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).

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

  PMID 36869353 · PMC9983196 · Genome biology · 2023 · 8 claims · 5 setups

  Has reproduction · 64

  HiCFlow, a new bioinformatic pipeline, performs de novo haplotype assembly, phasing, and visualization of allele-specific (parental) chromatin conformation directly from Hi-C data without requiring pre-phased haplotypes.

  1-7hb2 gm12878 imr-90 lines region hi-c genome-wide

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.

  PMID 34471117 · PMC8410849 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 97

  Chromosome 3D structure in S. ambofaciens correlates with genetic compartmentalization during exponential phase, with the central region segmented into domains and quiescent terminal compartments

  streptomyces complete ambofaciens 3c-seq rna-seq comparative

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 4 setups

  Has reproduction · 64

  Nimbus is an end-to-end software suite for amplicon-based NGS data that tracks source amplicons through alignment and variant calling, with tools for trimming, alignment, SNP/InDel calling, QC and visualization.

  blood twin na15510 haloplex snp whole-exome

• Detection of mutations in EGFR in circulating lung-cancer cells.

  PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

  Full-text index only

  The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

  blood archived nsclc plasma microfluidic allele-specific standard

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates.

  PMID 41350938 · PMC12811392 · The EMBO journal · 2026 · 7 claims · 3 setups

  Has reproduction · 78

  Newly transcribed human sncRNAs undergo widespread post-transcriptional adenylation in two distinct forms: transient oligoadenylation and stable monoadenylation.

  hek global nascent differential