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 161

System / cell line: reference ✕ Assay: genomic ✕ Clear

Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
A DNA microarray survey of gene expression in normal human tissues.

PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

normal common computational each two-color comparative unsupervised
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

PMID 18431496 · PMC2292242 · PloS one · 2008 · 8 claims · 4 setups

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South African HS:41 strains are clearly distinct from the other South African strains by comparative genomic analysis

clinical genomic jejuni multilocus microarray phylogenetic
A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

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Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

genomic hek293 hepg2 microsomes pcr site-directed luciferase
Enrichment of sequencing targets from the human genome by solution hybridization.

PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

genome genomic same technical capture solution-hybridization sequence
Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

PMID 15842735 · PMC1087844 · BMC medical genetics · 2005 · 7 claims · 3 setups

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MLPA was cheaper, more accurate and more precise than Real-Time PCR for detecting LDL receptor gene deletions

genomic real-time multiplex long-range
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 7 claims · 8 setups

Has reproduction · 86

HPVN24 is an avian pathogenic E. coli serotype O78:H9, sequence type ST23, with a 5.05 Mb genome and 50.57% GC content.

coli hpvn24 strain hemolysis antibiotic
A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

genomic genome pcr real-time fluorescence sequence
COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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COMP mutations were identified in 78% of families referred with PSACH

genomic sequence subset pcr bidirectional sequence
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

PMID 16887033 · PMC1559599 · BMC medical genetics · 2006 · 6 claims · 5 setups

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A multiplexed suspension bead array (Luminex) assay was developed to genotype 8 Ashkenazi-prevalent disease alleles including GBA c.1448T>C

genomic de-identified multiplex sanger clinical
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
Challenges and standards in integrating surveys of structural variation.

PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

genomic hapmap reference independent comparative snp fosmid
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide

Experiments

Analysis of copy number variation using quantitative interspecies competitive PCR.

A DNA microarray survey of gene expression in normal human tissues.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

Enrichment of sequencing targets from the human genome by solution hybridization.

Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

Personalized genomic medicine with a patchwork, partially owned genome.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

Challenges and standards in integrating surveys of structural variation.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.