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).

• Global mapping of the topography and magnitude of proteolytic events in apoptosis.

  PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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  PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

  jurkat sds-page fragmentation caspase-3

• An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

  PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

  brucella toxoplasma bacillus homo label-free mass genomic

• Structural genomics: a new era for pharmaceutical research.

  PMID 11864367 · PMC139010 · Genome biology · 2002 · 8 claims · 6 setups

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  Automation of crystal mounting, diffraction data collection, and structure determination/refinement is a critical factor enabling large-scale structural genomics projects.

  proteins target hiv x-ray thermal initio

• Back to basics.

  PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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  Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

  chromosome pendrin yeast carbonic genome gene mudpit

• Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

  PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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  P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

  falciparum coli native falciparum-infected rt-pcr recombinant peptide

• 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

• Genomics, proteomics and bioinformatics: all in the same boat.

  PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups

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  Microarray sensitivity has improved enough to analyze clinical samples as small as 10-50 nanograms, and many early microarray experiments may need to be repeated due to data quality issues

  clinical oligonucleotide-immobilized dendritic blood microarray chip combined

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• Tags for labeling protein N-termini with subtiligase for proteomics.

  PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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  Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

  jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• Mass spectrometry for proteomics.

  PMID 18718552 · PMC2642903 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  New instrumentation (Orbitrap) and new fragmentation methods (ETD) have enabled exciting new areas of proteomic application

  digested intact yeast large shotgun top-down quantitative

• Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

  PMID 8879195 · PMC2192830 · The Journal of experimental medicine · 1996 · 6 claims · 8 setups

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  The patient is a compound heterozygote for a p67-phox gene mutation: an in-frame deletion of lysine 58 on one allele and an 11-13 kb genomic deletion on the other allele.

  granulocytes granulocyte mononuclear leukocyte nbt cell-free western

• Unraveling the histone's potential: a proteomics perspective.

  PMID 18849650 · PMC2662511 · Epigenetics · 2008 · 8 claims · 8 setups

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  Mass spectrometry can determine the full repertoire of histone PTMs, their residue-specific location, and combinatorial patterns without requiring prior knowledge of the modification, unlike antibody-based methods

  histone overexpressed lysate top-down middle-down quantitative