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: sequences ✕ Assay: real ✕ Clear

The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

p493 rodent types quantitative chromatin northern
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

drosophila genome melanogaster real-time comparative gfp
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

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CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

randomly real human-chimpanzee simulated simulation comparative
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

paired colorectal genome normal quma auma bioinformatic
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

real combined pre-mirna training random independent repeated
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
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
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

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A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

cervix same spotted quantitative
Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

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Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

mcf7 promoter cdna quantitative computational
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

Has reproduction · 50

MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

bovine simulated cami trimming decontamination assembly
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups

Has reproduction · 83

MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences

simulated mock16 real snailgut novo transcript gene
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

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MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

mcf7 hct116 flcdna gis-pet chip-pet quantitative
Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

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All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation
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
HIV-1 sequence evolution in vivo after superinfection with three viral strains.

PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

blood seminal pbmcs biological strain-specific bulk in-house
The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

strongylocentrotus sprej purpuratus full-length cdna secondary real-time
Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

PMID 18957099 · PMC2582241 · Malaria journal · 2008 · 7 claims · 8 setups

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pfhrp2 and pfhrp3 genes show markedly higher polymorphism than the P. falciparum and P. vivax aldolase and pldh genes

falciparum vivax extracted febrile pcr nested species-specific

Experiments

The distribution of SNPs in human gene regulatory regions.

An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Genome assembly comparison identifies structural variants in the human genome.

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

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

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

HIV-1 sequence evolution in vivo after superinfection with three viral strains.

The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.