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).

• 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

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

  Full-text index only

  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

  PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 7 claims · 8 setups

  Has reproduction · 95

  Genome-scale identification detected 254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs, and other Rfam-classified sncRNAs) in the P. ostreatus CCEF00389 genome assembly

  pleurotus ostreatus ccef00389 sncrnas whole-genome rna-seq rfam

• DFAST and DAGA: web-based integrated genome annotation tools and resources.

  PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

  Has reproduction · 89

  DFAST is a web-based genome annotation pipeline with integrated quality assessment (CheckM) and taxonomic assessment (ANI) that produces DDBJ submission-ready files

  lactobacillus representative lab genomes genome average novo

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.

  genome normal drosophila long short-read whole-genome synthetic

• 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

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

  Full-text index only

  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.

  PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups

  Has reproduction · 87

  A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi

  mangrove sediment quality-filtered bacterial whole-genome physicochemical laser

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups

  Has reproduction · 87

  A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)

  euglena gracilis consensus bulk in-house novo

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.

  PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups

  Full-text index only

  Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.

  tuberculosis additional whole-genome spoligotyping comparative

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• 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

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig

• Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

  PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

  pooled individual liver serum viral pcr strand-specific