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).

• Hobbes: optimized gram-based methods for efficient read alignment.

  PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups

  Has reproduction · 83

  Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.

  genome hg18 example reference read-mapping character-substitution algorithmic

• randPedPCA: rapid approximation of principal components from large pedigrees.

  PMID 40877802 · PMC12392600 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 2 setups

  Has reproduction · 84

  Matrix-vector multiplication with the dense additive relationship matrix A can be performed implicitly and efficiently via forward/backward substitution using the sparse inverse relationship (Cholesky) factor L^-1, avoiding explicit construction of A.

  simulated kennel computational pedigree

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction.

  PMID 41734278 · PMC12975283 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  RUMINA improves detection accuracy of ultra-low frequency SNVs (0.01%-1%) compared to UMI-tools and UMICollapse

  hiv simulated empirical clinical simulated umi iclip

• DAESC + : high-performance, integrated software for single-cell allele-specific expression data.

  PMID 41851619 · PMC13169709 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  DAESC+ is a dual-module, end-to-end software package (DAESC-P for preprocessing, DAESC-GPU for differential analysis) for single-cell ASE data

  onek1k endoderm simulated single-cell differential runtime

• Cell neighborhood topology directs rare cell population identification.

  PMID 41912521 · PMC13199379 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  RareQ is a framework that quantifies neighborhood connectivity (Q), a cell-specific measure of kNN-graph cliquishness, to detect rare cell populations from single-cell and spatial omics data

  downsampled pbmc brain simulated scrna-seq cite-seq single-cell