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).

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• DNA sequencing: bench to bedside and beyond.

  PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

  bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes.

  PMID 15886392 · PMC1092276 · Nucleic acids research · 2005 · 7 claims · 4 setups

  Full-text index only

  LE-PCR (linking PCR combined with emulsion PCR) enables molecular determination of haplotypes at two linked polymorphic loci without specialized instrumentation beyond real-time PCR

  leukocyte capped genomic plasma linking quantitative emulsion

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

  PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

  Full-text index only

  RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

  tcga cell-line same gtex bulk whole-exome whole-genome

• MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

  PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

  Full-text index only

  MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

  psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer

• An enhanced single base extension technique for the analysis of complex viral populations.

  PMID 19834618 · PMC2759544 · PloS one · 2009 · 8 claims · 7 setups

  Full-text index only

  The MDAP single base extension microarray platform measures nucleotide frequency at each genomic position in a complex population without requiring prior knowledge of candidate SNPs

  transcribed poliovirus array-bound array single oligonucleotide sbe