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).

• Computational analysis of splicing errors and mutations in human transcripts.

  PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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  Retained introns are significantly shorter than constitutively spliced introns

  refseq genes intron exon computational splice prediction

• 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

• Designating eukaryotic orthology via processed transcription units.

  PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

  ortholog blat exon-intron blast-based

• Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

  PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

  refseq chicken random genome-wide quadparser regulatory

• Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

  PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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  More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

  dbest liver cultures refseq est oligoarray polymerase

• Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

  PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

  seraseq simulated small processed targeted simulated computation

• JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

  PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

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  Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

  encode genes invertebrate initio comparative training

• CEAS: cis-regulatory element annotation system.

  PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

  genome genomic chip-chip repeat-masked conservation

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated