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).

• A big circuit model.

  PMID 12940284 · PMC1316925 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  In early prostate carcinogenesis, apoptosis signals are primarily suppressed rather than growth rate being increased.

  prostate blood model genes microarray proteomic gene

• Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

  PMID 28446242 · PMC5406893 · Genome medicine · 2017 · 7 claims · 6 setups

  Has reproduction · 92

  Breast tumors exhibit two discrete GFRN activity phenotypes: a 'survival phenotype' with concordant HER2/IGF1R/AKT activation and a 'growth phenotype' with concordant EGFR/KRAS(G12V)/RAF1/BAD activation, which are typically mutually exclusive.

  mammary tcga hmecs breast rna-sequencing pathway western

• Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

  PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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  A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

  nsclc 293t il-3-independent mutational site-directed cytokine-independence

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

  PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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  Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

  gingivalis whole-cell comparative gene

• 25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

  PMID 12631391 · PMC154153 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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  Growth factor signalling (EGF/HER-2/MAPK, AKT) phosphorylates the oestrogen receptor and drives development of endocrine-resistant breast cancer

  xenograft serum frozen tumour xenograft mass cdna

• Utilization of genomic signatures to identify phenotype-specific drugs.

  PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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  A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

  nci-60 breast mda-mb-231 signature-drug gene signature

• Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.

  PMID 16261191 · PMC1246807 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  A comprehensive stoichiometric model of the MAP was built comprising 197 metabolites, 219 reactions, and 28 proteins

  stoichiometric map tuberculosis flux systematic drug

• Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

  PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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  A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

  panel breast 250-gene candidate genome growth pathway

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones

  crc cetuximab-sensitive sirna ffpe western growth colony

• Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

  PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

  Has reproduction · 80

  928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

  burkholderia pseudomallei bulk tmt-based rt-qpcr

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• Backseat drivers take the wheel.

  PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

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  Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

  pretreatment baf3 additional normal targeted baf3 immunoprecipitation

• Genomics against flatulence.

  PMID 17635535 · PMC1974822 · Environmental microbiology · 2007 · 8 claims · 8 setups

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  Methanogenic archaea (not bacteria) in the human gut, chiefly Methanobrevibacter smithii, produce the methane component of intestinal gas, most of which is released via the large intestine (up to 0.5 l day−1) rather than in breath.

  methanobrevibacter fecal metallosphaera pyrobaculum whole-genome serial respiratory

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

  PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

  sparced mcf10a deterministic hybrid comparison

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

  PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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  A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

  tuberculosis mtb protein-protein flux transposon

• Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

  PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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  Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

  resected thymic previously mass dideoxynucleotide array

• Adaptation, aging, and genomic information.

  PMID 20157529 · PMC2806027 · Aging · 2009 · 8 claims · 6 setups

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  Aging is caused primarily by the absence of adaptive genomic information for later-age survival and function, due to declining forces of natural selection with adult age; this absence secondarily produces misallocation and damage at every level of biological organization.

  drosophila large animal unspecified experimental demographic hormone

• In vivo application of RNA interference: from functional genomics to therapeutics.

  PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups

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  RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA

  mice tumor laser-induced herpetic cationic intraperitoneal aqueous