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 70

System / cell line: index ✕ Assay: sequence ✕ Clear

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
Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

tcp0 tcp2β blast-p phylogenetic structure
Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.

PMID 16280053 · PMC1410737 · Breast cancer research : BCR · 2005 · 8 claims · 8 setups

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There is no evidence that highly penetrant exonic or splice site mutations in FANCD2, BRIP1/BACH1, LMO4 or SFN contribute to familial breast cancer

germline lymphoblastoid dhplc sequencing rt-pcr
Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

clinical concatenated cereus isolates multilocus phylogenetic pcr
Mutation analysis of the ATR gene in breast and ovarian cancer families.

PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

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ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

index atr variant mutation direct variant
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
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

PMID 19915672 · PMC2772813 · PloS one · 2009 · 8 claims · 8 setups

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MLSA of 89 genes across 108 global MTBC strains yields a single, highly robust phylogeny with virtually no homoplasy, congruent across parsimony, NJ, ML, and Bayesian methods.

global mtbc miru-vntr multilocus spoligotyping 15-loci-miru-vntr
CHEK2 variants associate with hereditary prostate cancer.

PMID 14612911 · PMC2394451 · British journal of cancer · 2003 · 8 claims · 6 setups

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CHEK2 1100delC frameshift mutation is significantly more frequent in Finnish HPC patients than in population controls

index hpc unselected affected sscp sequencing minisequencing
The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

PMID 19050890 · PMC2690858 · Annals of hematology · 2009 · 7 claims · 7 setups

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HBG2:g.-109G>T is a novel promoter mutation causing a distinct ('Hellenic type') nd-HPFH

peripheral genomic nuclear mel cation reverse-phase denaturing
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
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
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

Has reproduction · 91

An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

gossypium longicalyx nine diploids whole-genome wgs read
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Evolution of motif variants and positional bias of the cyclic-AMP response element.

PMID 17288573 · PMC1796609 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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Canonical CRE positional bias toward the -1 to -150 bp TSS region is present in vertebrates (human, mouse, rat, chicken, frog, zebrafish) but absent in sea squirt, fruit fly and worm.

tss-spanning cres genome known genome-wide comparative cpg
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
Influence of two vaccination campaigns on genetic diversity of invasive Neisseria meningitidis isolates in northern Spain (1997-2008).

PMID 20041148 · PMC2794534 · PloS one · 2009 · 7 claims · 7 setups

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Overall diversity of the invasive meningococcal population, measured by ST/clonal complex frequencies, allele numbers, polymorphic sites, and index of association, remained relatively constant throughout the 12-year study period despite the two vaccination campaigns.

invasive non-serogroupable meningitidis mlst latex real-time pcr
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

dbsnp gpcr transmembrane sequence six-frame sift logistic
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell

Experiments

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

Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

Mutation analysis of the ATR gene in breast and ovarian cancer families.

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

CHEK2 variants associate with hereditary prostate cancer.

The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Genome-wide survey of allele-specific splicing in humans.

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

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Evolution of motif variants and positional bias of the cyclic-AMP response element.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Influence of two vaccination campaigns on genetic diversity of invasive Neisseria meningitidis isolates in northern Spain (1997-2008).

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.