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).

• BOAT: Basic Oligonucleotide Alignment Tool.

  PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

  same short-read snp

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

  PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

  hapmap bladder prostate simulated affymetrix simulation

• Method for determination of (-102C>T) single nucleotide polymorphism in the human manganese superoxide dismutase promoter.

  PMID 15598343 · PMC544190 · BMC genetics · 2004 · 6 claims · 4 setups

  Full-text index only

  A novel TaqMan allelic discrimination assay can reliably genotype the MnSOD -102C>T SNP from diverse DNA sources including blood, buccal swabs, frozen tissue, and paraffin blocks.

  genomic paraffin-embedded taqman pcr-restriction automated

• Invasive bacterial disease trends and characterization of group B streptococcal isolates among young infants in southern Mozambique, 2001-2015.

  PMID 29351318 · PMC5774717 · PloS one · 2018 · 7 claims · 6 setups

  Has reproduction · 97

  A notable young infant GBS disease burden persisted during 2001–2015 despite significant declines in overall IBD, neonatal mortality, and stillbirth rates.

  manhiça infants recovered stored demographic invasive gbs

• CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

  PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

  Has reproduction · 97

  CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

  simulated wgs reference same novo blast-based k-mer