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).

• LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

  PMID 17386085 · PMC1847688 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  LIMPIC is a computational method for detecting protein peaks from linear-mode MALDI-TOF-MS data using background noise reduction and baseline removal followed by non-uniform threshold peak detection and multi-spectra detection-rate classification.

  in-vitro plasma maldi-tof signal baseline

• scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

  PMID 41632596 · PMC12866930 · Briefings in bioinformatics · 2026 · 8 claims · 6 setups

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  scGACL, a GAN integrated with multi-scale contrastive learning, is proposed to overcome the over-smoothing problem in scRNA-seq imputation

  simulated real-world scrna-seq scrna-seq clustering gene

• scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

  PMID 41907409 · PMC13019583 · iScience · 2026 · 8 claims · 8 setups

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  scMILD identifies condition-associated cells using only sample-level labels via a dual-branch MIL architecture with a shared encoder

  simulated lupus covid-19 ulcerative simulated mixture scrna-seq

• nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.

  PMID 42057295 · PMC13141149 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.

  real simulated seven pipeline metagenomic simulated clinical

• Empirical Bayes analysis of quantitative proteomics experiments.

  PMID 19829701 · PMC2759080 · PloS one · 2009 · 8 claims · 4 setups

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  Developed a new empirical Bayes framework that models log2 SILAC protein ratios and is robust to non-Gaussian tails and data sparsity, unlike Gaussian mixture models or Efron's original spline-based approach

  hela predicted computational silac utr gaussian

• 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