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).

• 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

• The effect of 16S rRNA region choice on bacterial community metabarcoding results.

  PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 8 setups

  Has reproduction · 59

  The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, enabling more precise distance-based OTU clustering.

  bacterial extracted filtered combined 16s pcr extraction

• Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

  PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

  corbicula six sediment filtered 16s radseq picrust2

• An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

  PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

  Full-text index only

  Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

  unrelated shanghai tsnps snp allele linkage

• Gene expression study on peripheral blood identifies progranulin mutations.

  PMID 18551524 · PMC2773201 · Annals of neurology · 2008 · 7 claims · 3 setups

  Full-text index only

  PGRN is highly expressed in peripheral blood (97th percentile of all array genes)

  peripheral blood-derived microarray direct real-time

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

  PMID 35046988 · PMC8761809 · Frontiers in plant science · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  SLDMS is a novel method for computing overlapping regions of sequencing reads using suffix array (SA), longest common prefix (LCP) array, document array (DA), and a monotonic stack.

  sequencing concatenated pacbio-hifi third-generation running-time suffix overlap

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• A crowdsourced set of curated structural variants for the human genome.

  PMID 32559231 · PMC7329145 · PLoS computational biology · 2020 · 8 claims · 8 setups

  Has reproduction · 71

  1235 manually curated SVs were produced that can be used to evaluate SV callers or train machine learning models

  hg002 crowdsourced short-read mate-pair

• An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

  PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.

  pearl old oxford bionano illumina