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).

• Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

  PMID 41680825 · PMC12998095 · Biology direct · 2026 · 8 claims · 8 setups

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  A 48-gene cross-species hypertension (HTN) gene module identified from human and SHR rat scRNA-seq can classify ccRCC patients into two molecular subgroups with distinct survival and targeted therapy response

  aortic spontaneously tcga icgc single-cell bulk summary-data-based

• Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

  PMID 41736867 · PMC12927306 · iScience · 2026 · 8 claims · 8 setups

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  NARVI, a deep neural network trained on expression-velocity relationships of passed genes, can impute RNA velocity for dropped genes that conventional tools (e.g., scVelo, UniTVelo) fail to calculate

  hematopoietic lung erythroid bone scrna-seq cross-validation

• A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

  PMID 34140473 · PMC8211662 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 90

  The human post-implantation epiblast transitions from a naïve to a primed pluripotent state, with naïve markers (KLF4, KLF17, PRDM14, etc.) downregulated and primed markers (FGF2, DNMT3B, SOX11, etc.) upregulated between pre- and post-implantation stages

  embryo embryos single-cell logistic immunofluorescence

• Decoding the heterogeneity of human undifferentiated spermatogonia reveals RAS-dependent regulation of stem cell fate.

  PMID 41579373 · PMC13003925 · Cell reports · 2026 · 8 claims · 7 setups

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  FSD1 is a cell-surface pan-uSPG marker that enables FACS purification of the entire uSPG population

  testis seminiferous testicular fsd1+ single-cell immunofluorescence whole-mount

• scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

  PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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  scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

  single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type

• Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model.

  PMID 36321803 · PMC9708074 · eLife · 2022 · 7 claims · 5 setups

  Has reproduction · 72

  Follicle cell-specific Lgl knockdown (Lgl-KD) causes loss of apical-basal polarity and invasive multilayering of the follicular epithelium without long-distance metastasis

  drosophila single-cell bulk immunofluorescence

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.

  PMID 41622528 · PMC12916010 · Molecular biology and evolution · 2026 · 7 claims · 8 setups

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  Cattle and yak testes contain seven types of spermatogonia, ten spermatocyte subtypes, and ten spermatid types with largely conserved transcriptional programs governing spermatogenic fate transitions.

  testicular spermatocytes spermatids bc1 single-cell chromosome hematoxylin

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

  PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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  H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

  tumor hnacc epithelial accb single-cell scrna-seq copy

• Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR.

  PMID 41771837 · PMC12953643 · Signal transduction and targeted therapy · 2026 · 8 claims · 8 setups

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  KLF15 transcriptional activity shows the most significant change among TFs in pathological cardiomyocytes during progressive hypertrophic remodeling, reflecting less effective repression of disease-associated genes.

  ventricular heart cardiomyocytes cardiomyocyte single-cell rt-qpcr bulk

• Partially shared multi-modal embedding learns holistic representation of cell state.

  PMID 41741805 · PMC13021527 · Nature computational science · 2026 · 8 claims · 5 setups

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  APOLLO automatically learns partial information sharing between multiple data modalities using an autoencoder with a partially overlapping latent space trained via latent optimization.

  simulated paired single simulation scrna-seq multiplexed

• Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

  PMID 39730911 · PMC11681178 · Communications biology · 2024 · 8 claims · 8 setups

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  EMT involves temporal, stage-specific metabolic reprogramming with distinct dependencies in glycolysis and glutamine metabolism.

  a549 recon1 cancer lung bulk single-cell genome-scale

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• Sequential RNA polymerase II activation drives human hematopoiesis.

  PMID 41520338 · PMC13067999 · Cell reports · 2026 · 7 claims · 7 setups

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  sciCUT&Tag2in1 enables simultaneous single-cell combinatorial-indexing profiling of Pol II occupancy (Ser5/Ser2-phospho CTD) together with histone modifications (H3K4me1-2-3 or H3K27me3) in up to 50,000 cells per experiment

  g-csf-mobilized cd34+ 10-donor lineage-depleted scicut&tag2in1 individual souporcell

• Dissecting gene regulatory networks governing human cortical cell fate.

  PMID 41565813 · PMC12999477 · Nature · 2026 · 8 claims · 6 setups

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  ZNF219, a previously uncharacterized transcription factor, represses neural differentiation in human cortical radial glia

  cortical rhesus single-cell scrna-seq immunocytochemistry

• Autophagy Activators Normalize Aberrant Tau Proteostasis and Rescue Synapses in Human Familial Alzheimer's Disease iPSC-Derived Cortical Organoids.

  PMID 41591759 · PMC13042409 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 7 setups

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  An optimized CO differentiation protocol (Protocol 2, using 50% E6/50% hESC medium with constant rocking/orbital shaking) produces reproducible, larger, lower-necrosis organoids with consistent size across genotypes

  isogenic scrna-seq fixed cos single-cell pseudotime immunofluorescence

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups

  Has reproduction · 59

  TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene

  cd8+ tce manual gene principal

• Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

  PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups

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  New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach

  hela automated stepwise training-set-size