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).

• Rfam 15: RNA families database in 2025.

  PMID 39526405 · PMC11701678 · Nucleic acids research · 2025 · 8 claims · 6 setups

  Has reproduction · 68

  Rfamseq was expanded to 26,106 genomes, a 76% increase over Rfam 14.0, incorporating UniProt 2024_03 reference proteomes and additional viral genomes.

  rfamseq chains rfam hepatitis covariance structure-to-alignment covariation

• A novel mutation in the WFS1 gene identified in a Taiwanese family with low-frequency hearing impairment.

  PMID 17517145 · PMC1890544 · BMC medical genetics · 2007 · 7 claims · 6 setups

  Full-text index only

  A novel heterozygous missense mutation Y669H (2005T>C) in exon 8 of WFS1 was identified in affected family members but not in 100 controls (200 chromosomes)

  family genomic 10-member wfs1 pure direct pcr-rflp

• A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

  PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

  Full-text index only

  A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

  family k4425 embryonic scn9a-n641y linkage copy deletion

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• Autoimmune disease in a DFNA6/14/38 family carrying a novel missense mutation in WFS1.

  PMID 18688868 · PMC2586182 · American journal of medical genetics. Part A · 2008 · 8 claims · 5 setups

  Full-text index only

  A novel missense mutation c.2576G→A (p.R859Q) in WFS1 exon 8 causes autosomal dominant LFSNHL in this American family

  genomic wfs1 ceph affected pcr sanger population

• Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

  PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

  Full-text index only

  TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

  pakistani affected retina tissues linkage sanger race

• Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

  PMID 18997096 · PMC4836613 · Investigative ophthalmology & visual science · 2009 · 7 claims · 8 setups

  Full-text index only

  High T8993C mutant load (>77%) is associated with severe neurologic and/or retinal abnormalities, while low mutant load (42-54%) causes no detectable abnormalities.

  retina blood visual adaptive real-time genetic

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

  avian bird chicken covariance trna microrna

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups

  Has reproduction · 71

  A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).

  androctonus crassicauda paired-end coding homology

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• How accurately is ncRNA aligned within whole-genome multiple alignments?

  PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

  Full-text index only

  MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

  genome vertebrate nonhuman genomic sequence whole-genome covariance

• Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families.

  PMID 17900373 · PMC2082241 · BMC dermatology · 2007 · 8 claims · 4 setups

  Full-text index only

  This is the first SNP-based genome-wide linkage study of atopic dermatitis performed in an Asian population.

  japanese same genome-wide snp-based family-based targeted

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

  Full-text index only

  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal