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).

• 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

• 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

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

  PMID 12590655 · PMC149451 · BMC evolutionary biology · 2003 · 6 claims · 1 setups

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  RNA secondary structure folding shows a clear prevalence of antagonistic epistasis (β < 1) among reference sequences

  randomly

• Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

  PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

  Has reproduction · 85

  AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

  gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical

• Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

  PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

  random trans-acting tpo fibronectin minigene selex cdna

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

  archiveii bprna large-scale secondary cross-family self-supervised

• A surrogate-based approach for post-genomic partner identification.

  PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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  Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

  biotinylated tnf-β analysis secondary phage sequence secondary

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• Two novel myocilin mutations in a Chinese family with primary open-angle glaucoma.

  PMID 18776955 · PMC2530518 · Molecular vision · 2008 · 7 claims · 4 setups

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  Two novel MYOC mutations, Pro13Leu (38C→T) and Gln337Stop (1009C del), are likely responsible for POAG pathogenesis in this pedigree

  genomic family myoc pcr-rflp sequencing clinical

• Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

  PMID 19649175 · PMC2718852 · Molecular vision · 2009 · 8 claims · 6 setups

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  A heterozygous missense mutation c.607G>A in exon 6 of CRYBB2, causing p.Val187Met, is the probable causative mutation for congenital nuclear cataract in this family

  genomic basotho pcr restriction secondary

• Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.

  PMID 36513983 · PMC9749362 · BMC bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 99

  Long-read classifiers generally performed best among the 11 methods tested

  atcc zymobiomics taxonomic short-read