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 Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.

  PMID 41669879 · PMC13088316 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  SpecImmune is the first unified computational framework to simultaneously genotype HLA, KIR, IG, TCR, and CYP genes from long-read data.

  1kgp hprc hgsvc long-read targeted germline

• Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

  PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups

  Has reproduction · 75

  scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data

  aida merkel-cell 20k myeloma scrna-seq

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 4 setups

  Has reproduction · 50

  TOSCA is the first automated, modular open-source tumor-only somatic calling workflow for whole-exome and targeted panel sequencing, covering raw reads through variant classification.

  t-cell hcc1395 clinical targeted whole-exome

• From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.

  PMID 41810129 · PMC12969317 · Current research in microbial sciences · 2026 · 8 claims · 6 setups

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  Dietary variables had the largest effect on microbiota composition among lifestyle factors tested

  faecal 16s microbiota 16s volatile faecal

• Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer.

  PMID 41223332 · PMC13055634 · Cancer research · 2026 · 8 claims · 5 setups

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  HGSC tumors show high inter-patient heterogeneity in total de novo L1 insertion burden.

  hgsc pa-1 long-distance whole-genome validation

• Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.

  PMID 41776310 · PMC13004687 · Nature aging · 2026 · 8 claims · 7 setups

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  Young and estropausal female mice have distinct, separable gut microbial profiles (beta and alpha diversity) across multiple cohorts.

  fecal young gut vcd-induced 16s ovarian picrust2

• Screening of dystrophin gene deletions in Egyptian patients with DMD/BMD muscular dystrophies.

  PMID 11381192 · PMC3851408 · Disease markers · 2000 · 6 claims · 5 setups

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  Multiplex PCR screening of 18 dystrophin exons detected deletions in 55% of 100 Egyptian DMD/BMD families

  genomic egyptian same peripheral multiplex clinical electromyography

• Segmented filamentous bacteria are worldwide human gut commensals.

  PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

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  Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

  fecal sfb human-sfb-ml publicly pacbio maximum gram

• Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

  PMID 41540108 · PMC13004696 · Nature medicine · 2026 · 7 claims · 7 setups

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  GPRC5D antigenic drift/mutational events occurred in 68.4% of relapsed cases following anti-GPRC5D TCE therapy (13/19 evaluable patients)

  cd138+ pbmcs cohort bulk single-cell targeted

• A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

  PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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  A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

  genomic genome pcr real-time fluorescence sequence

• A chromosomally integrated bacteriophage in invasive meningococci.

  PMID 15967821 · PMC2212043 · The Journal of experimental medicine · 2005 · 8 claims · 7 setups

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  An 8-kb genetic island (NMA1792-NMA1799) is specifically associated with hyperinvasive meningococcal clonal complexes

  meningitidis culture czech patients comparative pcr nuclease

• Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

  PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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  Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

  formalin-fixed ffpe paired study direct pcr restriction

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II.

  PMID 19881469 · PMC4511341 · Journal of human genetics · 2009 · 8 claims · 6 setups

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  Screening all 72 exons of USH2A (long isoform) identifies significantly more mutations than screening only the short-isoform exons 1-21

  genomic ush2 ush2a sscp audiological ophthalmological

• Human stool contains a previously unrecognized diversity of novel astroviruses.

  PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

  Full-text index only

  Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

  stool consensus-pcr-positive negative one consensus specific sanger