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).

• 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

• Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

  PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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  Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

  a549 nsclc expansion wst-1 flow

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

  PMID 15778432 · PMC1067522 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Dinucleotide microsatellite alterations in human cancer fall into two distinct modes: Type A (length changes ≤6 bp) and Type B (changes ≥8 bp)

  msh2− mlh1− lymphomas colorectal fluorescent sequencing immunohistochemistry

• 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

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• PigGIS: Pig Genomic Informatics System.

  PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

  million pig matched wgs blastx repeat sequence

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

  PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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  A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

  colorectal cdna matched thyroid rt-pcr restriction genomic

• ARED 3.0: the large and diverse AU-rich transcriptome.

  PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

  records est est-derived combined computational est sequence

• Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

  PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

  archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence

• 'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

  PMID 18000506 · PMC2360265 · British journal of cancer · 2007 · 8 claims · 4 setups

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  'Classical' EGFR mutations (exon 18 G719X, exon 19 DEL19, exon 21 L858R) are associated with better clinical outcome (disease control) with gefitinib

  microdissected genomic ffpe advanced direct nested immunohistochemistry

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• Detection of venous thromboembolism by proteomic serum biomarkers.

  PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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  A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

  serum anova-selected citrated depleted direct artificial d-dimer

• Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.

  PMID 17439973 · PMC1888811 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  p53REs are not simple direct repeats of half-sites; the two half-sites couple to form a higher-order 20-bp full-site palindrome

  compiled genome artificial sequence computational simulated

• A novel mutation in BBS7 gene causes Bardet-Biedl syndrome in a Chinese family.

  PMID 19093007 · PMC2603185 · Molecular vision · 2008 · 7 claims · 5 setups

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  A novel mutation (1666 A>G, exon 15, S556R) in BBS7 causes BBS in this Chinese family

  at-risk eyes blood bbs7 clinical ophthalmologic genetic

• TAC3 and TACR3 mutations in familial hypogonadotropic hypogonadism reveal a key role for Neurokinin B in the central control of reproduction.

  PMID 19079066 · PMC4312696 · Nature genetics · 2009 · 8 claims · 5 setups

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  Homozygous loss-of-function mutations in TAC3 or TACR3 cause congenital hypogonadotropic hypogonadism in four consanguineous families

  consanguineous genomic hek293a hek293 genome sanger calcium

• SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

  PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results

  omim pmd swissprot msipi database sequence tandem