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).

• A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

  PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

  sparced mcf10a deterministic hybrid comparison

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome

• Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.

  PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups

  Has reproduction · 67

  The assembly of 21 unique macromolecular complexes (20 plus a reduced ribosome biogenesis model) was incorporated into the existing whole-cell kinetic model of Syn3A.

  jcvi-syn3a syn3a simulated hybrid chemical ordinary

• Topological approximate Bayesian computation for parameter inference of an angiogenesis model.

  PMID 35191485 · PMC9048691 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 3 setups

  Has reproduction · 100

  TDA summary statistics can be combined with ABC to infer parameters (ρ, χ) of the Anderson–Chaplain angiogenesis model

  square simplicial simulated computational persistent approximate

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups

  Has reproduction · 53

  spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.

  two-gene three-gene emt circuit simulation grn scrna-seq

• Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.

  PMID 29187638 · PMC5721160 · Journal of the Royal Society, Interface · 2017 · 7 claims · 8 setups

  Has reproduction · 49

  Numb (and Numbl) inhibits a full EMT by stabilizing a hybrid E/M phenotype, acting as a 'phenotypic stability factor'.

  notch-emt-numb h1975 independent mathematical multi-cell sirna

• Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

  PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

  Full-text index only

  Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

  yeast drosophila networks dppi reanalysis computer repeated