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 73

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

The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 8 claims · 8 setups

Has reproduction · 90

Phage Mimer is the first described lytic ssDNA (Microviridae) phage targeting Pectobacterium

phage conserved gpg cscl-gradient-purified whole-genome comparative intergenomic
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
Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

PMID 35073255 · PMC8828049 · eLife · 2022 · 8 claims · 7 setups

Has reproduction · 57

Prokaryotic community similarity follows a significant U-shape relationship over geographic distance up to 4000 km, decreasing within biotas but increasing across biotas after a tipping point of 1760-1920 km

soil grassland 16s plant soil
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Eighth major clade for hepatitis delta virus.

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

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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
TB database: an integrated platform for tuberculosis research.

PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups

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TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.

tuberculosis streptomyces tb-infected whole-genome sequence trna
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
A cell biological perspective on genome research.

PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.

saccharomyces caenorhabditis selected fruit genomic saturation physical
Characterization of the Schistosoma transcriptome opens up the world of helminth genomics.

PMID 14709167 · PMC395727 · Genome biology · 2003 · 8 claims · 5 setups

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Near-complete transcriptome complements have now been described for S. japonicum and S. mansoni

japonicum mansoni est blastx functional
Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

PMID 15314077 · PMC2211936 · The Journal of experimental medicine · 2004 · 7 claims · 5 setups

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Five distinct sets of B-CLL patients express strikingly similar (stereotyped) BCRs sharing common H and L chain V region gene segments and similar CDR3 length, composition, and junctional residues.

b-cll sequence cd5+ igv blast phylogenetic
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

five cichlid pairwise lake low-coverage blastx multi-species
HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

PMID 34025601 · PMC8134036 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

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ABAA reduces the number of false-positives with all metabarcoding methods tested

fungal same mock raw its1 blastn hierarchical
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

PMID 37129547 · PMC10191607 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 1 setups

Has reproduction · 83

VirPipe is a new bioinformatics pipeline for detecting viral genomes from Nanopore or Illumina sequencing input with streamlined installation and customization.

lung nanopore
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups

Has reproduction · 87

A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.

patients exome deep computer-assisted
A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

Has reproduction · 36

Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

phaeocystis strain yx04 globosa algicidal 16s scanning
Comparative genomics of multidrug resistance in Acinetobacter baumannii.

PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

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A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

baumannii resistance clinical whole-genome comparative sequence
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

PMID 18522722 · PMC2447851 · BMC genomics · 2008 · 8 claims · 4 setups

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A consensus Reference Human NumtS compilation (RHNumtS) was produced by comparing Blastn, MegaBlast and BLAT results with previously published compilations.

genome genomic blastn megablast blat
Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

hadv-37 predicted select genome cpg global
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

single glabripennis amino whole-genome gene busco

Experiments

The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

Genetic diversity among five T4-like bacteriophages.

Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Eighth major clade for hepatitis delta virus.

TB database: an integrated platform for tuberculosis research.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

A cell biological perspective on genome research.

Characterization of the Schistosoma transcriptome opens up the world of helminth genomics.

Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

Comparative genomics of multidrug resistance in Acinetobacter baumannii.

The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

Bases and spaces: resources on the web for accessing the draft human genome.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.