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 103

System / cell line: chromatin ✕ Assay: read ✕ Clear

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

Has reproduction · 90

A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

monocytes natural hematopoietic leukemia atac-seq hierarchical
Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.

PMID 41860998 · PMC13004010 · Science advances · 2026 · 8 claims · 6 setups

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Imatinib treatment induces transcriptional readthrough in K562 CML cells within 1 hour, before detectable gene expression or alternative splicing changes

k562 imatinib-resistant long-read short-read rt-qpcr
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
Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

Has reproduction · 91

Assembled the first chromosome-level genome of G. vermiculophylla: 77.5 Mb, 22 pseudochromosomes, contig N50 2.61 Mb, scaffold N50 3.16 Mb

vermiculophylla assembled predicted genome short-read nanopore hi-c
Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

stricta long-read short-read hi-c
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
Chromatin state architecture governs transcription factor accessibility across plant genomes.

PMID 41570051 · PMC12867329 · PLoS genetics · 2026 · 8 claims · 8 setups

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Chromatin states show a large degree of functional conservation between Arabidopsis thaliana and Marchantia polymorpha across more than 450 million years of land plant evolution

arabidopsis marchantia chromhmm atac-seq antibody-based
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
The chromosomal genome sequence of the common sea fan, Gorgonia ventalina (Linnaeus, 1758) (Malacalcyonacea: Gorgoniidae).

PMID 41625986 · PMC12856254 · Wellcome open research · 2026 · 7 claims · 6 setups

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A chromosome-level genome assembly was produced for Gorgonia ventalina with a total length of 339.18 Mb

gorgonia cobiont pacbio hi-c rna-seq
The genome sequence of the Purple Cloud, Actinotia polyodon (Clerck, 1759) (Lepidoptera: Noctuidae).

PMID 41696496 · PMC12902673 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosomal-level genome assembly was generated for Actinotia polyodon (Purple Cloud moth) from a single female specimen

actinotia 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

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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
The genome sequence of the Osiris Blue, Cupido osiris (Meigen, 1830) (Lepidoptera: Lycaenidae).

PMID 41798706 · PMC12963831 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly was produced for Cupido osiris (Osiris Blue butterfly)

cupido pacbio hi-c k-mer
The genome sequence of the Bicolour Sedge, Triaenodes bicolor (Curtis, 1834) (Trichoptera: Leptoceridae).

PMID 41852352 · PMC12993304 · Wellcome open research · 2026 · 7 claims · 8 setups

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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
The genome sequence of the Madeiran Speckled Wood, Pararge xiphia Hübner, 1819 (Lepidoptera: Nymphalidae).

PMID 41908930 · PMC13022564 · Wellcome open research · 2026 · 6 claims · 8 setups

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A chromosome-level genome assembly was generated for a male Pararge xiphia specimen, containing two haplotypes of 528.41 Mb and 523.51 Mb

organism pacbio assembled pacbio hi-c k-mer
The genome sequence of the Eastern Rock Grayling, Hipparchia syriaca (Staudinger, 1871) (Lepidoptera: Nymphalidae).

PMID 41913757 · PMC13033134 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly was generated for Hipparchia syriaca (Eastern Rock Grayling) from a female specimen collected in Măcin, Romania

organism pacbio assembled pacbio hi-c k-mer
The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.

PMID 41913758 · PMC13033139 · Wellcome open research · 2026 · 6 claims · 7 setups

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Genome assembly of Anodontia alba (buttercup lucine) with total length 1,862.85 Mb, 99.28% scaffolded into 18 chromosomal pseudomolecules

anodontia microbial pacbio hi-c sequencing
The genome sequence of the European Pepper moth, Duponchelia fovealis (Zeller, 1847) (Lepidoptera: Crambidae).

PMID 41929846 · PMC13040225 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level, haplotype-resolved genome assembly was generated for Duponchelia fovealis

organism pacbio assembled pacbio hi-c k-mer
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

Full-text index only

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 chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.

PMID 42116832 · PMC13157608 · Wellcome open research · 2026 · 7 claims · 8 setups

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Aurelia sp. 4 chromosomal genome assembly has a total length of 462.10 Mb with 99.99% of sequence scaffolded into 21 chromosomal pseudomolecules

aurelia microbial pacbio hi-c rna-seq

Experiments

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.

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

Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

Chromatin state architecture governs transcription factor accessibility across plant genomes.

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

The chromosomal genome sequence of the common sea fan, Gorgonia ventalina (Linnaeus, 1758) (Malacalcyonacea: Gorgoniidae).

The genome sequence of the Purple Cloud, Actinotia polyodon (Clerck, 1759) (Lepidoptera: Noctuidae).

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

The genome sequence of the Osiris Blue, Cupido osiris (Meigen, 1830) (Lepidoptera: Lycaenidae).

The genome sequence of the Bicolour Sedge, Triaenodes bicolor (Curtis, 1834) (Trichoptera: Leptoceridae).

The genome sequence of the Madeiran Speckled Wood, Pararge xiphia Hübner, 1819 (Lepidoptera: Nymphalidae).

The genome sequence of the Eastern Rock Grayling, Hipparchia syriaca (Staudinger, 1871) (Lepidoptera: Nymphalidae).

The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.

The genome sequence of the European Pepper moth, Duponchelia fovealis (Zeller, 1847) (Lepidoptera: Crambidae).

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 chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.