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).

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

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  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• 93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

  PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

  breast laser serum bladder cdna western seldi-tof

• Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

  PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

  peripheral hippocampal spinal peritumoral microarray protein-protein

• Current and future directions in genomics of amyotrophic lateral sclerosis.

  PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes by a discriminative index (DI) score representing classification power for distinguishing given groups, enabling intuitive selection of optimal biomarker genes.

  tcga melanoma lung head bulk single-cell rna-seq

• Tissue compartment analysis for biomarker discovery by gene expression profiling.

  PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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  TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

  kidney pure serial rt-pcr sage histo-morphometry

• 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

• A European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

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  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.

  cx3cr1-mφca-rep mcrfp-rep cx3cr1-mφgfp-rep peritoneal multi-photon confocal imaging

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups

  Has reproduction · 66

  Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.

  prostate pca bulk reverse ssgsea

• The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

  PMID 14580250 · PMC314415 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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  ADH and ductal carcinoma in situ (DCIS) are precursor lesions molecularly similar to adjacent invasive breast cancer

  locally adh brca1 malignant array chromosome-based cdna

• High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

  PMID 16432260 · PMC1345698 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  A 96-well high-throughput bisulfite modification (HTBM) method was developed and validated against single-sample bisulfite modification (SSBM), producing comparable methylation results even from as little as 3 ng DNA.

  genomic normal advanced bisulfite-treated methylation-specific bisulfite snp

• Role of FGFR3 in urothelial cell carcinoma: biomarker and potential therapeutic target.

  PMID 17912529 · PMC4876910 · World journal of urology · 2007 · 8 claims · 8 setups

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  Activating FGFR3 mutations occur frequently in bladder cancer and are strongly associated with low tumour grade and stage

  bladder normal urothelial mutation allele-specific laser

• QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

  PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

  pubmed ucsc laser-captured literature genome comparative

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman

• L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

  PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

  Has reproduction · 74

  L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

  coli growth crystal colony

• Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.

  PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.

  th-cre awake ibat plasma retrograde chemogenetic indirect