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).

• X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa.

  PMID 14641931 · PMC317313 · BMC pediatrics · 2003 · 7 claims · 5 setups

  Full-text index only

  This is the first fully characterized South African family with X-linked hyper-IgM syndrome (HIGM1)

  activated pbmcs genomic pcr flow rt-pcr long-range

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• The DNA sequence of the human X chromosome.

  PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

  Full-text index only

  The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

  pac selected chromosome clone-based shotgun comparative

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

  PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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  A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

  family patients peripheral-blood peripheral snp microsatellite sanger

• Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

  PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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  A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

  genomic family skeletal blood microsatellite direct multiplex

• Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

  PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

  kegg 8192x8192 user-submitted species pathway zoomable sequence

• DNA sequence and analysis of human chromosome 9.

  PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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  The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

  bac chromosome fibres chimpanzee clone-based restriction computational

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 7 claims · 8 setups

  Has reproduction · 80

  DME-mediated nicking enables DMN-seq (DMN+) to detect 5mC at single-base resolution by ligating adaptors only to 5mC-containing fragments generated by DME excision

  synthetic partially embryonic mesc dmn+ ubs-seq dmn–

• Mutation analysis of the Fanconi anaemia A gene in breast tumours with loss of heterozygosity at 16q24.3.

  PMID 10098735 · PMC2362253 · British journal of cancer · 1999 · 7 claims · 6 setups

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  The FAA gene is not the gene targeted by LOH at 16q24.3 in breast cancer

  breast tumour sscp exon-by-exon southern

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.

  PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups

  Has reproduction · 43

  N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management

  rice ir64 recombinant bulk biomass relative

• Differentiating human from animal isolates of Cryptosporidium parvum.

  PMID 9866750 · PMC2640237 · Emerging infectious diseases · 1998 · 7 claims · 5 setups

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  Two distinct genotypes of C. parvum (human/anthroponotic and bovine/zoonotic) exist, distinguishable by TRAP-C2 gene sequence differences at five nucleotide positions.

  parvum cloned aligned fecal pcr pcr-rflp sequencing

• LMPD: LIPID MAPS proteome database.

  PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

  uniprot kegg in-house oracle9i kegg database enzyme

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• Toxoplasma: the next 100years.

  PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups

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  Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling

  gondii mammalian cdna affymetrix sage