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).

• GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

  PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 96

  gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

  avian comparative correlation robustness

• Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.

  PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Has reproduction · 67

  Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.

  kyse150 bulk rna-seq-based differential

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

  PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

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  PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

  pancreatic same tumor pet sscp methylation-specific microsatellite

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

  PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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  PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

  hpv clinical biotinylated pcr mip molecular microarray

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

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

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

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  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

• GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

  PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

  ligand gpcr glida principal sequence gene

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

  PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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  TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

  pooled hcec-dm corneal 2-d western real-time

• Managing incidental findings in human subjects research: analysis and recommendations.

  PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

  Full-text index only

  Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

  affected large research consent linkage genomic structural

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Identification of Molecular Subtypes of Clear-Cell Renal Cell Carcinoma in Patient-Derived Xenografts Using Multi-Omics.

  PMID 40282537 · PMC12026142 · Cancers · 2025 · 8 claims · 7 setups

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  Each ccRCC PDX resembles one of the human molecular subtypes closely at both the transcript and protein levels.

  ccrcc differentially bulk lc-ms targeted

• Mutational landscape and molecular bases of echinocandin resistance in Saccharomyces cerevisiae.

  PMID 41766466 · PMC13147539 · Genetics · 2026 · 8 claims · 5 setups

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  The three echinocandin resistance hotspots of Fks1 form a single, solvent-exposed, water-filled binding cavity spanning hotspot 1, 2, and 3

  fks1 cerevisiae fks explicit-solvent site-directed deep-mutational

• Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson's and inflammatory bowel disease.

  PMID 41545356 · PMC12847817 · NPJ Parkinson's disease · 2026 · 8 claims · 5 setups

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  Spatial single-cell multiomic imaging of sigmoid colon reveals both shared and unique features of peripheral immune dysfunction in PD and IBD

  sigmoid plasma stool epithelial cosmx meso gene

• Therapeutic synergies that overcome carboplatin resistance in triple-negative breast cancer.

  PMID 41630032 · PMC13037280 · Journal of experimental & clinical cancer research : CR · 2026 · 8 claims · 8 setups

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  Four isogenic carboplatin-resistant (CR) PDX pairs (WHIM30, BCM-2147, BCM-3887, BCM-7482) were generated via serial in vivo carboplatin exposure to model acquired resistance in TNBC

  isogenic pdx ffpe carboplatin-resistant bulk single-cell nuclear

• Rete ridges form via evolutionarily distinct mechanisms in mammalian skin.

  PMID 41639458 · PMC12959975 · Nature · 2026 · 8 claims · 8 setups

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  Rete ridges form through a mechanism independent from hair follicles and sweat glands, via interconnected epidermal invaginations

  trunk pig multispecies gw12 histology comparative immunostaining