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).

Publications 1.3k Datasets 392.5k Experiments 701

Assay: time ✕ Clear

Approaching the genomics of risk-taking behavior.

PMID 20109660 · PMC3961474 · Advances in genetics · 2009 · 8 claims · 8 setups

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Candidate genes (e.g., DRD4, SERT, MAOA) explain only a small fraction of total genetic variation in risk-taking-related behaviors, motivating a whole-genome approach.

wild-caught three-spined sticklebacks open-field-like predator repeated-measures
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.

PMID 20064372 · PMC2892837 · Cell · 2009 · 8 claims · 8 setups

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A systematic yeast two-hybrid screen identified physical interactions between the 10 major PR8 influenza viral proteins and human proteins, implicating 87 human 'H1' proteins.

orfeome udorn bronchial hbecs yeast genome-wide sirna
Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

leukocytes leukocyte-derived archived comparison whole-genome quantitative snp
Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

saliva amplified extracted differentially genome quality extraction
Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems

hela jurkat exposed yeast quantitative antibody-based analog-sensitive
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
A genome-wide screen for copy number alterations in Aicardi syndrome.

PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

genomic subject array quantitative fluorescence
Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups

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Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2

genomic peripheral setx sanger dosage long-range
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

Has reproduction · 67

GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

oryza arabidopsis generic rna-seq workflow
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PMID 12962547 · PMC212256 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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RMA-generated gene expression values are markedly less variable and more reliable than MAS5.0- and MBEI-derived values

postmortem oligonucleotide real-time quality
The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

PMID 15661077 · PMC548512 · Respiratory research · 2005 · 6 claims · 3 setups

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IL-13 and IL-13R130Q modulate the same set of genes in human airway smooth muscle cells (HASMC)

airway hasmc cdna taqman flow
Angiotensin-converting enzyme gene insertion/deletion polymorphism in migraine patients.

PMID 18366776 · PMC2311324 · BMC neurology · 2008 · 6 claims · 3 setups

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ACE I/D genotype and allele distributions do not differ significantly between migraine patients and controls

genomic migraine pcr clinical
Germline mutations of the INK4a-ARF gene in patients with suspected genetic predisposition to melanoma.

PMID 14735200 · PMC2409576 · British journal of cancer · 2004 · 8 claims · 2 setups

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Seven germline INK4a-ARF changes (five novel) were found in 7 of 89 patients (8%) suspected of genetic predisposition to melanoma.

genomic pcr real-time
Limited clinical relevance of mitochondrial DNA mutation and gene expression analyses in ovarian cancer.

PMID 18842121 · PMC2571110 · BMC cancer · 2008 · 8 claims · 2 setups

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Somatic mutations in the mtDNA D-loop are found in 57% of ovarian cancer samples, mostly C-tract length changes and substitutions

ovarian sanger real-time
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

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Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

breast commercial vertebrate genes cdna activity computational
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

Has reproduction · 68

Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival

haploid pooled colony bulk pooled
SMAC, a computational system to link literature, biomedical and expression data.

PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

Has reproduction · 50

SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

pubmed invasive geo genes semantic computational gene
TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

PMID 34168290 · PMC8225889 · Communications biology · 2021 · 8 claims · 8 setups

Has reproduction · 85

TGF-β induces reprogramming of intracellular amino acid metabolism that is necessary to promote EMT in NSCLC cells

a549 metabolomics real-time western
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.

PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups

Has reproduction · 78

Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings

chinensis physiological relative bulk

Experiments

Approaching the genomics of risk-taking behavior.

A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.

Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

A genome-wide screen for copy number alterations in Aicardi syndrome.

Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

Angiotensin-converting enzyme gene insertion/deletion polymorphism in migraine patients.

Germline mutations of the INK4a-ARF gene in patients with suspected genetic predisposition to melanoma.

Limited clinical relevance of mitochondrial DNA mutation and gene expression analyses in ovarian cancer.

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

SMAC, a computational system to link literature, biomedical and expression data.

TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.