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).

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene

• 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.

  PMID 41609375 · PMC12915991 · mSystems · 2026 · 8 claims · 1 setups

  Full-text index only

  Pipeline selection for MAG reconstruction is a nontrivial decision that must align user needs with workflow factors such as sequencing data type, analytical functions, and computational environment.

  metagenomic computational

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

  holacanthella duospinosa genome transcriptome phylogenomics

• The genome sequence of the leafhopper, Arthaldeus pascuellus (Fallén, 1826) (Hemiptera: Cicadellidae).

  PMID 41625988 · PMC12859417 · Wellcome open research · 2026 · 6 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was generated for Arthaldeus pascuellus, the first high-quality genome for the genus Arthaldeus

  organism pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the Provence Hairstreak, Tomares ballus (Fabricius, 1787) (Lepidoptera: Lycaenidae).

  PMID 41710119 · PMC12910201 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A genome assembly was produced for a male Tomares ballus specimen consisting of two haplotypes (839.94 Mb and 831.10 Mb)

  organism pacbio assembled pacbio hi-c k-mer

• The genome sequence of the Spanish Festoon, Zerynthia rumina (Linnaeus, 1758) (Lepidoptera: Papilionidae).

  PMID 41769331 · PMC12946699 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  A genome assembly for Zerynthia rumina was produced, containing two haplotypes of 852.84 Mb and 775.60 Mb

  organism genomic assembled haplotype pacbio hi-c k-mer

• The genome sequence of the Short-tailed Blue, Cupido argiades (Pallas, 1771) (Lepidoptera: Lycaenidae).

  PMID 41815329 · PMC12972722 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for a female Cupido argiades specimen, comprising two haplotypes of 445.87 Mb and 384.46 Mb.

  organism pacbio assembled pacbio hi-c rna-seq

• The genome sequence of the Spanish Fritillary, Euphydryas desfontainii (Godart, 1819) (Lepidoptera: Nymphalidae).

  PMID 41835093 · PMC12988360 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for Euphydryas desfontainii from a single male specimen, comprising two haplotypes of 755.68 Mb and 751.57 Mb

  organism euphydryas pacbio hi-c k-mer

• nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

  PMID 36961337 · PMC10199315 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 88

  nf-core/isoseq is a new automated Nextflow-based pipeline that processes raw Iso-Seq subreads through to genome annotation (BED format) without requiring transcriptome assembly.

  organism-specific iso-seq reference mapped pacbio subread long-read

• A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

  PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing

  oryzae whole-genome genome orthology

• The genome sequence of the Chalk Yellow-face Bee, Hylaeus dilatatus (Kirby, 1802) (Hymenoptera: Colletidae).

  PMID 41657665 · PMC12881847 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A two-haplotype genome assembly of Hylaeus dilatatus was produced, with total lengths of 307.38 Mb (haplotype 1) and 314.32 Mb (haplotype 2)

  hylaeus pacbio assembled barcoding pacbio hi-c

• 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

• SEAseq: a portable and cloud-based chromatin occupancy analysis suite.

  PMID 35193506 · PMC8864840 · BMC bioinformatics · 2022 · 7 claims · 2 setups

  Has reproduction · 94

  SEAseq is a comprehensive, infrastructure-independent pipeline that performs the major analyses needed to process ChIP-Seq/CUT&RUN chromatin binding datasets in a single execution

  any chip-seq cut&run

• The genome sequence of the cryptorhynchine weevil, Kyklioacalles roboris (Stüben, 2003) (Coleoptera: Curculionidae).

  PMID 41696497 · PMC12895102 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for the cryptorhynchine weevil Kyklioacalles roboris

  kyklioacalles pacbio hi-c k-mer

• The genome sequence of the soldier beetle, Malthodes minimus (Linnaeus, 1758) (Coleoptera: Cantharidae).

  PMID 41769330 · PMC12949377 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Malthodes minimus genome assembly has a total length of 583.60 Mb, with 97.75% scaffolded into 7 chromosomal pseudomolecules including X and Y sex chromosomes

  malthodes pacbio assembled alternate pacbio hi-c barcoding

• pmid-41852352

  PMID 41852352 · PMC12993304 · 7 claims · 8 setups

  Full-text index only

  A genome assembly was generated for a male Triaenodes bicolor specimen, comprising two haplotypes of 615.75 Mb and 613.86 Mb.

  triaenodes pacbio hi-c barcoding

• A cell biological perspective on genome research.

  PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups

  Full-text index only

  Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.

  saccharomyces caenorhabditis selected fruit genomic saturation physical

• Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

  PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

  Has reproduction · 84

  The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

  single glabripennis amino whole-genome gene busco

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• pmid-41868653

  PMID 41868653 · PMC13003222 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level, haplotype-resolved genome assembly was produced for Charaxes jasius (Two-tailed Pasha), with haplotype 1 at 465.23 Mb and haplotype 2 at 401.60 Mb.

  charaxes hifi assembled haplotype pacbio hi-c k-mer