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).

• 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

• 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

• 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

• 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

• 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

• Genetic Surveillance Reveals Differential Evolutionary Dynamic of Anopheles gambiae Under Contrasting Insecticidal Tools Used in Malaria Control.

  PMID 41773559 · PMC12954828 · Molecular ecology · 2026 · 6 claims · 8 setups

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  Despite substantial reductions in indoor mosquito densities, nucleotide diversity and linkage-disequilibrium-based estimates showed no significant decline in effective population size after intervention

  anopheles gambiae simulated whole-genome principal linkage

• Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs.

  PMID 41779860 · PMC12959415 · Science advances · 2026 · 8 claims · 8 setups

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  Tapirs reverted from a cathemeral ancestor to a nocturnal/crepuscular niche, accompanied by coordinated sensory reallocation: regressive vision (corneal opacity, reduced acuity) with enhanced auditory and chemosensory systems.

  terrestris single-copy mammalian tapir whole-genome comparative ancestral

• Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.

  PMID 41802886 · PMC13014123 · Molecular biology and evolution · 2026 · 8 claims · 8 setups

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  Genomic structural variations and gene family expansions contributed little to morphological (mimicry) evolution in Epicopeiidae

  epicopeiidae mencia ancestral chromosome-level whole-genome hi-c comparative

• Genetic analysis of Mycobacterium abscessus reveals genomic diversity linked to global plasmid distribution.

  PMID 41858613 · PMC12995706 · iScience · 2026 · 8 claims · 8 setups

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  Three novel plasmids (pMAB625-1, pMAB625-2, pMAB625-3) were identified in M. abscessus isolates Abs1-5, absent from type strain ATCC 19977.

  abscessus candidate whole-genome long-read antimicrobial

• A telomere-to-telomere reference genome assembly of the Hypomesus nipponensis.

  PMID 41888540 · PMC13187195 · Scientific data · 2026 · 8 claims · 8 setups

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  A gap-free T2T genome assembly (HNIP-T2T) of H. nipponensis was generated, spanning 526.31 Mb with contig N50 of 20.23 Mb, anchored to 28 pseudochromosomes with zero gaps

  nipponensis hnip-t2t whole-genome pacbio ont

• 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

• Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

  PMID 41935313 · PMC13188593 · Animal microbiome · 2026 · 8 claims · 8 setups

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  Genome-wide CNV scanning of dairy vs non-dairy goats identified 62,860 CNVs, with 115 under strong selection (top 1% Fst/Vst).

  goat gmecs lps-induced whole-genome immunofluorescence lentiviral

• Germline sequence variation within the ribosomal DNA is associated with human complex traits.

  PMID 41966685 · PMC13261666 · Cell genomics · 2026 · 8 claims · 5 setups

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  Germline rDNA sequence variant frequencies associate with multiple human complex traits in the UK Biobank, independently of rDNA copy number

  biobank genomes synthetic 28s whole-genome short-read genome-wide

• The genome landscape of Hong Kong feral cattle as a unique genetic resource.

  PMID 42006315 · PMC13091034 · iScience · 2026 · 8 claims · 8 setups

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  HKF cattle harbor high genetic diversity despite a declining effective population size, indicating untapped genetic potential

  hkf autosomal wgs whole-genome pca runs

• Characterization of retrocopies in 663 individuals with esophageal squamous cell carcinoma.

  PMID 42058905 · PMC13122676 · iScience · 2026 · 8 claims · 7 setups

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  RIST, a new pipeline combined with GRIPper, refines retrocopy insertion site breakpoints and target-site duplication (TSD) detection, improving on existing tools (GRIPper2, sideRETRO)

  paired tool escc parent whole-genome nanopore sequencing

• The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

  PMID 11178241 · PMC138858 · Genome biology · 2000 · 8 claims · 4 setups

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  The V. cholerae O1 (El Tor) genome consists of two chromosomes with asymmetrically distributed gene functions

  vibrio whole-genome microarray expression

• Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

  PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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  A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

  panel breast 250-gene candidate genome growth pathway

• 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