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 77

System / cell line: across ✕ Assay: matched ✕ Clear

mtDNA nt13708A variant increases the risk of multiple sclerosis.

PMID 18270557 · PMC2217590 · PloS one · 2008 · 8 claims · 5 setups

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The mtDNA nt13708 G/A polymorphism (nt13708A allele) is significantly associated with increased risk of MS (OR=1.71, P=0.0002) across three well-matched European cohorts.

peripheral pooled mtdna snp meta-analysis complete
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 6 setups

Has reproduction · 67

An individualized Bayesian causal discovery framework can learn tumor-specific intercellular communication networks (ICNs) by combining single-cell gene expression module (GEM) discovery, bulk tumor deconvolution, and individualized causal network learning.

hnscc cd45+ cd8+ tcga single-cell bulk pseudo-time
Allelotype of squamous cell carcinoma of the head and neck: fractional allele loss correlates with survival.

PMID 7577465 · PMC2033926 · British journal of cancer · 1995 · 7 claims · 4 setups

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Allelic imbalance/LOH occurs most frequently on chromosome arms 3p, 9p, 17p and 18q (>45% LOH) in SCCHN

scchn subset microsatellite fractional survival
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups

Has reproduction · 53

A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.

metastatic top breast tnbc single-cell functional mutational
Metatranscriptomics of the human oral microbiome during health and disease.

PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

Has reproduction · 62

Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

patient-matched subset health rna-seq rrna comparison metatranscriptomics
A mutation in GJA8 (p.P88Q) is associated with "balloon-like" cataract with Y-sutural opacities in a family of Indian origin.

PMID 18587493 · PMC2435161 · Molecular vision · 2008 · 6 claims · 4 setups

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A heterozygous c.262C>A mutation in GJA8 (connexin 50), causing p.P88Q, is associated with a novel 'balloon-like' cataract phenotype with prominent Y-sutural opacities in an Indian family.

lens family genomic clinical family pcr
Chromosome alterations and E-cadherin gene mutations in human lobular breast cancer.

PMID 10584868 · PMC2374316 · British journal of cancer · 1999 · 8 claims · 5 setups

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LOH at chromosome 16q21-q22.1 occurs in 100% of informative lobular breast tumours, the highest frequency of any region tested

lobular pcr loh loh pcr-sscp sequencing
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
Performance of mitochondrial DNA mutations detecting early stage cancer.

PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

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The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

matched blood mtdna low-quantity mitochondrial capillary str
Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

PMID 18281252 · PMC2443276 · Carcinogenesis · 2008 · 7 claims · 4 setups

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Cigarette smoking is associated with a higher frequency of somatic mtDNA mutations in buccal cells

buccal subject ttge real-time pcr-based
Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

PMID 18621558 · PMC2697027 · European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery · 2008 · 8 claims · 3 setups

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AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals

aaa cases candidate genome-wide
Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

Has reproduction

Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics
Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 7 setups

Has reproduction · 49

S100A3 shows consistent discriminatory performance across the training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort

blood degs bulk single-gene gene
Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

sporadic msi-positive tumour unstable microsatellite denaturing sequencing
Development of a fluorescent multiplex assay for detection of MSI-High tumors.

PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry
Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

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Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

eye genomic tnnt1 cdna genomic snp
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

pancreatic computational targeted prevalence snp
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

matched excised additional formalin-fixed 2-d lc-ms quantitative

Experiments

mtDNA nt13708A variant increases the risk of multiple sclerosis.

An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

Allelotype of squamous cell carcinoma of the head and neck: fractional allele loss correlates with survival.

Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

Metatranscriptomics of the human oral microbiome during health and disease.

A mutation in GJA8 (p.P88Q) is associated with "balloon-like" cataract with Y-sutural opacities in a family of Indian origin.

Chromosome alterations and E-cadherin gene mutations in human lobular breast cancer.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Performance of mitochondrial DNA mutations detecting early stage cancer.

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

Development of a fluorescent multiplex assay for detection of MSI-High tumors.

Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

An integrated genomic analysis of human glioblastoma multiforme.

A comprehensive catalogue of somatic mutations from a human cancer genome.

Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.