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 6

System / cell line: algorithm ✕ Assay: direct ✕ Clear

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Evaluation of two methods for computational HLA haplotypes inference using a real dataset.

PMID 18230173 · PMC2268655 · BMC bioinformatics · 2008 · 8 claims · 5 setups

Full-text index only

PHASE v2.1.1 had the best overall performance in both haplotype construction and frequency calculation compared to Arlequin V3.0

genotypic unrelated computational direct
MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

PMID 32256520 · PMC7089958 · Frontiers in genetics · 2020 · 8 claims · 5 setups

Has reproduction · 50

MasterOfPores is a scalable, parallelizable, containerized (Docker/Singularity) NextFlow workflow for analyzing Oxford Nanopore direct RNA sequencing datasets

cerevisiae barcoded direct polya modification
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

Full-text index only

Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
An integrated genomic analysis of human glioblastoma multiforme.

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

Full-text index only

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 response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

Full-text index only

Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original

Experiments

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Evaluation of two methods for computational HLA haplotypes inference using a real dataset.

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

An integrated genomic analysis of human glioblastoma multiforme.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.