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).

• Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

  PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes

  orf coli rabbit cos-7 bioinformatic codon prokaryotic

• TassDB: a database of alternative tandem splice sites.

  PMID 17142241 · PMC1669710 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  TassDB is a relational database storing GYNGYN donor and NAGNAG acceptor tandem splice sites across eight species

  homo computational nagnag est maximum snp

• MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.

  PMID 41330639 · PMC12810180 · RNA (New York, N.Y.) · 2026 · 8 claims · 4 setups

  Has reproduction · 30

  CIMs are present and enriched in PIWI (piRNA) and Argonaute (miRNA) CLASH data and serve as molecular footprints of Argonaute binding on target mRNAs.

  elegans clash iclip sequencing

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

  PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups

  Has reproduction · 88

  C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.

  elegans clash bioinformatic iclip

• CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

  PMID 16995941 · PMC1592126 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  CROPPER is a web-based software resource that combines genomic data from heterogeneous sources using identifier and orthologous gene information from the Ensembl database.

  mus substantia transgenic mptp-lesioned western microarray self-organizing

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time