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 quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.
PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups
A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.
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Has reproduction · 84
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.
PMID 35624178 · PMC9142503 · Nature communications · 2022 · 7 claims · 5 setups
pcSecYeast, a proteome-constrained genome-scale model integrating metabolism, translation, and detailed secretory pathway processing (translocation, PTMs, folding, misfolding, degradation), was constructed for S. cerevisiae
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Has reproduction · 85
Predicting the pathogenicity of missense variants using features derived from AlphaFold2.
PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups
AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.
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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups
The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.
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High-accuracy proteome maps of human body fluids.
PMID 17140426 · PMC1794581 · Genome biology · 2006 · 8 claims · 5 setups
Large-scale, high-accuracy MS analyses of tear fluid, urine, and seminal plasma provide high-quality datasets useful for biomarker discovery
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Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.
PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups
DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)
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Reconstruction of pathways associated with amino acid metabolism in human mitochondria.
PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups
Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders
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LOCATE: a mammalian protein subcellular localization database.
PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups
LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.
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A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics.
PMID 18957120 · PMC2628390 · BMC bioinformatics · 2008 · 8 claims · 2 setups
Sili2DGel represents recursive gel matching results as a weighted undirected graph and identifies SAP by finding cliques and pseudocliques (dense subgraphs) after edge-weight filtering, strength-metric-based graph reduction, and cluster refinement.
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Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.
PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups
An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)
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The Universal Protein Resource (UniProt) in 2010.
PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups
UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.
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Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.
PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups
wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables
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Systems biology and the host response to viral infection.
PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups
Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets
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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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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.