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 42

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

TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

Has reproduction · 59

382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

semibalanus individual rocky barnacles pool-seq sanger temperature
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
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
Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

genomic pools training siddt individual pooled k-correction
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

pooled genome est novel tandem whole-genome est
A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

PMID 19823678 · PMC2757911 · PloS one · 2009 · 6 claims · 4 setups

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SLC10A2 is a novel susceptibility gene for cholelithiasis in humans

genomic pooled sanger maldi-tof genotype-phenotype
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

pooled genomic aneuploid dog mlga
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

hepatocellular p53 genomic hepatoma array-based pooled shrna
Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

normal aneuploid same genomiphi-amplified array-cgh
An optimized procedure for the design and evaluation of Ecotilling assays.

PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

genomic gene pcr cdna ecotilling sequence sanger
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
VarDetect: a nucleotide sequence variation exploratory tool.

PMID 19091032 · PMC2638149 · BMC bioinformatics · 2008 · 8 claims · 2 setups

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VarDetect is a stand-alone software tool that automatically detects nucleotide variation (SNPs) from fluorescence-based chromatogram traces using pre-calculated peak content ratios and artifact-handling rules.

genomic vardetect automatic software
Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

PMID 16055919 · PMC1182175 · Nucleic acids research · 2005 · 7 claims · 5 setups

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MDA genotyping call rates and accuracy are only marginally lower than for genomic DNA

genomic same monozygotic subset genome-wide genome
Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence

genomic driver coli individual whole-genome subtractive cloning
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

genomic gonystylus subset restriction-digested custom self-self blast
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

genomic domestic pooled colorectal snp pooling microsatellite
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal

Experiments

TEMP: a computational method for analyzing transposable element polymorphism in populations.

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

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

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

An optimized procedure for the design and evaluation of Ecotilling assays.

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

VarDetect: a nucleotide sequence variation exploratory tool.

Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

Paired-end mapping reveals extensive structural variation in the human genome.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.