

  type hela mm10 brain rna-seq genomic database

• Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

  PMID 41811178 · PMC12978698 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  Cell type-specific Bayesian and co-expression networks generated from BMSC-OB scRNA-seq data in Diversity Outbred mice can prioritize and contextualize genes underlying human BMD GWAS associations

  bmsc-ob genes mesenchymal gtex scrna-seq cellect iterativewgcna

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

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

  Full-text index only

  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

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

  liver mm39 bulk single-nuclei ahr