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).

• Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.

  PMID 41800729 · PMC12969758 · Molecular ecology resources · 2026 · 7 claims · 8 setups

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  VEHoP infers protein-coding regions from diverse input types (raw reads, draft genomes, transcriptomes, annotated genomes) and automates generation of orthologous alignments, concatenated supermatrices, and phylogenetic trees in a single pipeline run.

  ostreida crassostrea catfish insects phylogenomic sequencing reduced

• The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

  PMID 37036103 · PMC10084500 · GigaScience · 2022 · 8 claims · 8 setups

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  GEN-ERA is a unified, publicly available toolbox of 13 Nextflow workflows supported by 14 Singularity containers for reproducible microbial genomic/phylogenomic analyses in both bacteria and small eukaryotes.

  gloeobacterales gloeobacteraceae publicly ncbi-deposited phylogenomics ssu genome

• Epidemiology and phylogenomic characterization of the Clade IIb C.1 Mpox outbreak in Phnom Penh, Cambodia (2023-2024).

  PMID 41575511 · PMC12978180 · Emerging microbes & infections · 2026 · 8 claims · 8 setups

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  All Cambodian Mpox genomes belong to lineage C.1, nested within Clade IIb

  skin mpxv-positive raw cambodian real-time viral bioinformatic

• Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae).

  PMID 41595526 · PMC12841229 · Genes · 2026 · 8 claims · 7 setups

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  The E. seguinii mitogenome is the smallest and has the highest GC content of any known Eriobotrya species

  seguinii protein-coding mitogenomes whole-genome mitogenome repeat

• Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex.

  PMID 24883252 · PMC4034613 · PeerJ · 2014 · 8 claims · 8 setups

  Has reproduction · 54

  All three allopolyploid species are fixed hybrids combining the genomes of the two putative diploid parents hypothesized on the basis of previous crossing and molecular work.

  pooled perennial allopolyploid snp single-end read homoeologue

• Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae).

  PMID 41678355 · PMC13042277 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of the white-eyed mutant G. bimaculatus strain was generated using ONT + PacBio HiFi long reads integrated with Hi-C data

  bimaculatus nanopore pacbio hi-c

• 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

• First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

  PMID 41436027 · PMC12958814 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

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  This study produced the first genome assemblies of Neotropical Bombus (Thoracobombus) species, B. pauloensis and B. pullatus

  pauloensis masked long-read k-mer novo