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).

• Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.

  PMID 35072628 · PMC8887901 · eLife · 2022 · 8 claims · 3 setups

  Has reproduction · 57

  mRNA vaccination induces antibody binding to additional Spike epitopes (NTD and CTD in S1) beyond those seen after mild infection (FP and SH-H in S2)

  serum combined phage-dms principal

• Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

  PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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  The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

  faecal mcra pure pcr rflp 16s

• Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

  PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

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  DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

  scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico

• Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

  PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence

  genomic driver coli individual whole-genome subtractive cloning

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• Analysis of human sarcospan as a candidate gene for CFEOM1.

  PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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  Sarcospan sequence is unmutated in all six CFEOM1 families studied

  yac genomic extraocular genome pcr direct immunofluorescence

• Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

  PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

  duvernoy's nigriceps rna-seq differential extraction

• 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

• Identification of novel DNA sequence motifs that modulate transcription in T cells.

  PMID 41514212 · PMC12879379 · BMC genomics · 2026 · 8 claims · 8 setups

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  Identified 2,036 novel DNA motifs enriched in regulatory regions of T-cell-specific genes

  t-cell non-t-cell cd4+ sequences rna-seq dnase-seq h3k27ac

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

  PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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  Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

  blood schizophrenia sjl serum proteomic differential comparative

• Determining the quality and complexity of next-generation sequencing data without a reference genome.

  PMID 25514851 · PMC4298064 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  kPAL, an open-source alignment-free package, assesses sequencing data quality and complexity using k-mer frequency profiles and pairwise distances between them, without a reference sequence.

  rna-seq genome wgs exome k-mer rna-seq read

• Physiology engages with functional genomics - at last.

  PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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  Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

  wild-type caenorhabditis kidney pcr qtl enu copas

• Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

  PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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  Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

  zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative

• Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

  PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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  Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

  genomic commercial plco unrelated targeted long-range genotyping