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).

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

  PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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  Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

  genome genomic chromosome randomization

• SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

  PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

  melanocortin same paired test chromatogram tracediff weak

• Familial parkinsonism: study of original Sagamihara PARK8 (I2020T) kindred with variable clinicopathologic outcomes.

  PMID 18804399 · PMC2702757 · Parkinsonism & related disorders · 2009 · 6 claims · 4 setups

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  The same LRRK2 I2020T mutation can produce diverse neuropathologies (pure nigral degeneration, Lewy body pathology, or MSA-P) even when clinical presentation and PET findings are virtually identical across family members.

  living post-mortem pet neuropathologic immunohistochemistry

• The role of X-chromosome inactivation in female predisposition to autoimmunity.

  PMID 11056674 · PMC17816 · Arthritis research · 2000 · 6 claims · 2 setups

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  Skewed X-chromosome inactivation in the thymus could lead to inadequate thymic deletion of T cells reactive to X-linked polymorphic self-antigens, predisposing to autoimmunity

  peripheral fluorescent pcr

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

  PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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  Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

  lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

• A clinical genetic method to identify mechanisms by which pain causes depression and anxiety.

  PMID 16623937 · PMC1488826 · Molecular pain · 2006 · 8 claims · 4 setups

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  Pain-triggered depression/anxiety are mediated by distinct spino-parabrachial-hypothalamic-amygdalar neurochemical pathways compared to mood disorders independent of pain

  sciatica genomic snp sf-36 candidate-gene exploratory

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Conservation, variability and the modeling of active protein kinases.

  PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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  A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

  active-conformation same chak rio2 sequence-order pairwise structural

• RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

  PMID 19789336 · PMC2927135 · Cancer research · 2009 · 8 claims · 8 setups

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  K-RAS and N-RAS mutation status differentially determine the level of TNFα-induced apoptosis in an isogenic colon carcinoma cell panel

  isogenic same conditioned dld-1 flow luminex immunoblot