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 17

System / cell line: best ✕ Assay: sequencing ✕ Clear

Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 6 setups

Has reproduction · 99

Verrucomicrobia is a highly abundant phylum in north-temperate freshwater lakes, ranking 4th most abundant on average (range 1.7–41.7%)

bacterial same verrucomicrobia community 16s environmental linear
Enhanced protein isoform characterization through long-read proteogenomics.

PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups

Has reproduction · 79

A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization

jurkat jurkat-derived long-read transcript orf
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

Has reproduction · 89

Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa

aureus reduced genome cgmlst comparative
Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups

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There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.

jejuni ssh panel suppression blastx dot-blot
An atypical phenotype of Reis-Bücklers corneal dystrophy caused by the G623D mutation in TGFBI.

PMID 18636123 · PMC2467519 · Molecular vision · 2008 · 6 claims · 2 setups

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A heterozygous c.1915G>A mutation in exon 14 of TGFBI (p.G623D) causes an atypical form of RBCD in this Chinese family, distinct from previously reported phenotypes for the same mutation.

genomic family pcr clinical
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

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Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

fecal assembled predicted gut whole-genome gene reciprocal
Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

Has reproduction · 68

Siphonophorae is the first diverging clade within Hydroidolina.

hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
Three novel and the common Arg677Ter RP1 protein truncating mutations causing autosomal dominant retinitis pigmentosa in a Spanish population.

PMID 16597330 · PMC1456953 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Three novel RP1 truncating mutations (Gln686Ter, Lys705fsX712, Lys722fsX737) cause adRP

genomic adrp denaturing direct restriction
Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

PMID 19112530 · PMC2610289 · Molecular vision · 2008 · 8 claims · 5 setups

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Two novel heterozygous OPA1 mutations were identified: a splice-site mutation c.985-2A>G in family F1 and a nonsense mutation c.2197C>T (p.R733X) in family F2

genomic available leukocytes affected linkage pcr single
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis.

PMID 19093009 · PMC2603250 · Molecular vision · 2008 · 8 claims · 6 setups

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OCT detects foveal and lamellar macular retinoschisis more frequently than funduscopy alone

xlrs genomic optical full-field multifocal
Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

coli se11 rapd whole-genome gene
Clinical correlates of depressive symptoms in familial Parkinson's disease.

PMID 18785635 · PMC2872794 · Movement disorders : official journal of the Movement Disorder Society · 2008 · 7 claims · 5 setups

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Depressive symptoms are significantly associated with Hoehn and Yahr stage, motor impairment (UPDRS Part III), and functional disability/ADL measures (Blessed, UPDRS Part II)

familial clinical genotyping sequencing
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson

Experiments

Genetic diversity among five T4-like bacteriophages.

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

Enhanced protein isoform characterization through long-read proteogenomics.

Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

An atypical phenotype of Reis-Bücklers corneal dystrophy caused by the G623D mutation in TGFBI.

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

Three novel and the common Arg677Ter RP1 protein truncating mutations causing autosomal dominant retinitis pigmentosa in a Spanish population.

Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Gene losses during human origins.

Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis.

Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

Clinical correlates of depressive symptoms in familial Parkinson's disease.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.