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).

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

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  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Impaired vitamin D signaling reveals neutrophils as key drivers of prostate cancer dissemination.

  PMID 41957119 · PMC13179334 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

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  Serum vitamin D (25(OH)D3) levels are negatively associated with PSA levels in prostate cancer patients

  pca dlvp prostate facs-isolated clinical genetic immunohistochemistry

• The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

  PMID 42011021 · PMC13096693 · Clinical and translational medicine · 2026 · 6 claims · 8 setups

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  KRAS-mutant LUAD patients show significantly poorer pathological response and inferior long-term survival after neoadjuvant immunotherapy compared to KRAS-wildtype patients

  resected resectable epithelial cd4t_treg_tnfrsf4 scrna-seq retrospective cnv

• Understanding the mechanisms of drug-associated interstitial lung disease.

  PMID 15340376 · PMC2750813 · British journal of cancer · 2004 · 8 claims · 7 setups

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  Apoptosis of alveolar/bronchial epithelial cells via Fas-FasL and mitochondrial (cytochrome c/caspase-9) pathways is a key mechanism underlying drug-, chemotherapy-, and radiation-associated lung injury and fibrosis

  bronchial lung swiss mice immunohistochemistry toxicology pulmonary

• Intra-Tissue Bacteriome and Cellular Profiles in Periodontal Granulation Tissue From Osseous Defects and Extraction Sockets.

  PMID 41732956 · PMC13086548 · Journal of clinical periodontology · 2026 · 7 claims · 6 setups

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  Osseous defect granulation tissue (GT) and inflamed gingival tissue (PT) exhibit periodontal health-associated, commensal-enriched bacteriome profiles, while root (RT) and socket (ST) granulation tissues show periodontopathogen enrichment and commensal depletion

  periodontal 16s subjects 16s single-cell histology

• A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

  PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

  patients bulk colorectal epithelial clinical bulk single-cell

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

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  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

  PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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  The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

  coli hep-2 pslm862 eaec colony hep-2 pcr

• Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

  PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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  S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

  enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes differentially spliced during SARS-CoV-2 infection show a similar functional (GO) profile to those differentially spliced in SARS-CoV and MERS infection, affecting a diverse set of genes tied to virus biology.

  mrc5 calu-3 nasal lung bulk

• Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

  PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

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  Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

  serum prns-1-1 n-linked maldi solid tandem

• Proteomic profiling in ovarian cancer.

  PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

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  No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

  serum tumor rolling mass microarray

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• Integrative analysis of RUNX1 downstream pathways and target genes.

  PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

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  Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

  lymphoblastic hela runx1 aml cdna microarray affymetrix

• Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

  PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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  FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

  armd dutch fibulin pef6-ssflag mutation computational site-directed

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.

  PMID 42013848 · PMC13198233 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Consensus meta-program (MP) expression patterns stratify LUAD patients with rare and reference oncogenic mutations into ICI-MP-H and ICI-MP-L subgroups reflecting differential predicted ICI benefit

  luad matched tcga epithelial single-cell multiplex bulk

• A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

  PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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  MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

  skin blister punch donor scrna-seq 250-plex seqfish