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).

• SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data.

  PMID 42015285 · PMC13231777 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  SpaNiche integrates smoothed cell-type abundance and ligand-receptor expression matrices via graph-regularized joint NMF, across multiple spatial views, to identify colocalization patterns

  lymph colorectal prostate cerebral simulated spatial scrna-seq

• An "omics" approach to uropathogenic Escherichia coli vaccinology.

  PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

  Full-text index only

  An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

  upec vaccination comparative two-dimensional

• Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

  PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

  Full-text index only

  Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

  ceacam1 meningitidis influenzae ha3 homology site-directed receptor

• Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

  PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

  Full-text index only

  Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

  mcf7 promoter cdna quantitative computational

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

  Full-text index only

  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

  Full-text index only

  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

  PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

  ensembl genomic simulation pcr maldi-tof

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

  PMID 18697827 · PMC3711528 · Journal of medical genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Four novel JARID1C mutations (p.A77T, p.V504M, p.E468GfsX2, p.R1481GfsX9) were identified in males with mental retardation across three screened cohorts.

  genomic family carrier jarid1c dhplc allele-specific restriction

• Single cell profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

  PMID 42023148 · PMC13097095 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  PCNSL and sDLBCL contain five distinct malignant B-cell subtypes (B0-B4) with discrete differentiation trajectories

  pcnsl malignant bulk sdlbcl scrna-seq infercnv cytotrace2

• Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

  PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 20

  AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

  ipf common key rats microarray network protein-protein

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

  Full-text index only

  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Maternal Fine Particulate Matter Exposure Impairs Inguinal White Adipose Tissue Plasticity in Middle-Aged Male Mouse Offspring.

  PMID 41648986 · PMC12918713 · ACS nano · 2026 · 7 claims · 8 setups

  Full-text index only

  Maternal PM2.5 exposure induces insulin resistance in middle-aged male (but not female) offspring despite normal body weight/obesity status

  pregnant iwat adsc whole-body body histology

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  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

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

  Full-text index only

  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data.

  PMID 41484206 · PMC12905373 · EMBO molecular medicine · 2026 · 6 claims · 7 setups

  Full-text index only

  INS R6C is a recessive loss-of-function mutation causing diabetes only in homozygous individuals, not a dominant mutation as previously classified.

  blood serum large-scale computational targeted autoantibody population

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

  PMID 42108258 · PMC13158306 · Signal transduction and targeted therapy · 2026 · 8 claims · 5 setups

  Full-text index only

  iS2C2 integrates the S2C2 cell-cell communication algorithm with LLMs to generate biologically interpretable hypotheses from scRNA-seq and spatial transcriptomics data

  single-cell algorithm domain scrna-seq single-cell perturbation llm-based

• 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

• The Proteomic Code: a molecular recognition code for proteins.

  PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

  Full-text index only

  The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

  anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide