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).

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

  Has reproduction · 68

  Siphonophorae is the first diverging clade within Hydroidolina.

  hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

  PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

  Has reproduction · 30

  Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

  mapped simulated rna-seq ict1 computational benchmarking 3'-seq

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

  PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 52

  A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

  vespid single-copy brain caste-biased bulk orthology principal

• Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.

  PMID 41641705 · PMC12873609 · Nucleic acids research · 2026 · 7 claims · 8 setups

  Full-text index only

  Screening 202 cyanobacterial genomes identified 402 CRSs matching known RNA families (Rfam and Rho-independent terminators) and 409 novel CRSs.

  cyanobacterial peptide aligned local comparative genome sequence

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• 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

• 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

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• The genome sequence of a window fly, Scenopinus jerei Pohjoismäki & Haarto, 2021 (Diptera: Scenopinidae).

  PMID 41953045 · PMC13054250 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  This assembly provides the first genomic resource for the family Scenopinidae (window flies)

  organism idscejere3 assembled pacbio hi-c rna-seq

• The chromosomal genome sequence of the feather duster worm, Sabellastarte sp. h YS-2021 (Sabellida: Sabellidae) and its associated microbial metagenome sequences.

  PMID 42255362 · PMC13234546 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A chromosomal-level genome assembly was generated for Sabellastarte sp. h YS-2021, with 97.94% of the sequence scaffolded into 14 chromosomal pseudomolecules

  sabellastarte microbial pacbio hi-c rna-seq

• The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.

  PMID 41835092 · PMC12988363 · Wellcome open research · 2026 · 7 claims · 7 setups

  Full-text index only

  A chromosome-level genome assembly of Lycopodina hypogea was generated, with total length 235.10 Mb and 98.85% of sequence scaffolded into 15 chromosomal pseudomolecules.

  lycopodina microbial hypogea pacbio hi-c rna-seq

• The genome sequence of the cabbage seedpod weevil, Ceutorhynchus obstrictus (Marsham, 1802) (Coleoptera: Curculionidae).

  PMID 42109707 · PMC13153772 · Wellcome open research · 2026 · 8 claims · 4 setups

  Full-text index only

  A chromosome-level genome assembly for Ceutorhynchus obstrictus was generated with total length 728.81 Mb

  organism dissected pacbio hi-c rna-seq

• High-quality genome assembly and annotation of the white-cheeked goby, Rhinogobius duospilus (Herre, 1935) (Gobiiformes: Oxudercidae).

  PMID 41248690 · PMC12869079 · G3 (Bethesda, Md.) · 2026 · 6 claims · 7 setups

  Full-text index only

  This is the first high-quality chromosome-level reference genome for R. duospilus

  duospilus pacbio hi-c rna-seq

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

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

  Full-text index only

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

  yunnanensis pacbio hi-c illumina

• A high-quality chromosome-level genome assembly of a feather star Glyptometra sp. from a deep seamount.

  PMID 41786724 · PMC13079724 · Scientific data · 2026 · 8 claims · 8 setups

  Full-text index only

  This is the first chromosome-level genome assembly of a feather star (Glyptometra sp. CNS01629) from a deep seamount

  genomic arm middle assembled k-mer whole-genome pacbio

• 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

  Full-text index only

  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