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).

• Viral and host determinants of RNA virus vector replication and expression.

  PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

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  BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

  bmv saccharomyces wild-type immunogold genome-wide northern

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

  PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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  Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

  saccharomyces higher yeast mitochondria genome-wide rnai gene

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference

• High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

  PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

  saccharomyces plasmid pooled individual yeast pcr-based restriction

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• Phosphoproteomics: new insights into cellular signaling.

  PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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  Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

  yeast hela beta2-adrenergic erk phosphopeptide targeted silac

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.

  PMID 20064372 · PMC2892837 · Cell · 2009 · 8 claims · 8 setups

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  A systematic yeast two-hybrid screen identified physical interactions between the 10 major PR8 influenza viral proteins and human proteins, implicating 87 human 'H1' proteins.

  orfeome udorn bronchial hbecs yeast genome-wide sirna

• 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

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  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

  PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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  A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

  cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• Assembling a jigsaw puzzle with 20,000 parts.

  PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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  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.

  yeast caenorhabditis escherichia proteome-wide microarray yeast rnai

• Helicobacter pylori: after the genomes, back to biology.

  PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

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  STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

  helicobacter diffuse signature-tagged genome yeast

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• Proteomic view of mitochondrial function.

  PMID 18331620 · PMC2374722 · Genome biology · 2008 · 8 claims · 8 setups

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  Most modulators of basal mitochondrial function identified in the Drosophila RNAi screen are located outside the mitochondrion, since only 17 of 152 hits had a clear mitochondrial function.

  drosophila saccharomyces caenorhabditis yeast genome-wide phenotypic morphology

• Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

  PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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  Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

  yeast specified normal coli chip-on-chip chip-sequencing correlation-based

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

  PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

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  Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

  cerevisiae lists yeast genome-wide functional protein-protein

• The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

  PMID 17145711 · PMC1751528 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  GermOnline is a cross-species systems browser providing comprehensive curated information on genes and gene products relevant for sexual reproduction across nine model organisms including human.

  saccharomyces mus rodent classical tiling comparative