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 36

System / cell line: previously ✕ Assay: analysis ✕ Clear

The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

tumor ovarian kgn high sanger taqman
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Investigating the genetic association between ERAP1 and ankylosing spondylitis.

PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

patients cases genotype comparison snp meta-analysis resequencing
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
Analysis of X chromosome inactivation in autism spectrum disorders.

PMID 18361425 · PMC4867005 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 6 claims · 5 setups

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No significant excess of skewed XCI was found in mothers of children with ASD or in affected girls compared to controls

genomic multiplex mecp2 four chromosome non-parametric mutation
Shotgun metagenomic analysis of the oral microbiomes of children with noma.

PMID 41860897 · PMC13029773 · PLoS neglected tropical diseases · 2026 · 8 claims · 6 setups

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Noma oral microbiomes show marked dysbiosis with significant enrichment of Treponema, Porphyromonas, and Bacteroides, and depletion of Streptococcus and Rothia, compared to healthy controls

oral saliva noma previously shotgun comparative metagenome
Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

PMID 11104560 · PMC2363466 · British journal of cancer · 2000 · 8 claims · 2 setups

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MBD4 mutations occur in 89% (17/19) of RER+ sporadic colorectal carcinomas when microdissected tumor sites are analyzed

microdissected frozen pcr comparison
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.

PMID 33777521 · PMC7977378 · PeerJ · 2021 · 8 claims · 1 setups

Has reproduction · 95

nf-core/eager is a complete redesign and extension of the EAGER pipeline in Nextflow, built within the nf-core framework to ensure high-quality, sustainable software development.

skeletal whole-genome
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 96

gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

avian comparative correlation robustness
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

otx sea elegans endo16 windowed reporter comparative
Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

nsclc matched lung quantitative pcr genomic
Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

PMID 17324265 · PMC1810516 · BMC medical genetics · 2007 · 8 claims · 3 setups

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Developed a real-time TaqMan PCR method that quantifies PARK2 exon 1-12 copy number by comparing amplification signal to the β-globin internal control gene

genomic same real-time prior
Cell Specific eQTL Analysis without Sorting Cells.

PMID 25955312 · PMC4425538 · PLoS genetics · 2015 · 7 claims · 4 setups

Has reproduction · 90

A genotype x predicted-cell-count interaction (GxE) meta-analysis across whole blood datasets can detect neutrophil-specific cis-eQTLs without cell sorting

blood neutrophils cis-eqtl cell-count rna-seq
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Genomic organization of zebrafish microRNAs.

PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

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Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

zebrafish candidate hairpin blast secondary comparative
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

normal prostate microarray cdna cross-tissue gene
TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

ovarian sporadic paraffin-embedded mutation survival extraction
SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

chromosome 16p array probe-by-probe sw-array

Experiments

The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

Molecular analysis of Plasmodium ovale variants.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Investigating the genetic association between ERAP1 and ankylosing spondylitis.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Analysis of X chromosome inactivation in autism spectrum disorders.

Shotgun metagenomic analysis of the oral microbiomes of children with noma.

Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

Cell Specific eQTL Analysis without Sorting Cells.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Genomic organization of zebrafish microRNAs.

Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.