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).

• miRBase: tools for microRNA genomics.

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

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  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

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

  PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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  A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

  pre-mirnas test conserved-hairpin cross-species secondary svm cross-species

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Genomic organization of zebrafish microRNAs.

  PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

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  Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

  zebrafish candidate hairpin blast secondary comparative

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

  PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

  real combined pre-mirna training random independent repeated

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

  PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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  miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

  conserved putative mirna-target normal comparative machine mirna

• Comparative genomic analysis of prion genes.

  PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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  SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

  vertebrate multi-tissue aligned sprn comparative gene cdna

• Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

  PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

  genome affymetrix antisense mirna computational microarray sage

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

  PMID 36694127 · PMC9875403 · BMC bioinformatics · 2023 · 8 claims · 4 setups

  Has reproduction · 76

  Existing circRNA workflows are limited: none delineate circRNA-miRNA interactions and only one performs differential expression analysis, requiring users to supplement missing analysis types with in-house expertise

  paired-end rna-seq mature circrna read circrna mirna

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

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

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

  Has reproduction · 100

  34 lncRNA-associated loci are conserved between birds and mammals, and 12 of these were validated in chicken by RNA-seq.

  avian bird chicken covariance-model trna mirna

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

  tissues conditions randomized est-based mirna randomization

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger