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 38

System / cell line: in-silico ✕ 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
The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

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Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

143b ffpe blood cloned southern pcr rt-pcr
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

genomic gonystylus subset restriction-digested custom self-self blast
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

metazoan identified amphimedon nematostella genome sequence gene
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

PMID 18616530 · PMC4732719 · Clinical genetics · 2008 · 8 claims · 8 setups

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TMC1 mutations were identified in seven of the families/patients segregating hearing loss linked to DFNA36/DFNB7-11

families affected tmc1 tjp2 genetic sequencing multiplex
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

refseq macaca genomic rhesus exon pcr molecular
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

consensus sap query all-against-all blast cross-database
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
Unlocking the microbial studies through computational approaches: how far have we reached?

PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

Has reproduction

Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

clinical bacteriophage vaginal hbv ngs random whole-genome
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
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

hpv clinical biotinylated pcr mip molecular microarray
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
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.

PMID 19046425 · PMC2625370 · BMC genomics · 2008 · 6 claims · 7 setups

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Identified a 12-bp Bacteroidetes DNA barcode and a 26-bp degenerate Firmicutes DNA barcode within the 16S rRNA gene

16s brain cystic caecal barcode 16s metagenome
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
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter

Experiments

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

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

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

Unlocking the microbial studies through computational approaches: how far have we reached?

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

Human SNPs resulting in premature stop codons and protein truncation.

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

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

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.

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

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.