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).

Publications 1.3k Datasets 392.5k Experiments 24

System / cell line: hifi ✕ Assay: novo ✕ Clear

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

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

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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 Spanish Fritillary, Euphydryas desfontainii (Godart, 1819) (Lepidoptera: Nymphalidae).

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

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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
The genome sequence of the Two-tailed Pasha, Charaxes jasius (Linnaeus, 1767) (Lepidoptera: Nymphalidae).

PMID 41868653 · PMC13003222 · Wellcome open research · 2026 · 8 claims · 8 setups

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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
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

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

organism idscejere3 assembled pacbio hi-c rna-seq
The genome sequence of the Lesser Horseshoe Bat, Rhinolophus hipposideros (Bechstein, 1800) (Chiroptera: Rhinolophidae).

PMID 42004187 · PMC13090764 · Wellcome open research · 2026 · 8 claims · 6 setups

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A phased, chromosome-level genome assembly was produced for Rhinolophus hipposideros as part of the Bat1K and Darwin Tree of Life projects.

rhinolophus pacbio hi-c sequencing
The genome sequence of the Portuguese Dappled White, Euchloe tagis (Hübner, 1804) (Lepidoptera: Pieridae).

PMID 42028159 · PMC13100615 · Wellcome open research · 2026 · 7 claims · 8 setups

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A chromosome-level genome assembly was generated for Euchloe tagis (Portuguese Dappled White) as part of Project Psyche

euchloe pacbio hi-c k-mer
The genome sequence of the Northern Grizzled Skipper, Pyrgus centaureae (Rambur, 1839) (Lepidoptera: Hesperiidae).

PMID 42038589 · PMC13109703 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly was produced for Pyrgus centaureae (Northern Grizzled Skipper) as part of Project Psyche.

pyrgus pacbio hi-c rna-seq
The genome sequence of the Southern White Admiral, Limenitis reducta (Staudinger, 1901) (Lepidoptera: Nymphalidae).

PMID 42078575 · PMC13129534 · Wellcome open research · 2026 · 7 claims · 8 setups

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A chromosome-level genome assembly was generated for a female Limenitis reducta specimen, comprising two phased haplotypes.

reducta pacbio assembled haplotype pacbio hi-c k-mer
The genome sequence of the nematode Ostertagia ostertagi (Stiles, 1892) (Rhabditida, Trichostrongylidae).

PMID 42094077 · PMC13139848 · Wellcome open research · 2026 · 8 claims · 7 setups

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A chromosome-level genome assembly was generated for a single male specimen of Ostertagia ostertagi (isolate MOo2).

single pooled unassembled assembled pacbio hi-c k-mer
The genome sequence of Schreibers's Long-fingered Bat, Miniopterus schreibersii (Kuhl, 1817) (Chiroptera: Miniopteridae).

PMID 42180417 · PMC13197751 · Wellcome open research · 2026 · 8 claims · 7 setups

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A chromosome-level genome assembly was produced for Miniopterus schreibersii from a single male individual, comprising two phased haplotypes.

miniopterus assembled pacbio hi-c rna-seq
The genome sequence of Geoffroy's Bat, Myotis emarginatus (Geoffroy, 1806) (Chiroptera: Vespertilionidae).

PMID 42238844 · PMC13227098 · Wellcome open research · 2026 · 8 claims · 7 setups

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A chromosome-level genome assembly was generated for Myotis emarginatus (Geoffroy's Bat) as part of the Darwin Tree of Life Project

myotis pacbio hi-c rna-seq
MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism

arabidopsis grapevine pangenome invertebrate genome novo gene
Genetic polyploid phasing from low-depth progeny samples.

PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 73

WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

solanum illumina pacbio wh-ppg
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat

Experiments

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

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

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

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

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

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

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

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

The genome sequence of the Two-tailed Pasha, Charaxes jasius (Linnaeus, 1767) (Lepidoptera: Nymphalidae).

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

The genome sequence of the Lesser Horseshoe Bat, Rhinolophus hipposideros (Bechstein, 1800) (Chiroptera: Rhinolophidae).

The genome sequence of the Portuguese Dappled White, Euchloe tagis (Hübner, 1804) (Lepidoptera: Pieridae).

The genome sequence of the Northern Grizzled Skipper, Pyrgus centaureae (Rambur, 1839) (Lepidoptera: Hesperiidae).

The genome sequence of the Southern White Admiral, Limenitis reducta (Staudinger, 1901) (Lepidoptera: Nymphalidae).

The genome sequence of the nematode Ostertagia ostertagi (Stiles, 1892) (Rhabditida, Trichostrongylidae).

The genome sequence of Schreibers's Long-fingered Bat, Miniopterus schreibersii (Kuhl, 1817) (Chiroptera: Miniopteridae).

The genome sequence of Geoffroy's Bat, Myotis emarginatus (Geoffroy, 1806) (Chiroptera: Vespertilionidae).

MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

Genetic polyploid phasing from low-depth progeny samples.

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.