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).

• High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

  PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

  Has reproduction · 85

  SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

  atlantic low-coverage genotyping genome

• Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.

  PMID 42046229 · PMC13171174 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Duplex-Indel is a Snakemake pipeline for somatic Indel calling from Tn5 transposase-based duplex sequencing data that requires consensus support from both DNA strands to minimize technical artifacts.

  colo829-t colo829-bl colo829-blt duplex tn5 bulk cosine

• scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data.

  PMID 41982479 · PMC13075984 · Bioinformatics advances · 2026 · 7 claims · 4 setups

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  scGeno, a categorical HMM, infers chromosome-level genotype states in mixed-genotype organisms by modeling sequential single-cell allelic expression ratios along chromosomes

  wild-type dnmt1 synthetic embryo single-cell posterior down-sampling

• bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

  PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

  tcga gtex stem embryonic paired semi-synthetic single-cell

• TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.

  PMID 41883585 · PMC13011251 · Molecular therapy. Nucleic acids · 2026 · 8 claims · 8 setups

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  TiSMeD integrates 6,782 methylomes, 16,894 transcriptomes, and 241 proteomes across 48 normal human tissues into a searchable database

  normal plasma case-control tcga methylation transcriptome proteomics