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).

• Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

  PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

  hepg2 liver chip-seq quantitative co-immunoprecipitation

• Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

  PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

  ulcerans collection snp whole-genome comparative read

• Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

  PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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  Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

  peripheral array custom snp

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• Cone-rod dystrophy and a frameshift mutation in the PROM1 gene.

  PMID 19718270 · PMC2732717 · Molecular vision · 2009 · 7 claims · 6 setups

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  A novel homozygous frameshift insertion in PROM1 (c.1349insT) causes cone-rod dystrophy with high myopia in this consanguineous family

  patients genomic chromosomes clinical fluorescein full-field

• Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

  PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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  A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

  multiplex affected subjects cluster-specific family-based continuous wisconsin

• Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

  PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups

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  2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups

  postmortem trypsin-digested individual subjects difference mass micro

• Examination of tetrahydrobiopterin pathway genes in autism.

  PMID 19674121 · PMC2784255 · Genes, brain, and behavior · 2009 · 8 claims · 6 setups

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  PTS (6-pyruvoyl-tetrahydropterin synthase) shows significant nominal association with autism (p=0.009), not restricted to affected-male-only subset

  non-hispanic subset trios case snp two-point pedigree

• Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

  PMID 19656662 · PMC2744841 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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  Pyrosequencing™ can substitute for traditional sequencing methods, providing rapid (<1 h) and reliable detection of antibiotic resistance mutations in P. aeruginosa

  clinical extracted pcr fluoroquinolone-resistant kirby–bauer multiplex sanger

• High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

  PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

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  High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

  tumour serum nsclc comparative snp methylation

• Different molecular patterns in glioblastoma multiforme subtypes upon recurrence.

  PMID 19644652 · PMC2811648 · Journal of neuro-oncology · 2010 · 7 claims · 5 setups

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  Type 1 GBM (p53 mutation, no EGFR amplification) and type 2 GBM (EGFR amplification, no p53 mutation) conserve their original molecular pattern at relapse.

  paired gbm sequencing semiquantitative microsatellite

• CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

  PMID 41400832 · PMC12790814 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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  CholeraSeq is an automated, V. cholerae-specific Nextflow pipeline that processes WGS outbreak data from raw reads/assemblies to high-quality SNPs and phylogenies in near-real-time.

  cholerae recombination-masked pis read reference-based recombination

• The Genetic and Morphological Basis of Local Adaptation to Elevational Extremes in an Alpine Finch.

  PMID 41624103 · PMC12853319 · Ecology and evolution · 2026 · 8 claims · 6 setups

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  Birds in the warmer Piute Pass population were predicted to have longer wings and larger beaks per Allen's rule

  sierra body blood same morphometric feather whole-genome

• Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features.

  PMID 41667493 · PMC13002996 · Nature communications · 2026 · 8 claims · 8 setups

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  6-base-CUT&Tag (6B-C&T) simultaneously maps G, A, T, C, 5mC, and 5hmC at antibody-targeted chromatin features on the same DNA fragment

  e14tg2a synthetic mescs mesc 6-base-cut&tag standard exonuclease

• WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations.

  PMID 41685638 · PMC13042275 · G3 (Bethesda, Md.) · 2026 · 8 claims · 7 setups

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  WeavePop is a novel Snakemake-based, reproducible, scalable workflow that performs reference-based read mapping, assembly, annotation, small variant calling/effect prediction, and CNV detection for eukaryotic haploid organisms

  neoformans reference-based read windowed

• CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

  PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

  bmmc pbmc foetal cis-regulatory enhancer-promoter scalability

• 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

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

  PMID 41792463 · PMC13084053 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

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  Combining cfDNA methylome (EwingSign) and fragmentome analysis detects all clinically confirmed relapse events in EwS/CIC patients

  plasma cfdna t7-mbd-seq ichorcna fragment