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).

• Challenges and standards in integrating surveys of structural variation.

  PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

  Full-text index only

  There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

  genomic hapmap reference independent comparative snp fosmid

• Validation of analytic methods for biomarkers used in drug development.

  PMID 18829475 · PMC2744124 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

  Full-text index only

  Analytical method validation (assessing assay performance/reproducibility) is a distinct process from clinical qualification (linking a biomarker to biological processes and clinical endpoints), though the two are intertwined.

  specified biological cancer-associated biofluids immunohistochemistry immunoassay microarray

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

  Full-text index only

  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• Randomised trial of a decision aid and its timing for women being tested for a BRCA1/2 mutation.

  PMID 14735173 · PMC2410151 · British journal of cancer · 2004 · 6 claims · 3 setups

  Full-text index only

  The DA had no impact on well-being (anxiety, depression, cancer-related distress, general health)

  women brca1 same randomised comparative validated

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

  Full-text index only

  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative

• Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

  PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

  Full-text index only

  Mutations in the OAZ3 gene are not a common cause of male infertility

  genomic coding inferred oaz3 direct sscp haplotype

• The flexible pocketome engine for structural chemogenomics.

  PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

  Full-text index only

  A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

  pdb bacteriorhodopsin enr asn automated virtual energy-based

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

  Full-text index only

  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Next-generation sequencing.

  PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups

  Full-text index only

  Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment

  individuals metastatic acute oestrogen whole-exome whole-genome large-scale