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).

• Searching for SNPs with cloud computing.

  PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

  Full-text index only

  Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

  han local short simulated whole-genome cloud

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

  PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

  Has reproduction · 73

  De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

  suaeda rna-seq novo blastx

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• A bioinformatic pipeline for simulating viral integration data.

  PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups

  Has reproduction · 96

  A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.

  aav2 host simulated integration simulated junction-crossing

• RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

  PMID 41222189 · PMC12857227 · GigaScience · 2026 · 8 claims · 8 setups

  Full-text index only

  RNA-SeqEZPZ is the first open-source tool offering a point-and-click interface with interactive plots, spanning raw FASTQ reads through differential gene and pathway analysis.

  generic paired-end aligned gene bulk adapter read

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• ArGD: An Integrated Database and Analysis Platform for Artocarpus Genomics and Transcriptomics.

  PMID 41595510 · PMC12840728 · Genes · 2026 · 7 claims · 6 setups

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  ArGD is the first publicly accessible platform centrally integrating genomic data for the genus Artocarpus

  seven artocarpus five user-submitted functional bulk differential