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).

• Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

  PMID 38883333 · PMC11179850 · Horticulture research · 2024 · 7 claims · 7 setups

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  A haplotype-resolved telomere-to-telomere (T2T) genome of plum (P. salicina cv. 'Fengtangli') was assembled into two gap-free haplotypes of 251.25 and 251.29 Mb.

  plum four appm genes pacbio hi-c k-mer

• Extensive variation between chromosomes of North American and European hop.

  PMID 42204144 · PMC13216280 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 87

  Chromosome-scale, haplotype-resolved genome assemblies of the hybrid hop cultivar Apollo were generated using hifiasm, ALLHiC, and TRITEX pipelines with PacBio HiFi and Hi-C data

  hop feral biparental accessions pacbio busco fluorescence

• The genome sequence of Menetries' Clouded Yellow, Colias thisoa Ménétriès, 1832 (Lepidoptera: Pieridae).

  PMID 41716938 · PMC12914173 · Wellcome open research · 2026 · 8 claims · 7 setups

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  A chromosome-level, haplotype-resolved genome assembly was generated for Colias thisoa as part of Project Psyche

  colias pacbio assembled scaffolded pacbio hi-c k-mer

• 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

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  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 Basking Shark, Cetorhinus maximus (Gunnerus, 1765) (Lamniformes: Cetorhinidae).

  PMID 41938266 · PMC13044535 · Wellcome open research · 2026 · 8 claims · 7 setups

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  The Cetorhinus maximus genome was assembled into two haplotypes with total lengths of 3993.85 Mb (hap1) and 3817.33 Mb (hap2)

  heart pacbio assembled 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

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

  organism dissected pacbio hi-c rna-seq

• The Nuclear and Mitochondrial Genomes of the Lined Rockskipper, Istiblennius lineatus (Teleostei: Blenniidae).

  PMID 42117780 · PMC13195801 · Genome biology and evolution · 2026 · 7 claims · 8 setups

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  A chromosome-scale nuclear genome assembly of I. lineatus (643.23 Mb, 24 pseudochromosomes) was generated using PacBio HiFi reads and Arima Hi-C scaffolding.

  istiblennius lineatus pacbio hi-c rna-seq

• Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.

  PMID 42203797 · PMC13216315 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated 20 near-complete haplotypes from 10 Japanese male individuals using PacBio HiFi, ONT ultra-long, and Omni-C reads, all with contig N50 exceeding 100 Mbp

  japanese pacbio oxford omni-c

• Improved chromosome-level genome assembly of the American cockroach, Periplaneta americana.

  PMID 41123565 · PMC12774602 · G3 (Bethesda, Md.) · 2026 · 8 claims · 7 setups

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  Produced the first chromosome-level genome assembly of P. americana, scaffolded into 17 chromosome-scale scaffolds consistent with karyotype

  leg midgut assembled blattodea pacbio hi-c bulk

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• 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

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

  duospilus pacbio hi-c rna-seq

• Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.

  PMID 41491791 · PMC12771794 · BMC microbiology · 2026 · 6 claims · 6 setups

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  Swab material (Core Swab A, Core Swab B, Pap Brush) causes minimal variation in bacterial composition, DNA yield, and host DNA contamination.

  vaginal artificial clinical 16s pacbio extraction host

• Chemically guided single-cell transcriptomics reveals sulfotransferase-mediated scaffold remodeling in securinine biosynthesis.

  PMID 41577683 · PMC12929733 · Nature communications · 2026 · 8 claims · 8 setups

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  FsMS is a ketoreductase that reduces premenisdaurilide to menisdaurilide

  suffruticosa synthetic nicotiana pacbio single-cell d2o

• ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.

  PMID 41626876 · PMC12862641 · Genome biology and evolution · 2026 · 7 claims · 8 setups

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  High-quality chromosome-level reference genomes were assembled for four previously unsequenced Culex species

  whole-organism assembled annotated individual pacbio hi-c poly

• Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.

  PMID 41634861 · PMC12955163 · Genome biology · 2026 · 8 claims · 8 setups

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  PHap is a new pipeline that enables haplotype-resolved, near-T2T assembly of autopolyploid genomes using only standard HiFi, ONT-UL, and Hi-C sequencing data

  autotetraploid parental huashu4 pacbio hi-c illumina

• Haplotype-resolved chromosome-level genome assembly of an autohexaploid oil camellia tree Camellia osmantha.

  PMID 41663440 · PMC12996448 · Scientific data · 2026 · 8 claims · 8 setups

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  First haplotype-resolved chromosome-level genome assembly generated for a hexaploid oil camellia (C. osmantha 'Yidan')

  leaves fresh pacbio root pacbio hi-c whole-genome

• A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.

  PMID 41673035 · PMC13002930 · Scientific data · 2026 · 8 claims · 7 setups

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  Generated a chromosome-scale, phased reference genome of Argania spinosa using PacBio HiFi long reads combined with Hi-C scaffolding

  argania pacbio assembled pacbio hi-c rna-seq

• A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.

  PMID 41678351 · PMC13042314 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  A haplotype-complete, chromosome-level genome assembly of octoploid U. humidicola cv. Tully was generated from PacBio HiFi reads alone

  humidicola chromosomes urochloa additional pacbio busco proteome

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• The genome sequence of the tub gurnard, Chelidonichthys lucerna (Linnaeus, 1758) (Perciformes: Triglidae).

  PMID 41625984 · PMC12856256 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A genome assembly was generated for Chelidonichthys lucerna (tub gurnard) with two haplotypes of 649.07 Mb (hap1) and 651.58 Mb (hap2)

  chelidonichthys pacbio hi-c sequencing