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).

• Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

  PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

  baumannii ranked lpta representative pooled string mic

• Contributions from molecular/biochemical approaches in epidemiology to cancer risk assessment and prevention.

  PMID 1486845 · PMC1519598 · Environmental health perspectives · 1992 · 8 claims · 8 setups

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  Genotoxicity of chemicals is a continuous, graded property (agent score) rather than a simple dichotomy of mutagenic vs. nonmutagenic chemicals

  chemical drosophila normal uv-sensitive short-term drosophila excision

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.

  PMID 32003771 · PMC7203754 · Bioinformatics (Oxford, England) · 2020 · 7 claims · 4 setups

  Has reproduction · 37

  A novel Bayesian peak deconvolution algorithm gives unbiased likelihood estimations for peak locations and derives probability-based z-scores.

  lines simulated invariant l1000 l1000 simulated liss

• 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

• Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

  PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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  Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

  tcp0 tcp2β blast-p phylogenetic structure

• 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: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• 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

• 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