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).

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

  PMID 41882679 · PMC13019944 · Genome biology · 2026 · 8 claims · 7 setups

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  The majority of long-range intronic RNA duplexes detected genome-wide are mediated by inverted Alu-repeat elements.

  k562 hek293t chimpanzee computational splash eclip-seq

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

  PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

  Has reproduction · 90

  PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

  heart genome rna-seq rt-pcr

• Competition for the conserved branch point sequence influences physiological outcomes in pre-mRNA splicing.

  PMID 41860977 · PMC13004596 · eLife · 2026 · 8 claims · 8 setups

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  SF1 and QKI compete for a subset of intron branch sites with the sequence ACUAA in mammalian cells

  hepg2 computational hek293 c2c12 rna-seq motif western

• A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.

  PMID 41884004 · PMC13010111 · iScience · 2026 · 8 claims · 8 setups

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  Malignant cells cluster predominantly by tumor of origin, while non-malignant cells from the same tumors cluster by cell type independent of patient

  malignant non-malignant ovarian normal scrna-seq alternative paired

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic