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).

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

  PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

  homologous human-mouse same gene comparative parameter micro-exon

• Gapless provides combined scaffolding, gap filling, and assembly correction with long reads.

  PMID 37142439 · PMC10166144 · Life science alliance · 2023 · 8 claims · 5 setups

  Has reproduction · 73

  gapless is a new tool that combines assembly correction, scaffolding, and gap filling in one pipeline using PacBio or Oxford Nanopore long reads.

  coli dolphin supernova four long-read read-alignment

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.

  PMID 33729159 · PMC8012062 · eLife · 2021 · 8 claims · 7 setups

  Has reproduction · 94

  The SCLC regulatory network is multistable and its steady states map onto four experimentally observed phenotypes (ASCL1high/NEUROD1low, ASCL1low/NEUROD1high, ASCL1high/NEUROD1high, ASCL1low/NEUROD1low)

  sclc randomized ccle gse73160 boolean racipe network

• Calculating expected DNA remnants from ancient founding events in human population genetics.

  PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

  Full-text index only

  Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

  simulated forward-based size

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene