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 105

System / cell line: same ✕ Assay: genome ✕ Clear

Eighth major clade for hepatitis delta virus.

PMID 17073101 · PMC3294742 · Emerging infectious diseases · 2006 · 7 claims · 7 setups

Full-text index only

Three HDV isolates (dFr644, dFr2072, dFr2736) form a monophyletic group distinct from HDV-1 through HDV-7, constituting a new eighth major clade (HDV-8) of the Deltavirus genus.

serum-derived complete same shd rt-pcr sequence phylogenetic
A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

Has reproduction · 76

58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

asfv b602l porcine sardinian whole-genome sanger haemoadsorption
Genome sequences and great expectations.

PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

Full-text index only

Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

complete annotated haemophilus automated benchmarking temporal
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

Full-text index only

1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

Has reproduction · 99

getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

genome complete same coronavirus nuclescore resistance mlst
POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

Full-text index only

Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

Full-text index only

Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

Full-text index only

A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

domestic red same white partial comparative pcr
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

Full-text index only

Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

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

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

Full-text index only

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

genomic same monozygotic subset genome-wide genome
A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

Full-text index only

Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

snp irish french fst-based microsatellite genome-wide
A genome wide linkage scan of metacarpal size and geometry in the Framingham Study.

PMID 18449921 · PMC2574919 · American journal of human biology : the official journal of the Human Biology Council · 2008 · 8 claims · 4 setups

Full-text index only

Metacarpal geometric indices (length, midshaft width, MCT, MCI, MZ) show significant heritability, ranging from 0.51 (MCT) to 0.82 (length)

hand individuals same radiogrammetry genome-wide variance
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

Full-text index only

Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.

PMID 34110280 · PMC8461470 · Microbial genomics · 2021 · 8 claims · 8 setups

Has reproduction · 50

rMAP is a pipeline capable of profiling the resistomes of ESKAPE pathogens using Illumina WGS data

eskape same novo snp phylogenetic
Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

Has reproduction · 85

First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

liver-derived muscle heart pooled 10x oxford hi-c
Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families.

PMID 17900373 · PMC2082241 · BMC dermatology · 2007 · 8 claims · 4 setups

Full-text index only

This is the first SNP-based genome-wide linkage study of atopic dermatitis performed in an Asian population.

japanese same genome-wide snp-based family-based targeted
Genetic linkage study of high-grade myopia in a Hutterite population from South Dakota.

PMID 17327828 · PMC2633468 · Molecular vision · 2007 · 6 claims · 5 setups

Full-text index only

AD non-syndromic high-grade myopia in the Hutterite family MYO-101 shows significant linkage to a locus on chromosome 10q21.1

hutterite same pcdh15 genome-wide fine-point candidate
WebScipio: an online tool for the determination of gene structures using protein sequences.

PMID 18801164 · PMC2644328 · BMC genomics · 2008 · 7 claims · 4 setups

Full-text index only

WebScipio, a web interface to Scipio, determines gene structure from a query protein sequence against an assembled eukaryotic genome with quality approaching manual annotation.

homo pongo callithrix mus spliced
Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

Full-text index only

A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

fregene-simulated 80k-snp 480k 192k simulated null whole-genome
PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

Full-text index only

PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

case-control same wtccc genome-wide benchmark stratified

Experiments

Eighth major clade for hepatitis delta virus.

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

Genome sequences and great expectations.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

POCUS: mining genomic sequence annotation to predict disease genes.

A comprehensive catalogue of somatic mutations from a human cancer genome.

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

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

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

A genome wide linkage scan of metacarpal size and geometry in the Framingham Study.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families.

Genetic linkage study of high-grade myopia in a Hutterite population from South Dakota.

WebScipio: an online tool for the determination of gene structures using protein sequences.

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.