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: strain ✕ Assay: blast ✕ Clear

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

e2348 hep-2 blast colony transformation
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

PMID 18317809 · PMC2329726 · Molecular genetics and genomics : MGG · 2008 · 8 claims · 7 setups

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Strain 83972 is best described as a 'deconstructed pathogen' rather than a true commensal that acquired fitness properties

coli microarrays microarray comparative processing
Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

hcv 5'ncr serum maximum sequence recombination
Molecular correlates of host specialization in Staphylococcus aureus.

PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

aureus sequenced et3-1 bovine whole-genome comparative substitution
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

PMID 18700039 · PMC2529317 · BMC genomics · 2008 · 8 claims · 6 setups

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Complete genome of P. zucineum HLK1T consists of a 3,996,255 bp circular chromosome and a 382,976 bp circular plasmid encoding 3,861 proteins, 42 tRNAs, and one 16S-23S-5S rRNA operon

phenylobacterium zucineum bacteria genome cog comparative
Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology

tigr xanthomonas xcc ann wu-blast whole-genome
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
The genome of the simian and human malaria parasite Plasmodium knowlesi.

PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

knowlesi predicted type whole-genome comparative pfam
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

PMID 19930606 · PMC2785843 · BMC genomics · 2009 · 8 claims · 7 setups

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Reannotation excluded 608 CDSs from the original RefSeq annotation, mostly unfunctional 'hypothetical'/'putative' genes

coli c0139r blastp rps-blast initio
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 100

The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.

amorphophallus 6-month-old bacterial aroidearum pathogenicity pectinolytic 16s
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

saccharomyces higher yeast mitochondria genome-wide rnai gene
Versatile and open software for comparing large genomes.

PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level
The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

coli hep-2 pslm862 eaec colony hep-2 pcr
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

Experiments

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

Molecular correlates of host specialization in Staphylococcus aureus.

Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

Sequence polymorphisms cause many false cis eQTLs.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

Versatile and open software for comparing large genomes.

The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

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.