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).

• Competitive enzymatic reaction to control allele-specific extensions.

  PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups

  Full-text index only

  Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.

  genomic immobilized four individuals multiplex protease-mediated effect

• Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

  PMID 28398514 · PMC5499547 · Nucleic acids research · 2017 · 6 claims · 6 setups

  Has reproduction · 77

  A sequence-independent biotin–streptavidin (SAv) roadblocking strategy using randomly biotinylated DNA templates can stall TECs across all template positions for cotranscriptional SHAPE-Seq, simplifying template preparation and reducing cost.

  coli randomly radiolabeled cotranscriptional exonuclease

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

  PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

  Has reproduction · 88

  CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

  synthetic sw480 circrnas rt-qpcr circrna primer

• SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells.

  PMID 32770939 · PMC7430845 · BMC genomics · 2020 · 8 claims · 5 setups

  Has reproduction · 94

  SOX10 binds preferentially at proximal promoter elements directly over TSSs in Schwann cells in vivo, identifying candidate SOX10-regulated promoters.

  sciatic schwann differentiating tn5prime chip-seq gene

• R2DT is a framework for predicting and visualising RNA secondary structure using templates.

  PMID 34108470 · PMC8190129 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  R2DT is a template-based computational framework/pipeline that predicts and visualises RNA 2D structure in standardised, community-accepted layouts

  rnacentral query input aligned covariance trna-specific structure-guided

• Description of a PCR-based technique for DNA splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C.

  PMID 16137330 · PMC1208860 · BMC biotechnology · 2005 · 7 claims · 7 setups

  Full-text index only

  Two adjacent Ara-C molecules incorporated into a PCR primer produce mild template-dependent polymerization termination, generating 5' overhangs usable for cohesive-end ligation.

  plasmid pcr gel-isolated ligated pcr gel ligation

• Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

  PMID 17537826 · PMC1933130 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  StSNP integrates dbSNP, PDB, KEGG, and NCBI Entrez data into a single web server for nsSNP analysis

  glutathione aldehyde sequences dbsnp comparative sequence-structure database

• Evolutionary trace annotation of protein function in the structural proteome.

  PMID 20036248 · PMC2831211 · Journal of molecular biology · 2010 · 8 claims · 7 setups

  Full-text index only

  ET-ranked residue clusters can be used to build 3D templates that predict GO function in enzymes and non-enzymes alike, without prior knowledge of functional mechanism.

  structural pdb pairs annotated evolutionary template support

• Primase-based whole genome amplification.

  PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

  genomic plasmids circular agarose picogreen dye-terminator

• nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

  PMID 36961337 · PMC10199315 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 88

  nf-core/isoseq is a new automated Nextflow-based pipeline that processes raw Iso-Seq subreads through to genome annotation (BED format) without requiring transcriptome assembly.

  organism-specific iso-seq reference mapped pacbio subread long-read

• Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.

  PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 83

  Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD

  tcga gse13213 gse31210 multiomics closest ssgsea

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Prediction, syntax and semantic grounding in the brain and large language models.

  PMID 41807493 · PMC12979642 · Scientific reports · 2026 · 8 claims · 6 setups

  Has reproduction · 86

  Nouns show significant pre-onset neural activity, suggesting enhanced anticipatory processing of this word class.

  healthy cortex german pre-trained magnetoencephalography electroencephalography source

• Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

  PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

  Has reproduction · 68

  viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

  transgenic elegans four gfp genetic template-independence

• Multiplexed genetic analysis using an expanded genetic alphabet.

  PMID 15319316 · PMC1592527 · Clinical chemistry · 2004 · 7 claims · 6 setups

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  MultiCode PLx is a three-step platform (PCR, target-specific extension, liquid chip decoding) performed in a single reaction vessel and completed in ~3 h

  genomic synthetic subset newborn multicode eracode automated

• Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

  PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

  pcr-amplified same sequence luciferase bioluminometric bati comparison

• Analysis of the human Alu Ye lineage.

  PMID 15725352 · PMC554112 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Two new Alu subfamilies, Ye4 and Ye6, were discovered, complementing the previously described Ye5 subfamily.

  draft genomic non-human geographically blast sequence pcr

• Assaying chromosomal inversions by single-molecule haplotyping.

  PMID 16721377 · PMC2690135 · Nature methods · 2006 · 8 claims · 4 setups

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  Haplotype Fusion PCR (HF-PCR) juxtaposes sequences flanking an inversion breakpoint on single DNA molecules via emulsion PCR, generating orientation-specific fusion products diagnostic of inversion genotype

  genomic yac haplotype pulsed template

• External contamination in single cell mtDNA analysis.

  PMID 17668059 · PMC1930155 · PloS one · 2007 · 8 claims · 6 setups

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  External DNA contamination is a real and non-negligible problem in single-cell mtDNA sequence analysis

  single current laboratory reagent mtdna two-step nested