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).

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

  PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

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  A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

  oocytes genomic fbhm population rt-pcr est direct

• Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.

  PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups

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  OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.

  real tailored blood algorithm snp

• Science review: searching for gene candidates in acute lung injury.

  PMID 15566614 · PMC1065043 · Critical care (London, England) · 2004 · 8 claims · 8 setups

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  The candidate gene approach combined with an ortholog gene database and gene ontology analysis identifies ALI candidate genes, with blood coagulation and inflammation ontologies most highly represented

  lung canine pulmonary alveolar microarray gene immunoassay

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• SNPs in cancer research and treatment.

  PMID 14970847 · PMC2410167 · British journal of cancer · 2004 · 8 claims · 8 setups

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  SNPs and haplotype-tagging SNPs (ht-SNPs) provide a resource for investigating genetic contributions to cancer susceptibility and outcome while reducing genotyping burden versus testing every SNP

  lung bladder colon prostate candidate snp-based haplotype

• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

  PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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  There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

  genomic pcr large outbred comparative denaturing pcr

• A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

  PMID 16321154 · PMC1326206 · BMC neurology · 2005 · 7 claims · 6 setups

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  CFS, PGI and fibromyalgia are highly overlapping symptom complexes likely reflecting a shared underlying pathophysiological mechanism rather than distinct diseases

  pooled individual cerebrospinal subjects capillary trypsin elisa

• A critical reassessment of the role of mitochondria in tumorigenesis.

  PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups

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  A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.

  hepatocellular papillary prostate tissues mtdna mutational

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

  PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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  COMP mutations were identified in 78% of families referred with PSACH

  genomic sequence subset pcr bidirectional sequence

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

  PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 67

  Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

  cytoscape generated prior-knowledge iris software datarail logic

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• EGFR mutation status in tumour-derived DNA from pleural effusion fluid is a practical basis for predicting the response to gefitinib.

  PMID 17060940 · PMC2360588 · British journal of cancer · 2006 · 7 claims · 4 setups

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  EGFR mutations can be detected by direct sequencing of DNA extracted from cell-free pleural effusion fluid supernatant in NSCLC patients

  cell-free pleural nsclc direct extraction clinical

• Human metapneumovirus, Australia, 2001-2004.

  PMID 16965711 · PMC3291208 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

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  HMPV had a 7.1% average annual incidence among 10,025 respiratory samples tested over 4 years

  nasopharyngeal npa hmpv-positive reverse direct multiplex