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).

• BayesRare: Bayesian mixture model for population-level rare cell type detection in multi-subject single-cell RNA sequencing data.

  PMID 41632592 · PMC12867491 · Briefings in bioinformatics · 2026 · 8 claims · 4 setups

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  BayesRare is a hierarchical Bayesian mixture model framework for population-level rare cell type detection in multi-subject scRNA-seq data

  synthetic breast kidney parkinson's scrna-seq

• Cell neighborhood topology directs rare cell population identification.

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

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  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

• saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

  PMID 41709279 · PMC13019952 · Genome biology · 2026 · 8 claims · 5 setups

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  Replacing the library-size offset with the log of the total gene count in NB-based bulk RNA-seq models (edgeR/DESeq2) lets the mean-model parameters be interpreted as transcript/exon usage, unlocking these tools for differential usage and aberrant splicing without DEXSeq-style subject-specific blocking covariates.

  simulated bulk cohort aberrant differential exon

• DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

  PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups

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  DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.

  individual pooled individuals gatk-called whole-genome overlapped simulated

• GDSim: accurate simulation for single-cell transcriptomes based on the guided diffusion model.

  PMID 41978379 · PMC13076945 · Briefings in bioinformatics · 2026 · 8 claims · 4 setups

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  GDSim, a label-guided diffusion-based deep generative network, can simulate scRNA-seq data that closely reflects the true distribution of original data

  real simulated annotated scrna-seq subtype differential