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 33

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Information extraction from full text scientific articles: where are the keywords?

PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

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The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

corpus same articles keyword validation qualitative
Mitochondrial diversity within modern human populations.

PMID 17439969 · PMC1888801 · Nucleic acids research · 2007 · 8 claims · 5 setups

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Modern humans show extremely low divergence from the mitochondrial consensus sequence, differing on average by only 21.6 nucleotide sites

full-length mitochondrial mtdna additional sequence site-by-site regional
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Calculating expected DNA remnants from ancient founding events in human population genetics.

PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

simulated forward-based size
DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

PMID 18254956 · PMC2270804 · BMC medical genetics · 2008 · 8 claims · 5 setups

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Three LOXL1 SNPs previously associated with pseudoexfoliation in Nordic populations are significantly associated with pseudoexfoliation syndrome and pseudoexfoliation glaucoma in a U.S. ethnically diverse population

patients randomly cohort pxf taqman direct full-gene
Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

hiv-1 polyclonally shannon cross-clade ctl
Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 8 setups

Has reproduction · 80

After ~2 decades of ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin, especially centromeric/peri-centromeric satellite and micro-satellite DNA

pbmc single cd4 pbmc-derived flip-seq mip-seq prip-seq
Characterization of in vivo somatic mutations at the hypoxanthine phosphoribosyltransferase gene of a human control population.

PMID 8513767 · PMC1519656 · Environmental health perspectives · 1993 · 7 claims · 4 setups

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In vivo hprt mutants from 63 independent donors were molecularly characterized by cDNA and genomic DNA PCR/sequencing.

peripheral hprt-mutant pcr limiting cdna multiplex
A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups

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Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines

falciparum red northern static rt-pcr
Eighth major clade for hepatitis delta virus.

PMID 17073101 · PMC3294742 · Emerging infectious diseases · 2006 · 7 claims · 7 setups

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Three HDV isolates (dFr644, dFr2072, dFr2736) form a monophyletic group distinct from HDV-1 through HDV-7, constituting a new eighth major clade (HDV-8) of the Deltavirus genus.

serum-derived complete same shd rt-pcr sequence phylogenetic
Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

pbmc his-tagged cem mammalian pcr electrophoretic western
PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

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All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

vcjd scjd scottish controls pcr-rflp full chi-squared
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

ligand gpcr glida principal sequence gene
A common genetic factor for Parkinson disease in ethnic Chinese population in Taiwan.

PMID 17187665 · PMC1764029 · BMC neurology · 2006 · 6 claims · 4 setups

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The G2385R variant in LRRK2 contributes significantly to the etiology of PD in ethnic Han Chinese individuals

peripheral g2385r patients genotype pcr full clinical
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
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

Experiments

Information extraction from full text scientific articles: where are the keywords?

Mitochondrial diversity within modern human populations.

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Calculating expected DNA remnants from ancient founding events in human population genetics.

DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

Characterization of in vivo somatic mutations at the hypoxanthine phosphoribosyltransferase gene of a human control population.

A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

Eighth major clade for hepatitis delta virus.

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

A genome annotation-driven approach to cloning the human ORFeome.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

A common genetic factor for Parkinson disease in ethnic Chinese population in Taiwan.

The distribution of SNPs in human gene regulatory regions.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

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.