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).

• Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

  PMID 41850291 · PMC13030954 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Metapipeline-DNA automates germline and somatic DNA sequencing analysis end-to-end, from raw reads through preprocessing, feature detection, QC, and visualization.

  pcawg giab pcawg-5 tumor-normal whole-genome germline somatic

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

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  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc

• 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

• From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland.

  PMID 41940667 · PMC13188883 · Applied and environmental microbiology · 2026 · 8 claims · 8 setups

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  Wastewater surveillance captures community circulation of ESBL-E. coli that overlaps with clinically relevant circulating strains

  esbl-producing esbl-e coli genome core-genome ezclermont

• 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

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• 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

• TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

  PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

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  TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

  drosophila combined motif chip-seq whole-animal

• 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

• 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

• CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance.

  PMID 41564866 · PMC12866162 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CHD1 and MAP3K7 loss additively sensitizes cancer cells to IFN-γ-induced death

  a375 crc-9 ht-29 vcap whole-genome autologous incucyte

• A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.

  PMID 24809511 · PMC4014436 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  The Helicosporidium nuclear genome is small and compact (~2.5-fold smaller than Chlorella and Coccomyxa) yet shows almost no evidence of functional/metabolic reduction.

  helicosporidium ten whole-genome transcriptome gene

• 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 chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae).

  PMID 41673002 · PMC13002913 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of Z. scutellata was generated using Illumina short reads, PacBio HiFi long reads, and Hi-C scaffolding

  scutellata single assembled whole-genome pacbio hi-c

• Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.

  PMID 41738836 · PMC13154841 · GigaScience · 2026 · 8 claims · 6 setups

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  Detection accuracy of eccDNA/circRNA tools is highly influenced by sequencing depth, alignment algorithm, and experimental enrichment protocol

  genome transcriptome muscle dnase1l3 simulated circle-seq atac-seq

• A disease model resource reveals core principles of tissue-specific cancer evolution.

  PMID 41741657 · PMC13149333 · Nature · 2026 · 8 claims · 8 setups

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  The Mouse Cancer Cell line Atlas (MCCA) is a broad-utility resource of 590 comprehensively characterized mouse cancer cell line models spanning 22 lineages and 46 disease types, accessible via a web portal (www.mcca.tum.de)

  mcca tumour immunocompetent paca whole-genome microscopy-based histopathology

• Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.

  PMID 41760692 · PMC13066446 · Scientific data · 2026 · 7 claims · 9 setups

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  A. haimaensis genome was assembled to chromosome level (4.27 Gb, scaffold N50 195.52 Mb, anchored to 22 chromosomes) using PacBio HiFi, Illumina, and Hi-C sequencing

  acharax haimaensis illumina pacbio hi-c