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).

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• Genomics and public health: development of Web-based training tools for increasing genomic awareness.

  PMID 15888236 · PMC1327719 · Preventing chronic disease · 2005 · 7 claims · 4 setups

  Full-text index only

  Web-based training tools (Genomics for Public Health Practitioners and Six Weeks to Genomic Awareness) can increase genomic awareness among public health practitioners nationwide.

  michigan health visitors six post-session voluntary web

• Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

  PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups

  Full-text index only

  Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.

  mammalian aligned constrained sequence evolutionary comparative

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

  Full-text index only

  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• Policy implications of genetic information on regulation under the Clean Air Act: the case of particulate matter and asthmatics.

  PMID 16507451 · PMC1392222 · Environmental health perspectives · 2006 · 8 claims · 4 setups

  Full-text index only

  The Clean Air Act mandates protection of sensitive subpopulations, including asthmatics, from air pollution health effects, creating an opening for genetic susceptibility data in regulation.

  u.s epa asthma asthmatic statutory regulatory literature

• The ENCODE Project at UC Santa Cruz.

  PMID 17166863 · PMC1781110 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  The UCSC ENCODE portal serves as the primary repository and access point for sequence-based ENCODE pilot phase data

  genome mammals lines tissues radical sequence chromatin

• Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

  PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

  Has reproduction · 95

  The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

  catharanthus pacbio smrt pot experimental endpoint smrt

• Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

  PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 7 claims · 8 setups

  Has reproduction · 86

  HPVN24 is an avian pathogenic E. coli serotype O78:H9, sequence type ST23, with a 5.05 Mb genome and 50.57% GC content.

  coli hpvn24 strain hemolysis antibiotic

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

  Full-text index only

  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.

  PMID 36242054 · PMC9563170 · Microbiome · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  Three MAGs from a stratified salt crust represent a novel order, Nucleotidisoterales, within Ca. Nanohaloarchaeota

  stratified salt nanohaloarchaeota reconstructed 16s metagenomic phylogenomic