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).

• Technical challenges in using human induced pluripotent stem cells to model disease.

  PMID 19951687 · PMC2921621 · Cell stem cell · 2009 · 8 claims · 8 setups

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  hiPSCs generated from patient somatic cells (skin, blood) can be differentiated into disease-relevant cell types to model disease pathogenesis in vitro

  ipscs humanized hemophilia parkinsonian tetraploid transplantation neuronal

• 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

• Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

  PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  JMJD6 is an epigenetic vulnerability/fitness gene in RCC, identified by integrating GeCK CRISPR screening data with TCGA/ICGC RCC cohorts.

  tumor rcc 786-o balb crispr mtt sirna

• Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

  PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

  Has reproduction · 79

  TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

  cecum fecal shotgun humann

• A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence With Existing Human Data.

  PMID 41566898 · PMC12824456 · Brain and behavior · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Chronic stress induces a robust, cross-paradigm PFC transcriptional signature characterized by downregulation of glia/myelin and vascular pathways and suppression of immediate-early gene activity

  c57 c57bl post-weaning pfc microarray rna-seq random

• Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

  PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups

  Has reproduction · 77

  Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.

  appswe app gut 16s open picrust2

• Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

  PMID 29907695 · PMC6068466 · The EMBO journal · 2018 · 8 claims · 8 setups

  Has reproduction · 46

  B16F1 and B16F10 melanoma subclones functionally exchange EVs in vivo, transferring Cre mRNA cargo detectable via a Cre-LoxP color-switch reporter system

  co-injected b16f1 locally 16.5k intravital cre-loxp rt-pcr

• The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

  PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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  Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

  fecal postnatal luminal pooled 16s shotgun body

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master

• Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.

  PMID 40276518 · PMC12018310 · Frontiers in immunology · 2025 · 7 claims · 6 setups

  Has reproduction

  Intrinsic microbiota (chiefly genera Burkholderia and Ralstonia) reside in the heart and liver of SPF mice, with the heart having lower bacterial abundance than the liver

  spf heart ileum metagenomic culturomics 16s

• Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.

  PMID 37602956 · PMC10548174 · The EMBO journal · 2023 · 6 claims · 5 setups

  Has reproduction · 91

  E14.5 DFPs have a repressed transcriptional profile marked by high H3K27me3 and inaccessible chromatin at lineage-specific genes

  skin dermal single-cell chamber chip-seq

• msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.

  PMID 36123620 · PMC9487059 · BMC bioinformatics · 2022 · 6 claims · 8 setups

  Has reproduction · 100

  msPIPE is a new end-to-end pipeline integrating pre-processing, alignment & methylation calling, and downstream DNA methylation analysis (profiling, HMR, DMR, functional enrichment) with publication-quality figure output for WGBS data

  blood rod sperm old wgbs hypomethylated differential

• Toxicogenomics research consortium sails into uncharted waters.

  PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

  strains nervous mice liver microarray gene toxicogenomic

• 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

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.

  PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)

  ipf degs differentially bleomycin-induced bulk methylation kegg

• Two committees tackle toxicogenomics.

  PMID 12501852 · PMC1241123 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  NIEHS funded a $37 million, five-year Toxicogenomics Research Consortium (TRC) linking the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to coordinate gene-expression research on environmental health effects.

  strains nervous mice liver microarray gene toxicogenomic

• Genetics of osteoarticular disorders, Florence, Italy, 22-23 February 2002.

  PMID 12223106 · PMC128940 · Arthritis research · 2002 · 8 claims · 8 setups

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  OP and OA are common, polygenic, multifactorial quantitative disorders influenced by both low-penetrance genetic variants and environmental factors

  patients twin families dutch association magnetic genome-wide

• Gene losses during human origins.

  PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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  A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

  pseudogene chimpanzee human-specific population comparative phylogenetic fisher's

• Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

  PMID 20031542 · PMC3097376 · Circulation. Cardiovascular genetics · 2008 · 7 claims · 8 setups

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  Rare Mendelian mutations (e.g., in sarcomere genes, ion channels, FBN1, LMNA) cause specific rare cardiovascular conditions (hypertrophic/dilated cardiomyopathy, long-QT syndrome, thoracic aortic aneurysm, progeria) but explain little of common CVD risk.

  community-based subjects dallas mice exon community-based gene