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).

• Differential diagnosis between chronic pancreatitis and pancreatic cancer: value of the detection of KRAS2 mutations in circulating DNA.

  PMID 12189555 · PMC2376157 · British journal of cancer · 2002 · 8 claims · 4 setups

  Full-text index only

  KRAS2 mutations are significantly more frequent in serum DNA of pancreatic cancer patients than chronic pancreatitis controls

  serum serum-extracted allele-specific fluorimetric immunoassay

• Discovering the phylodynamics of RNA viruses.

  PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

  Full-text index only

  A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

  h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome

• A single-cell survey of Drosophila blood.

  PMID 32396065 · PMC7237219 · eLife · 2020 · 8 claims · 6 setups

  Has reproduction · 94

  scRNA-seq of Drosophila larval hemocytes across unwounded, wounded, and wasp-infested conditions resolves 17 clusters spanning plasmatocytes, crystal cells, lamellocytes, and a non-hemocyte population.

  drosophila single-cell quantitative bulk

• The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue.

  PMID 28346411 · PMC5699924 · Nature medicine · 2017 · 8 claims · 8 setups

  Has reproduction · 78

  12,13-diHOME is a cold-induced lipokine that stimulates BAT activity

  plasma bat serum mice lc-ms correlation 18f-fdg

• Prospective health care: the second transformation of medicine.

  PMID 16522218 · PMC1431721 · Genome biology · 2006 · 8 claims · 7 setups

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  Predictive biomarkers (genomic, proteomic, metabolomic) will enable quantification of disease risk and anticipation of onset before pathological damage occurs.

  cancer circulating breast population gene-expression proteomic 21-gene

• miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

  PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  miEAA 2.0 extends miRNA enrichment analysis to ten species (previously only Homo sapiens), accepting both precursor and mature miRNA input.

  kidney blood model geo bulk small agilent

• A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.

  PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups

  Has reproduction · 62

  A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform

  pbmc bronchial nasal skin gene rna-seq

• 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

• Macrophage migration inhibitory factor and autism spectrum disorders.

  PMID 18676531 · PMC3816765 · Pediatrics · 2008 · 8 claims · 4 setups

  Full-text index only

  Functional MIF promoter polymorphisms (-794 CATT repeat and -173 G/C SNP) are genetically associated with ASD, particularly with stereotypical/repetitive behavior components

  asd plasma genetic sandwich

• Resistance to thyroid hormone with missense mutation (V349M) in the thyroid hormone receptor beta gene.

  PMID 18363280 · PMC2686955 · The Korean journal of internal medicine · 2008 · 8 claims · 7 setups

  Full-text index only

  The patient's resistance to thyroid hormone (RTH) was caused by a novel missense mutation (V349M, c.1045G>A) in exon 11 of the TRβ gene, the first such case reported in Korea.

  serum pituitary-thyroid thyroid sellar thyroid trh magnetic

• pyrpipe: a Python package for RNA-Seq workflows.

  PMID 34085037 · PMC8168212 · NAR genomics and bioinformatics · 2021 · 8 claims · 3 setups

  Has reproduction · 79

  pyrpipe enables development of flexible, reproducible, and easy-to-debug RNA-Seq computational pipelines purely in Python, in an object-oriented manner

  circulating zea bulk novo

• Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

  PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

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  Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

  generic simulated hiv-1 stochastic dynamic regression

• Cold-Induced Lipoprotein Clearance in Cyp7b1-Deficient Mice.

  PMID 35478959 · PMC9038073 · Frontiers in cell and developmental biology · 2022 · 7 claims · 8 setups

  Has reproduction · 83

  Cyp7b1 deficiency blunts cold-induced hepatic Cyp7b1 upregulation and plasma bile acid synthesis

  liver plasma interscapular bat qrt-pcr western bile

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 8 claims · 6 setups

  Has reproduction · 69

  An ensemble feature selection strategy using consensus of feature relevance across 8 classifier types identifies a 100-miRNA signature from a 1046-feature TCGA dataset

  tcga geo mirnas mirna feature bibliographic

• Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

  PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups

  Has reproduction · 76

  High expression of IFN-I signaling/response genes (IFNAR1, IFNAR2, STAT1, MX1, OAS1) predicts favorable relapse-free survival in B-ALL patients

  cog b-all eμ-myc crispra gene-expression-based flow mass

• Molecular markers for early detection of cervical neoplasia.

  PMID 15322318 · PMC3839269 · Disease markers · 2004 · 8 claims · 8 setups

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  HPV testing has very high negative predictive value but insufficient specificity as a stand-alone screening test, motivating the search for additional molecular markers of cervical neoplasia.

  serum plasma cervical elisa serum pcr

• Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

  PMID 16277682 · PMC1297578 · Arthritis research & therapy · 2005 · 6 claims · 4 setups

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  The M404V mutation in p62/SQSTM1 exon 8 segregates with the polyostotic form of PDB in the F01 Italian family

  genomic serum affected pcr pcr biochemical clinical

• Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

  PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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  277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

  umbilical ucb zebrafish microarray fluorescence-activated quantitative

• Adapting to a changing world: RAG genomics and evolution.

  PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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  RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

  rag-1 patients zebrafish vertebrate comparative site-directed clinical

• Genetics and proteomics: deciphering gene association studies in critical illness.

  PMID 16934133 · PMC1750993 · Critical care (London, England) · 2006 · 8 claims · 8 setups

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  Most critical illnesses are complex traits (multifactorial), unlike single-gene Mendelian diseases.

  severe families caucasian tnf genetic linkage microarray