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).

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• From genomics to chemical genomics: new developments in KEGG.

  PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.

  enzymatic substrate kegg complete chemical number ortholog

• VIRGO: computational prediction of gene functions.

  PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

  cerevisiae sapiens leave-one-out gene protein-protein

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

  PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups

  Has reproduction · 91

  A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.

  coli yxja refolded flow bulk cotranscriptional

• Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.

  PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups

  Has reproduction · 81

  Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells

  h460 nsclc swath-ms western machine

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• A search for structurally similar cellular internal ribosome entry sites.

  PMID 17591613 · PMC1950536 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Cellular IRES are not defined by an overall conserved structure (unlike viral IRES) but instead depend on short RNA motifs and shared trans-acting factors (ITAFs)

  transcribed hek 293t enzymatic chemical structural

• 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