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).

• Proteomic profiling of the amniotic fluid to detect inflammation, infection, and neonatal sepsis.

  PMID 17227133 · PMC1769412 · PLoS medicine · 2007 · 8 claims · 8 setups

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  Higher MR scores (severe, 3-4) are associated with significantly shorter amniocentesis-to-delivery intervals than minimal (1-2) or no (0) inflammation

  amniotic placental blood seldi-tof elisa clinical

• Epidermal growth factor receptor abnormalities in the pathogenesis and progression of lung adenocarcinomas.

  PMID 19138956 · PMC3369271 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 4 setups

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  EGFR mutations and protein overexpression are early phenomena in the pathogenesis of lung adenocarcinoma, occurring in histologically normal bronchial/bronchiolar epithelium (NBE)

  lung microdissection fluorescence immunohistochemistry

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device.

  PMID 19053073 · PMC3010182 · Electrophoresis · 2008 · 8 claims · 7 setups

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  LDR-FSCE (combining LDR with free-solution conjugate electrophoresis) enables single-base resolution separation of LDR products without a polymer sieving matrix

  genomic synthetic k-ras ldr-dt pcr solid-phase ligase

• The molecular landscape of ASPM mutations in primary microcephaly.

  PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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  ASPM mutations are the most common cause of MCPH

  consanguineous genomic parents one polymorphic sanger family

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Cataloging coding sequence variations in human genome databases.

  PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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  A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

  coding hapmap concurrent nssnps database hapmap amino

• Profiling humoral immune responses to P. falciparum infection with protein microarrays.

  PMID 18937256 · PMC3021802 · Proteomics · 2008 · 7 claims · 5 setups

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  A protein microarray platform of 250 Pf proteins, individually expressed cell-free and printed unpurified, can profile serum antibody responses across donor groups of differing immune status

  sera coli genomic microarray immuno-dot elisa

• Tubulin proteomics: towards breaking the code.

  PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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  Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

  bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page

• Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

  PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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  PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

  porcine paec umbilical huvec methyltransferase sds-page fragmentation

• 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

• DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

  PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

  fresh-frozen same sssi-methylated mixture digital conventional classic

• The incentive salience of alcohol: translating the effects of genetic variant in CNR1.

  PMID 18606956 · PMC2856651 · Archives of general psychiatry · 2008 · 7 claims · 6 setups

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  The C allele of rs2023239 is associated with greater CB1 receptor binding in the prefrontal cortex

  postmortem buccal heavy moderate-to-heavy receptor snp functional

• Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

  PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

  sap sequence-derived humvar same decision independent greedy

• Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

  PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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  Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

  normal genome-wide same omim microarray sage computational

• Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

  PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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  The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

  faecal mcra pure pcr rflp 16s

• Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

  PMID 18450818 · PMC2425492 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Pyknons (recurrent, genome-specific, ≥16nt motifs with ≥30 intact intergenic/intronic copies and ≥1 exonic copy) span a substantial fraction of previously uncharacterized intronic space (7.4% human, 4.4% mouse)

  pyknon computational comparative term

• A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

  PMID 18435860 · PMC2397416 · BMC genomics · 2008 · 7 claims · 4 setups

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  A two-way ANOVA model with a treatment x probe-set interaction term can automatically determine whether sibling probe sets for a gene behave similarly (non-significant interaction, consolidate) or differently (significant interaction, treat as independent)

  retina thyroid spermatogonial differentially two-way paired anova-based