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).

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

  PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

  orthologous literature sequence pairwise

• INTERFEROME: the database of interferon regulated genes.

  PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

  Full-text index only

  INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

  chimp ifn-treated tissues irg microarray in-house basal

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

  PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction

  An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

  udn blood skin snvs whole-genome bulk splice-altering

• 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

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome