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).

• 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

• Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.

  PMID 42206012 · PMC13202175 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups

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  AVITI and NovaSeq X Plus are highly comparable overall for variant-calling performance in WGS

  tumor mm1s aviti chr20 whole-genome pacbio small

• 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

• scSNViz: visualization and analysis of cell-specific expressed SNVs.

  PMID 41533688 · PMC12866635 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 7 setups

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  scSNViz is an R package for exploration, quantification, and visualization of expressed SNVs from cell-barcoded scRNA-seq data, supporting VAF estimation, SNV clustering, and 2D/3D visualization.

  prostate non-small cholangiocarcinoma neuroblastoma scrna-seq cell-level single-cell

• A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.

  PMID 41924242 · PMC13037781 · Bio-protocol · 2026 · 7 claims · 5 setups

  Has reproduction · 100

  ECCFP significantly improves eccDNA detection sensitivity, accuracy, and runtime efficiency compared to other pipelines

  nanopore trimmed aligned base sequencing adapter

• Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.

  PMID 34435438 · PMC9290141 · Molecular ecology resources · 2022 · 6 claims · 6 setups

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  Bisulphite conversion of unmethylated cytosines to thymines violates strand-complementarity assumptions of SNP callers and confounds true C->T SNPs with unmethylated cytosines, complicating SNP calling from bisulphite sequencing data.

  blood bismark-aligned bwa-mem-based gem3-based whole-genome snp

• Virus variant quantification with Orthanq.

  PMID 41639627 · PMC12930645 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, including in samples with mixed infections

  simulated real mixture sequencing sequencing-based pangenome variant

• The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

  PMID 36262335 · PMC9557141 · F1000Research · 2022 · 7 claims · 3 setups

  Has reproduction · 59

  The third BCM & DNAnexus hackathon produced nine software projects for SV analysis, of which eight are presented in this paper.

  long-read re-sequenced genomic long-read k-mer read-based

• Alignoth: portable and interactive visualization of read alignments.

  PMID 41392197 · PMC12777968 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  Alignoth is a command-line tool that generates self-contained, portable HTML reports of DNA sequencing read alignment pileups, with export to PNG, SVG, PDF, and JSON.

  synthetic test genomic report browser output

• Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.

  PMID 41796349 · PMC13081257 · Genome biology · 2026 · 8 claims · 5 setups

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  BADGER, an automated snakemake pipeline, was developed to simulate high-fidelity pedigrees and raw ancient DNA sequence data for benchmarking genetic relatedness methods

  genomes simulated pedigree ancient read

• scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

  PMID 42085187 · PMC13157062 · STAR protocols · 2026 · 8 claims · 6 setups

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  scPASU is a Snakemake-based workflow that quantifies APA from standard 3′ scRNA-seq data without requiring specialized library preparation

  ureter processed scrna-seq read poly

• Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.

  PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 7 setups

  Has reproduction · 92

  Draft genome sequences of three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri, one S. sonnei) are reported as a resource for AMR surveillance.

  shigella bacterial antimicrobial whole-genome

• RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

  PMID 42172220 · PMC13196991 · PloS one · 2026 · 8 claims · 8 setups

  Has reproduction · 63

  RAGER integrates widely-used bioinformatics tools into an automated Snakemake-based pipeline for joint analysis of RNA-seq and ATAC-seq data

  embryonic cd34+ shared promoter rna-seq atac-seq gsea

• Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

  PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

  six same polished each nanopore illumina novo

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome

• 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

• The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.

  PMID 41625985 · PMC12859430 · Wellcome open research · 2026 · 8 claims · 8 setups

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  The Phakellia ventilabrum genome assembly spans 211.92 Mb with 99.97-99.98% scaffolded into 25 chromosomal pseudomolecules

  phakellia pacbio genome microbial pacbio hi-c sequencing

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

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

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  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 fin whale, Balaenoptera physalus (Linnaeus, 1758) (Artiodactyla: Balaenopteridae).

  PMID 41657664 · PMC12877476 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly was produced for Balaenoptera physalus (fin whale) from a male specimen collected in Orkney, Scotland, as part of the Darwin Tree of Life project

  balaenoptera pacbio hi-c k-mer

• The genome sequence of the Gold Spangle, Autographa bractea (Denis & Schiffermüller), 1775 (Lepidoptera: Noctuidae).

  PMID 41710118 · PMC12910202 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level, haplotype-resolved genome assembly was produced for Autographa bractea (Gold Spangle)

  autographa pacbio hi-c k-mer