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).

• Discovery and characterization of Alu repeat sequences via precise local read assembly.

  PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups

  Has reproduction · 69

  Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads

  hgdp insertion-supporting candidate assembled genome discordant novo

• Determination of complete chromosomal haplotypes by bulk DNA sequencing.

  PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 97

  A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

  rpe-1 na12878 aneuploid linked-read hi-c bulk

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

  Full-text index only

  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• Searching for SNPs with cloud computing.

  PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

  Full-text index only

  Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

  han local short simulated whole-genome cloud

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene