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).

• Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

  PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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  Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

  peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning

• Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

  PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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  Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

  ptk2 t84 escherichia computational expression immunofluorescence immunoblotting

• Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

  PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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  A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

  primate hepg2 32p-labeled sequence rt-pcr luciferase

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

  PMID 19832989 · PMC2770483 · BMC microbiology · 2009 · 8 claims · 5 setups

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  The relative proportion of the three Pfmsp1 block2 allelic families (K1, Mad20, RO33) in Dielmo showed no significant temporal fluctuation over a 10-year period (1990-99).

  plasmodium dielmo semi-nested direct cross-sectional

• Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

  PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

  genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin

• Bcipep: a database of B-cell epitopes.

  PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

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  Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

  synthetic antigenic anti-peptide sequence

• Co-circulation and evolution of polioviruses and species C enteroviruses in a district of Madagascar.

  PMID 18085822 · PMC2134956 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  Madagascar VDPVs are intertypic/interspecies recombinants with Sabin 2-derived sequence in the 5'-half of the genome and HEV-C-derived sequence in the 3'-half

  vdpv mad04 pvr-tg21 hep-2c rt-pcr monoclonal plaque

• Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

  PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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  PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

  falciparum escherichia coli-expressed recombinant pcr recombinant sds-page

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

  PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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  A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

  coli hela filamentous scfv gfp sds-page fluorescence

• Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

  PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

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  Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

  hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389

• The Proteomic Code: a molecular recognition code for proteins.

  PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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  The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

  anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide

• A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

  PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups

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  A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.

  genomic laser-capture cell-free hela sscp loss transcription

• Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

  PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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  Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

  hiv-1 longitudinal 0-month single pseudovirus single site-directed

• Endemic Venezuelan equine encephalitis in northern Peru.

  PMID 15200823 · PMC3323213 · Emerging infectious diseases · 2004 · 8 claims · 8 setups

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  Four VEE complex lineages cocirculate in the Peruvian Amazon region: subtype ID (Panama genotype and Colombia/Venezuela genotype), subtype IIIC, and a newly proposed subtype IIID

  veev pe2 subtype cotton sscp pcr phylogenetic

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• The identification and characterization of a novel protein, c19orf10, in the synovium.

  PMID 17362502 · PMC1906808 · Arthritis research & therapy · 2007 · 8 claims · 8 setups

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  c19orf10 is a novel protein produced in significant amounts by fibroblast-like synoviocytes (FLSs), identified via proteomic analysis

  fibroblast-like coli balb chicken two-dimensional recombinant monoclonal

• TP53 mutations, amplification of P63 and expression of cell cycle proteins in squamous cell carcinoma of the oesophagus from a low incidence area in Western Europe.

  PMID 11531258 · PMC2364124 · British journal of cancer · 2001 · 8 claims · 5 setups

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  TP53 mutations were detected in 36% (12/33) of SCCE from the low-incidence Lyon area, lower than the 56-80% reported in high-incidence areas

  microdissected deparaffinized oesophageal genomic ttge immunohistochemistry western

• Influenza A (H3N2) outbreak, Nepal.

  PMID 16102305 · PMC3320503 · Emerging infectious diseases · 2005 · 7 claims · 6 setups

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  Nepal H3N2 outbreak isolates show antigenic drift, with ~40% antigenically distinct from the A/Wyoming/3/03 vaccine strain by hemagglutination inhibition

  influenza throat ha1 amino hemagglutination rt-pcr rapid