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).

• p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

  PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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  p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

  frozen plasmids single extracted p53 sanger laser

• Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

  PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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  IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

  saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

• "Reverse ecology" and the power of population genomics.

  PMID 18752601 · PMC2626434 · Evolution; international journal of organic evolution · 2008 · 8 claims · 7 setups

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  Population genomic data can be used to rapidly identify genes targeted by adaptive natural selection, an approach termed 'reverse ecology'.

  cerevisiae melanogaster sapiens simulans likelihood mcdonald-kreitman mkprf

• 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

• Structure of protein interaction networks and their implications on drug design.

  PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

  budding pin yeast protein-protein graph-theoretic gene

• Genomic mutation rates: what high-throughput methods can tell us.

  PMID 19644920 · PMC2952423 · BioEssays : news and reviews in molecular, cellular and developmental biology · 2009 · 8 claims · 8 setups

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  High-throughput DNA analyses yield genome mutation rate estimates markedly higher than those obtained with pre-genomic strategies

  cerevisiae elegans melanogaster mammals fluctuation mutation indirect

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Bacteriophage Mu integration in yeast and mammalian genomes.

  PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

  cerevisiae ab2.2 hela fes29 electroporation southern transposition

• 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

• The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

  PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.

  interaction yeast edge-betweenness chi-squared robustness

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Protein under-wrapping causes dosage sensitivity and decreases gene duplicability.

  PMID 18208334 · PMC2211539 · PLoS genetics · 2008 · 7 claims · 6 setups

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  Protein under-wrapping extent is negatively correlated with gene duplicability (family size) across six organisms (E. coli, yeast, worm, fly, human, thale cress)

  coli cerevisiae sapiens elegans structural comparative functional

• Reconstruction of human protein interolog network using evolutionary conserved network.

  PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

  ppi sequences interaction predicted interolog orthology quasi-clique

• Adaptations to climate in candidate genes for common metabolic disorders.

  PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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  A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

  individuals population genic compiled snp spearman bayesian

• Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

  PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

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  This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

  acropora millepora coral snp genetic segregation

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise