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).

• 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

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  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

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

  PMID 41765919 · PMC13066037 · Scientific data · 2026 · 8 claims · 8 setups

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  B. polycarpa genome was assembled de novo using PacBio HiFi reads and Hi-C data to a size of 585.68 Mb with contig N50 of 12.62 Mb

  polycarpa illumina pacbio hi-c

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• A chromosome-level reference genome of an endangered plant Craigia yunnanensis.

  PMID 41771874 · PMC13065974 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly of C. yunnanensis was generated using PacBio HiFi sequencing and Hi-C scaffolding

  yunnanensis pacbio hi-c illumina

• Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires.

  PMID 41140028 · PMC12774592 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  Generated long-read genome assemblies for two P. theobromicola isolates (MB01960, P0449) and short-read assemblies for five additional isolates

  theobromicola additional cacao genomes long-read short-read rna-seq

• Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

  PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

  stricta long-read short-read hi-c