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 55

System / cell line: non-synonymous ✕ Clear

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

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Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

brucella sequenced concatenated allelic multilocus ratio neighbour-joining
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

private disease uniprot snps database controlled sequence
Functional analysis of novel SNPs and mutations in human and mouse genomes.

PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

apoe 11-nucleotide sequence genomic manual automated exonic
An optimized procedure for the design and evaluation of Ecotilling assays.

PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

genomic gene pcr cdna ecotilling sequence sanger
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
The background of mitochondrial DNA haplogroup J increases the sensitivity of Leber's hereditary optic neuropathy cells to 2,5-hexanedione toxicity.

PMID 19936068 · PMC2774515 · PloS one · 2009 · 8 claims · 7 setups

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Haplogroup J1 background greatly increases sensitivity of LHON cells (11778/ND4 and 14484/ND6 mutations) to 2,5-HD toxicity

cybrids fibroblasts digitonin-permeabilized cybrid mtt atp complete
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

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

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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
mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

mitochondrial aligned compilation sequence multi-locus
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups

Has reproduction · 94

Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path

jejuni core whole-genome core k-mer
Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

PMID 19015641 · PMC2633425 · Oncogene · 2009 · 8 claims · 8 setups

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E884K works in concert with L858R in-cis, in a dominant fashion, to differentially alter EGFR downstream signaling and inhibitor sensitivity in an inhibitor-specific manner

cos-7 kinase japanese western cellular mts
RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic

Experiments

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

An optimized procedure for the design and evaluation of Ecotilling assays.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

The background of mitochondrial DNA haplogroup J increases the sensitivity of Leber's hereditary optic neuropathy cells to 2,5-hexanedione toxicity.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

Web-based resources for comparative genomics.

Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

RPS4Y gene family evolution in primates.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.