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 14

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

An SVM-based system for predicting protein subnuclear localizations.

PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

single-localization multi-localization same svm sequence
Metagenomic analysis of human diarrhea: viral detection and discovery.

PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

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Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

stool divergent extract preparations sequence-independent maximum enzyme
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
Application of proteomics methods for pathogen discovery.

PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

hlf sequences synthetic conventional 2d-dige gelc-ms
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.

PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups

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SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA

serum clustered pooled trypsin-digested seldi-tof cart immunoprecipitation
High-throughput crystallography for structural genomics.

PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

recombinant recalcitrant hundred family hydrogen situ site-directed
CGH-Profiler: data mining based on genomic aberration profiles.

PMID 16042799 · PMC1183191 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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CGH-Profiler circumvents ISCN nomenclature by importing CGH data from different vendor systems and converting it into a table format suitable for statistical analysis.

tumour cgh metaphase comparative metaphase
Rare mutations predisposing to familial adenomatous polyposis in Greek FAP patients.

PMID 15833136 · PMC1097718 · BMC cancer · 2005 · 8 claims · 6 setups

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A 250 Kbp deletion spanning intron 5 to beyond exon 15 of APC was identified in one FAP patient using MLPA, karyotyping, and FISH.

genomic peripheral metaphase dhplc sequencing rt-pcr
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

extracts pooled same non-assigned pcr parallel conventional
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

pcr-amplified same sequence luciferase bioluminometric bati comparison
Base editing in human cells with monomeric DddA-TALE fusion deaminases.

PMID 35821233 · PMC9276701 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 95

mDdCBEs built from non-toxic full-length DddA_tox variants enable mitochondrial DNA base editing with efficiencies of up to 50% upon transient expression in human cells

hek293t nih3t3 targeted clonal aav2
Competitive enzymatic reaction to control allele-specific extensions.

PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups

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Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.

genomic immobilized four individuals multiplex protease-mediated effect
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative

Experiments

An SVM-based system for predicting protein subnuclear localizations.

Metagenomic analysis of human diarrhea: viral detection and discovery.

Conservation, variability and the modeling of active protein kinases.

Application of proteomics methods for pathogen discovery.

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.

High-throughput crystallography for structural genomics.

CGH-Profiler: data mining based on genomic aberration profiles.

Rare mutations predisposing to familial adenomatous polyposis in Greek FAP patients.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

Base editing in human cells with monomeric DddA-TALE fusion deaminases.

Competitive enzymatic reaction to control allele-specific extensions.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).