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).

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron

• Proteomics of human neurodegenerative diseases.

  PMID 18800015 · PMC2710115 · Journal of neuropathology and experimental neurology · 2008 · 8 claims · 8 setups

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  Proteomic techniques applied to autopsy brain and CSF from patients with neurodegenerative diseases provide insight into pathogenesis and enable biomarker discovery

  detergent-extractable thioflavin-s-stained tau-2-immunostained snca-immunoreactive 2-dimensional laser lc-ms-ms

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• The role of medical structural genomics in discovering new drugs for infectious diseases.

  PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

  bacteria plasmodium candidate burkholderia high-throughput animal compound-target

• Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

  PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups

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  An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.

  pepseeker local known swissprot tandem peptide pmf

• A global view of protein expression in human cells, tissues, and organs.

  PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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  A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

  normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised

• IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

  PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

  standard thp-1 replicate lc-ms manual cross-instrument

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative