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).

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• 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

• The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

  PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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  The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

  coli hep-2 pslm862 eaec colony hep-2 pcr

• Angiotensin I-converting enzyme mutation (Trp1197Stop) causes a dramatic increase in blood ACE.

  PMID 20011602 · PMC2788243 · PloS one · 2009 · 8 claims · 8 setups

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  A novel heterozygous Trp1197Stop (W1197X) mutation in the ACE gene causes a 13-fold increase in blood ACE activity in an African-American family

  plasma genomic cho heparinized ace plate conformational

• Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

  PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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  S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

  enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative

• Acetylation goes global: the emergence of acetylation biology.

  PMID 19920250 · PMC2812806 · Science signaling · 2009 · 8 claims · 4 setups

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  Whole-proteome acetylome mapping (via SILAC-coupled high-resolution MS) shows the acetylome approaches the size and complexity of the phosphoproteome, indicating acetylation is a widespread regulatory modification rather than a niche one.

  proteome proteome-wide liver anti-acetyllysine silac-based silac-coupled

• Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

  PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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  Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

  tumors cancer tumor lung direct database quantitative

• Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

  PMID 19723304 · PMC2748065 · BMC medical genetics · 2009 · 7 claims · 4 setups

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  Three NOD1 Exon 6 SNPs (W219R, L349P, L370R) show statistically significant association with ulcerative colitis compared to controls

  genomic pcr patients dhplc cloning pcr-rflp

• Ecotype diversity and conversion in Photobacterium profundum strains.

  PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

  photobacterium profundum predicted orthologous whole-genome pulsed-field comparative

• Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay.

  PMID 18036208 · PMC2253505 · BMC medical genetics · 2007 · 7 claims · 3 setups

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  Improved short, non-overlapping TaqMan MGB probes accurately and simultaneously discriminate the H63D, S65C and C282Y HFE polymorphisms without cross-interference between the closely spaced codon 63/65 SNPs.

  genomic real-time rflp sequencing

• Proposed methods for testing and selecting the ERCC external RNA controls.

  PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups

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  A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)

  candidate linearized transcripts pools sequence transcription quality

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75.

  PMID 7642699 · PMC2199968 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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  The 36-amino acid cytoplasmic tail of gp75 alone is sufficient to direct intracellular retention and targeting of chimeric CD8 proteins to the endosomal/lysosomal compartment in fibroblasts

  melanoma sk-mel-19 immunoprecipitated coli immunofluorescence immunoelectron protease

• Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

  PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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  Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

  falciparum cdna c18 genomic rt-pcr southern genomic

• Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

  PMID 8879195 · PMC2192830 · The Journal of experimental medicine · 1996 · 6 claims · 8 setups

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  The patient is a compound heterozygote for a p67-phox gene mutation: an in-frame deletion of lysine 58 on one allele and an 11-13 kb genomic deletion on the other allele.

  granulocytes granulocyte mononuclear leukocyte nbt cell-free western

• Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

  PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

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  The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

  c3h genomic bac multiple-tissue genetic yac direct

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

  PMID 17264116 · PMC1851657 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cruciform extrusion propensity of PATRRs depends on both length and central symmetry of the repeat.

  plasmids same single-stranded patrr-containing cruciform endonuclease secondary

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene