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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A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.
PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups
PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11
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From single cells to whole organisms.
PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups
The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods
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Assembling a jigsaw puzzle with 20,000 parts.
PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups
Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.
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A new era for proteomics research?
PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups
Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable
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Pathway analysis of kidney cancer using proteomics and metabolic profiling.
PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups
31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue
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Proteomic approaches for studying alcoholism and alcohol-induced organ damage.
PMID 23584750 · PMC3860448 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 7 setups
Chronic alcohol abuse produces persistent changes in brain function (tolerance, dependence, craving) likely resulting from alterations in gene and protein expression
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Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.
PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups
31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis
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Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.
PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups
Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome
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Interactome networks: the state of the science.
PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups
Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia
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Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.
PMID 18617507 · PMC2577208 · Molecular & cellular proteomics : MCP · 2008 · 8 claims · 8 setups
Nuclear Ran GTPase was identified by mass spectrometry as a novel interacting partner of VRK1 and VRK2B
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Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.
PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups
A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date
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Human Protein Reference Database--2009 update.
PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups
HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data
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HUPO Highlights.
PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups
Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing
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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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Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.
PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups
Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides
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Whither genomics?
PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups
Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype
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Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.
PMID 19122847 · PMC2585750 · Circulation. Arrhythmia and electrophysiology · 2008 · 7 claims · 5 setups
A missense R99H mutation in KCNE3 was identified in a Brugada Syndrome proband and cosegregates with the phenotype in the family (4/4 phenotype-positive, 0/3 phenotype-negative members carried it)