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).

• PICDGI: A framework for predicting cancer driver genes through dynamic gene-gene interaction modeling of single-cell data.

  PMID 42044093 · PMC13119913 · PLoS computational biology · 2026 · 8 claims · 3 setups

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  PICDGI is a Bayesian framework that predicts driver-like regulatory genes by integrating dynamic gene-gene interaction modeling with scRNA-seq data, without using DNA mutation calls

  lung pediatric same scrna-seq moran's

• 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

• 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

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  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

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

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  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

  PMID 41933362 · PMC13173987 · BioData mining · 2026 · 8 claims · 7 setups

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  Single-cell analysis of integrated ovarian cancer datasets identifies 9 distinct mononuclear phagocyte clusters (MPC1-MPC9), of which MPC3, MPC5, and MPC7 are hypermetabolic

  ovarian mpc annotated tcga-oc single-cell gene pseudotime

• Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

  PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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  A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

  larc scrna-seq scissor+ single-cell bulk pseudotime

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial

• DAESC + : high-performance, integrated software for single-cell allele-specific expression data.

  PMID 41851619 · PMC13169709 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  DAESC+ is a dual-module, end-to-end software package (DAESC-P for preprocessing, DAESC-GPU for differential analysis) for single-cell ASE data

  onek1k endoderm simulated single-cell differential runtime

• An optimized protocol for efficient derivation of pancreatic islets from multiple human pluripotent stem cell lines.

  PMID 41997152 · PMC13163220 · Stem cell reports · 2026 · 8 claims · 8 setups

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  Shortening the S4 pancreatic progenitor stage duration enhances subsequent S5 endocrine progenitor (EP) differentiation efficiency

  hs980 hpsc-derived eight sc-islets flow static dynamic

• An artificial intelligence optimized hepatic differentiation unveils NR5A2 and AP-1 transcriptional regulation in hepatic maturation.

  PMID 41962865 · PMC13185932 · The Journal of biological chemistry · 2026 · 7 claims · 8 setups

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  A CNN-based AI algorithm trained on bright-field images of hepatic progenitor cells (HPCs) accurately predicts successful vs. failed differentiation without immunostaining or lineage tracing

  hpsc-derived hlcs cnn-based qpcr flow