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).

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon

• Recurring mutations found by sequencing an acute myeloid leukemia genome.

  PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

  Full-text index only

  Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

  aml-m1 tumor bone additional whole-genome snp gene-expression

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 6 setups

  Has reproduction · 86

  Plasmid types II and III have more stable size, larger core genomes, and phylogenies that track the chromosome, indicating predominantly vertical transmission

  rhizobium extrachromosomal plasmidome gse long-read k-mer genome

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

  PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 7 claims · 5 setups

  Has reproduction · 78

  Genomic profiling can identify malignant transformation in MGUS/SMM patients, distinguishing 'genomic MM' from 'genomic MGUS' despite identical clinical/morphologic presentation

  cd138+ mgus whole-exome whole-genome copy-number

• The formation of avian montane diversity across barriers and along elevational gradients.

  PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.

  forest population individuals single whole-genome f_st principal

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 5 setups

  Has reproduction · 100

  WGS-derived antibiotic resistance gene (ARG) coverage can be used to predict antimicrobial resistance in Gram-negative bacteria via machine learning

  gram-negative in-house args curated shotgun genome phenotypic

• A chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• 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

• Coverage of whole proteome by structural genomics observed through protein homology modeling database.

  PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

  orfs predicted modeled representative homology transmembrane intrinsic

• Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

  PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

  Full-text index only

  The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology

  tigr xanthomonas xcc ann wu-blast whole-genome

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

  Full-text index only

  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• Genomic signatures of migratory preference and historical whaling in eastern South Pacific humpback whales.

  PMID 41986456 · PMC13161203 · Communications biology · 2026 · 7 claims · 8 setups

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  Nuclear genomic data show no clear population structure among feeding grounds, indicating panmixia despite divergent migratory destinations

  megaptera same unrelated regional whole-genome relatedness population

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates

  sdsd sdse isolates genomes genome core-genome multilocus

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp 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

• PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

  PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 8 claims · 8 setups

  Has reproduction · 76

  Drug repurposing screen of the LINCS transcriptional signature database identified PI3K/mTOR/Akt inhibitors as the most prominent pharmacological class capable of repressing REDD1/FKBP51 expression.

  keratinocytes hacat skin ear computational rt-pcr western

• The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

  PMID 41671394 · PMC12951522 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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  Gouania slender and stout morphotypes evolved convergently at least twice within the genus, confirmed by 3D morphometrics and phylogenomics

  pelvic individuals draft gouania geometric barcoding phylogenomics