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).
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T cell receptor usage and fine specificity of human immunodeficiency virus 1-specific cytotoxic T lymphocyte clones: analysis of quasispecies recognition reveals a dominant response directed against a minor in vivo variant.
PMID 8666925 · PMC2192525 · The Journal of experimental medicine · 1996 · 8 claims · 6 setups
Despite heterogeneous TCR usage among clones from different HLA-B14 subjects, the fine specificity for the gp41/584-592 epitope and its variants is strikingly similar.
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A mouse plasma peptide atlas as a resource for disease proteomics.
PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups
A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.
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A surrogate-based approach for post-genomic partner identification.
PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups
Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.
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The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.
PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups
Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments
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Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.
PMID 18774841 · PMC2707264 · Journal of proteome research · 2008 · 8 claims · 5 setups
Using MS/MS ion intensities with stable isotope labeling (SILT) decreases the effects of contamination from unrelated co-eluting compounds compared to precursor ion intensity methods.
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Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.
PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups
CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.
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iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells.
PMID 19159641 · PMC2716563 · Advances in enzyme regulation · 2009 · 7 claims · 4 setups
Egln1 knockdown induces P1465 hydroxylation and Ser5 phosphorylation of Rpb1 only in VHL(+) cells, not VHL(-) cells
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Genomics, proteomics and bioinformatics: all in the same boat.
PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups
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
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Proteomics technologies and challenges.
PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups
The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.