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 third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

  PMID 36262335 · PMC9557141 · F1000Research · 2022 · 7 claims · 3 setups

  Has reproduction · 59

  The third BCM & DNAnexus hackathon produced nine software projects for SV analysis, of which eight are presented in this paper.

  long-read re-sequenced genomic long-read k-mer read-based

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Detecting natural selection by empirical comparison to random regions of the genome.

  PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

  ceu genomic simulated long-read snp population

• Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

  PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

  Has reproduction · 68

  200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

  african lion crater simulated genome principal admixture

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel