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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Decision tree-driven tandem mass spectrometry for shotgun proteomics.
PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups
A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone
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Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.
PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups
18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.
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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
An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.
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Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.
PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups
A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.
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The most frequent short sequences in non-coding DNA.
PMID 19966278 · PMC2831315 · Nucleic acids research · 2010 · 8 claims · 2 setups
Short frequent sequences (9-14 bases) in non-coding DNA may play a role in maintaining chromosome structure and function
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Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.
PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups
Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells
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Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.
PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups
Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma
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Proteomic analysis of human aqueous humor using multidimensional protein identification technology.
PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups
Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome
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Human spermatozoa contain multiple targets for protein S-nitrosylation: an alternative mechanism of the modulation of sperm function by nitric oxide?
PMID 17683036 · PMC2777308 · Proteomics · 2007 · 7 claims · 5 setups
Human sperm proteins undergo S-nitrosylation upon exposure to NO donors, detectable by the biotin switch assay
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The use of laser capture microscopy in proteomics research--a review.
PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups
LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis
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Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis.
PMID 18534013 · PMC2440737 · BMC cell biology · 2008 · 6 claims · 4 setups
A modified differential detergent extraction method (pelleting nuclei/intact cells at low speed before detergent solubilization) yields DRM fractions with markedly reduced nuclear protein contamination compared to the conventional method.
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Induction of calcification by serum depletion in cell culture: a model for focal calcification in aortas related to atherosclerosis.
PMID 18230165 · PMC2248577 · Lipids in health and disease · 2008 · 8 claims · 8 setups
Serum depletion induces calcification (mineral Ca/P deposition) in rabbit aortic smooth muscle cell culture
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Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.
PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups
Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.
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Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.
PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups
An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis
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Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.
PMID 18849548 · PMC4260454 · Experimental biology and medicine (Maywood, N.J.) · 2008 · 6 claims · 6 setups
50 μM HU treatment of SS RBC membranes causes statistically significant changes in a discrete set of membrane proteins, distinct from HbF induction.
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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.