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).

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• Determining the quality and complexity of next-generation sequencing data without a reference genome.

  PMID 25514851 · PMC4298064 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  kPAL, an open-source alignment-free package, assesses sequencing data quality and complexity using k-mer frequency profiles and pairwise distances between them, without a reference sequence.

  rna-seq genome wgs exome k-mer rna-seq read

• The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

  PMID 41765919 · PMC13066037 · Scientific data · 2026 · 8 claims · 8 setups

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  B. polycarpa genome was assembled de novo using PacBio HiFi reads and Hi-C data to a size of 585.68 Mb with contig N50 of 12.62 Mb

  polycarpa illumina pacbio hi-c

• 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

• Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.

  PMID 41528732 · PMC12958813 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  High-quality de novo genome assemblies were generated for A. andreniformis and A. florea using a hybrid ONT long-read + Illumina short-read sequencing approach.

  andreniformis polished illumina unmasked genomic sequencing genome

• Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.

  PMID 41803406 · PMC13103082 · Communications biology · 2026 · 8 claims · 8 setups

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  A high-quality, chromosome-scale genome assembly of H. arachnoideus was generated using PacBio HiFi and Hi-C sequencing.

  arachnoideus pacbio high-throughput illumina

• Chromosome-level genome assembly of the blackchin tilapia (Sarotherodon melanotheron).

  PMID 41942530 · PMC13234295 · Scientific data · 2026 · 7 claims · 7 setups

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  A chromosome-level genome assembly of blackchin tilapia was generated with total length 1,027.41 Mb and scaffold N50 of 38.87 Mb, with 93.42% of sequence anchored to 22 chromosomes.

  muscle ten illumina assembled illumina ont hi-c

• Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.

  PMID 42049241 · PMC13124242 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Chromosome-level, phased diploid genome assemblies were generated for BJ and IMR-90 fibroblast cell lines spanning 5.9 and 6.0 Gbp with diploid QV exceeding 60

  imr-90 pacbio oxford hi-c

• A high-quality chromosome-level genome assembly of the endangered species Magnolia amoena.

  PMID 41781393 · PMC13076695 · Scientific data · 2026 · 8 claims · 8 setups

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  Generated a high-quality chromosome-level genome assembly of the endangered/vulnerable species Magnolia amoena using DNBSEQ-T7, PacBio HiFi, and Hi-C data

  amoena pooled short-read pacbio hi-c

• The chromosome-level genome assembly of Sitobion avenae Fabricius (Hemiptera: Aphididae).

  PMID 41981000 · PMC13249962 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly of Sitobion avenae was generated using PacBio HiFi, Illumina short-read, and Hi-C scaffolding data.

  sitobion winged illumina avenae pacbio illumina hi-c

• Unlocking the microbial studies through computational approaches: how far have we reached?

  PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

  Has reproduction

  Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

  clinical bacteriophage vaginal hbv ngs random whole-genome

• Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

  PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

  Has reproduction · 90

  Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

  cephalopholis analysis next-generation pacbio ont

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• Centromere organization and epigenetic regulation in Aristolochia fimbriata.

  PMID 41761339 · PMC13049873 · Genome biology · 2026 · 8 claims · 8 setups

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  A complete gapless telomere-to-telomere (T2T) genome assembly of A. fimbriata was constructed, substantially improving on the previous v1 assembly.

  aristolochia fimbriata pacbio hi-c cenh3

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

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

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

  yunnanensis pacbio hi-c illumina

• An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.

  PMID 41792167 · PMC13087180 · Scientific data · 2026 · 8 claims · 8 setups

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  An improved chromosome-level genome assembly of C. savignyi was generated using Illumina short reads, ONT long reads, and Hi-C data.

  savignyi illumina oxford hi-c

• Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).

  PMID 41824659 · PMC13089509 · Plant physiology · 2026 · 7 claims · 8 setups

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  A near-complete telomere-to-telomere genome assembly of E. cheiri was generated (244.33 Mb, 6 chromosomes)

  cheiri brassicaceae illumina pacbio hi-c

• Chromosome-Level Genome Assembly and Annotation of Piptanthus nepalensis (Hook.) Sweet.

  PMID 41912568 · PMC13199499 · Scientific data · 2026 · 7 claims · 8 setups

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  A chromosome-scale genome assembly of P. nepalensis was generated by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C chromatin interaction data.

  nepalensis assembled illumina whole-genome hi-c rna-seq

• 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 a parasitoid wasp, Netelia inedita (Kokujev, 1899) (Hymenoptera: Ichneumonidae).

  PMID 41938268 · PMC13049423 · Wellcome open research · 2026 · 7 claims · 8 setups

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  A genome assembly was generated for a female Netelia inedita specimen as part of the Darwin Tree of Life project

  netelia assembled pacbio hi-c sequencing