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).

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 99

  Existing Nanopore methylation detection tools present a tradeoff between false positives and false negatives and show high dispersion relative to expected methylation frequency values.

  coli individual lymphoblastoid na12878 nanopore per-read consensus

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

  PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

  Full-text index only

  C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

  chimpanzee intergenic genome-wide chi-square nucleotide-content

• Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features.

  PMID 41667493 · PMC13002996 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  6-base-CUT&Tag (6B-C&T) simultaneously maps G, A, T, C, 5mC, and 5hmC at antibody-targeted chromatin features on the same DNA fragment

  e14tg2a synthetic mescs mesc 6-base-cut&tag standard exonuclease

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc