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).

• Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

  PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

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  ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

  acl differentially study flow single-cell immunofluorescence

• Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.

  PMID 41593733 · PMC12918531 · Genome biology · 2026 · 8 claims · 5 setups

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  Generated the first single-cell transcriptome atlas (scRNA-seq + spRNA-seq) of grapevine leaves during P. viticola infection across four early time points (0, 3, 6, 12 hpi)

  vitis guard cabernet tissue-specific single-cell spatial pseudo-time

• Expression spectrum of TE-driven transcripts in human adult tissues.

  PMID 41593763 · PMC12924553 · Genome biology · 2026 · 8 claims · 8 setups

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  TE-driven transcripts are broadly expressed across human adult tissues and contribute to both housekeeping and tissue-specific gene regulation

  tissues paired sequences genome bulk differential chip-seq

• Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

  PMID 41599741 · PMC12845513 · Pharmaceuticals (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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  A PIGA-knockout (PIGA-KO) THP-1 cell model was successfully established using CRISPR/Cas9 RNP technology as a PNH model

  thp-1 literature-validated pnh cxcl8 crispr rt-qpcr bulk

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

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  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

  PMID 41620539 · PMC12916760 · Scientific reports · 2026 · 8 claims · 9 setups

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  76 overlapping genes were identified between COPD-associated DEGs and oxidative stress-related genes.

  lung genecards differentially bronchial bulk database functional

• Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

  PMID 41674383 · PMC12895067 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

  ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted

• Lactate metabolism-related interaction perturbation network enables robust stratification of hepatocellular carcinoma.

  PMID 41689750 · PMC13009326 · Discover oncology · 2026 · 8 claims · 8 setups

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  An LM-related gene interaction perturbation network can stratify HCC into four robust molecular subtypes (Cluster1-4)

  tcga-hcc gse76427 gene consensus immune

• Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

  PMID 41701761 · PMC12928580 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  Driver2Comm is a computational framework that identifies intrinsic-extrinsic (IE) pathways functionally connecting cancer cell driver genes with their associated CCC signatures in the TME using single-cell transcriptomics data.

  pdac genes tcga single-cell copy fisher's

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• Unravelling Synaptic and Metabolic Mechanisms of Cognitive Resilience in Asymptomatic Alzheimer's Disease Across Two Alzheimer's Disease Cohorts.

  PMID 41723778 · PMC12996523 · Cellular and molecular neurobiology · 2026 · 6 claims · 6 setups

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  Integrating DEG, DET, and DUT analyses (rather than DEGs alone) provides a more comprehensive view of the molecular mechanisms of AsymAD, since some genes/transcripts are only detected by transcript-level methods.

  postmortem combined ppi hippocampus bulk functional protein-protein

• pmid-41732268

  PMID 41732268 · PMC12925236 · 8 claims · 8 setups

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  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal

• pmid-41734278

  PMID 41734278 · PMC12975283 · 8 claims · 4 setups

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  RUMINA improves detection accuracy of ultra-low frequency SNVs (0.01%-1%) compared to UMI-tools and UMICollapse

  hiv simulated empirical clinical simulated umi iclip

• pmid-41736152

  PMID 41736152 · PMC13001359 · 7 claims · 8 setups

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  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

• pmid-41736863

  PMID 41736863 · PMC12927097 · 8 claims · 8 setups

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  A unified liver organoid cell atlas of 217,025 high-quality cells was constructed by integrating scRNA-seq data from 15 organoid samples across 9 studies with human fetal liver data (5-19 weeks gestation)

  liver fetal endoderm-derived mesoderm-derived scrna-seq pseudotime pearson

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

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

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  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

• SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

  PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

  gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish

• 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

• Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).

  PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups

  Has reproduction · 62

  TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR

  potato rna-seq gene alternative

• Identifying the important HIV-1 recombination breakpoints.

  PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

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  Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

  inter-subtype parental copy-choice probabilistic comparative