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 569

System / cell line: frequency ✕ Clear

G-quadruplexes: the beginning and end of UTRs.

PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

genome 5'-utr simulated protein-coding computational high-resolution utr
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups

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A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.

urothelial hapmap snp plot baf
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
High quality catalog of proteotypic peptides from human heart.

PMID 18803417 · PMC2765113 · Journal of proteome research · 2008 · 8 claims · 4 setups

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A catalog of 4476 proteotypic peptides representing 2558 human heart proteins was generated from MudPIT analyses of nonfailing and failing left-ventricular explants

left-ventricular unfractionated heart mudpit selected preparation
BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

PMID 18782444 · PMC2553419 · BMC cancer · 2008 · 8 claims · 7 setups

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KRAS, BRAF and PIK3CA mutations occur in the majority of colorectal polyps and are mutually exclusive

formalin-fixed colorectal sporadic polyps pcr bisulfite pentaplex
Developmental and genetic regulation of human surfactant protein B in vivo.

PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

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Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene
"Reverse ecology" and the power of population genomics.

PMID 18752601 · PMC2626434 · Evolution; international journal of organic evolution · 2008 · 8 claims · 7 setups

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Population genomic data can be used to rapidly identify genes targeted by adaptive natural selection, an approach termed 'reverse ecology'.

cerevisiae melanogaster sapiens simulans likelihood mcdonald-kreitman mkprf
Clinical heterogeneity and genotype-phenotype correlations in hereditary spastic paraplegia because of Spatacsin mutations (SPG11).

PMID 18717728 · PMC7254873 · European journal of neurology · 2008 · 8 claims · 4 setups

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Spatacsin (SPG11) mutations are a frequent cause of complex ARHSP, occurring in 3 of 8 screened families

genomic patients sanger brain clinical
Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.

PMID 18712882 · PMC2614079 · Chemical research in toxicology · 2008 · 8 claims · 6 setups

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hAGT expression increases mutations and cytotoxicity following BDO exposure, and hAGT-DNA cross-links form in the presence of BDO

recombinant wt-hagt [35s]-labelled trg8 sds-page time-course forward
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
Pathogenic mitochondrial DNA mutations are common in the general population.

PMID 18674747 · PMC2495064 · American journal of human genetics · 2008 · 7 claims · 6 setups

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At least 1 in 200 healthy humans harbors a pathogenic mtDNA mutation with potential to cause disease in offspring of female carriers

neonatal independent m.1555a→g-positive mutation-positive high-throughput last-cycle cloning
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

PMID 18648522 · PMC2480479 · Molecular vision · 2008 · 8 claims · 4 setups

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A rare CHX10 missense variant (c.728G>A, Gly243Asp) was identified in one PACG patient and absent in 215 controls, and is a possible disease-causing variant

genomic same chx10 pacg pcr case-control cross-species
Current and future directions in genomics of amyotrophic lateral sclerosis.

PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

american sals dutch irish genome laser expression
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

PMID 18557994 · PMC2481495 · Breast cancer research : BCR · 2008 · 8 claims · 8 setups

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Mutation frequencies in ATM, BRIP1, PALB2 and CHEK2 are many times higher in women with strong breast cancer family history (familial cases) than in population controls.

women familial finnish unselected germline international statistical
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans.

PMID 18510744 · PMC2424074 · BMC genetics · 2008 · 7 claims · 4 setups

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Sequencing the TPI1 locus in 357 German long-lived individuals identified 17 polymorphisms, 15 of which were rare and previously unknown

blood-derived cohort pcr snplex taqman

Experiments

G-quadruplexes: the beginning and end of UTRs.

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

High quality catalog of proteotypic peptides from human heart.

BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

Developmental and genetic regulation of human surfactant protein B in vivo.

"Reverse ecology" and the power of population genomics.

Clinical heterogeneity and genotype-phenotype correlations in hereditary spastic paraplegia because of Spatacsin mutations (SPG11).

Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

Pathogenic mitochondrial DNA mutations are common in the general population.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

Current and future directions in genomics of amyotrophic lateral sclerosis.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

Massively parallel pyrosequencing in HIV research.

Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans.