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).

• 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

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• 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

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups

  Has reproduction · 75

  geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data

  stool deduplicated reference whole-genome taxonomic functional

• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

  PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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  Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

  mda-mb231 epithelial breast early-stage cdna quantitative facs

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• Innate immune modulation by RNA viruses: emerging insights from functional genomics.

  PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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  Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

  embryonic liver brain serial gene-expression computational

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups

  Has reproduction · 50

  A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation

  pre-treatment domingo geo bulk bulk external spatial

• Early days: genomics and human responses to infection.

  PMID 16679048 · PMC7108404 · Current opinion in microbiology · 2006 · 8 claims · 8 setups

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  DNA microarray-based transcript profiling of primate/human responses to infection has begun to yield new insights into host-pathogen interactions but is limited by unresolved methodological challenges.

  peripheral liver gastric brain microarray

• Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

  PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

  genomic postmortem nimhgi esr1 targeted case-control family-based

• Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

  PMID 26969729 · PMC4812528 · Molecular systems biology · 2016 · 7 claims · 6 setups

  Has reproduction · 67

  Cell adhesion (cell-cell and cell-ECM) pathways are significantly and consistently dysregulated in women who develop familial breast cancer across multiple omic data types and tissues.

  peripheral pbmcs normal snap-frozen gene exome western

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• 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

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A 15-gene immune infiltration-related signature (IRS) predicts overall survival in breast cancer, with higher IRS indicating worse prognosis

  tcga metabric geo breast immune bulk microarray