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).

• Assessment of dispersion metrics for estimating single-cell transcriptional variability.

  PMID 41770747 · PMC12970974 · PLoS computational biology · 2026 · 7 claims · 4 setups

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  The variance-to-mean ratio (VMR/Fano factor) scales approximately linearly with increasing dispersion and is independent of dataset size.

  simulated manivannan lana-elola yuzwa computational scrna-seq

• Optimized mixed Markov models for motif identification.

  PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  OMiMa can incorporate more than NNSplice's pairwise dependencies

  simulated regulatory splice biological motif pairwise

• Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage.

  PMID 41779826 · PMC12959883 · eLife · 2026 · 8 claims · 5 setups

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  DeepTX is an interpretable, scalable deep learning inference framework that links mechanistic transcription models to scRNA-seq data to infer genome-wide transcriptional burst kinetics

  synthetic embryonic colorectal computational stochastic scrna-seq deep

• Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.

  PMID 42024616 · PMC13188987 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  MUSTARD is a trajectory-guided dimensionality reduction method for multi-sample, multi-condition scRNA-seq data that simultaneously captures gene expression variation along pseudotime and across samples

  simulated covid-su covid-stephenson tuberculosis data-driven scrna-seq pseudobulk-pca

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

  PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

  simulated classical degs naive simulated bulk real

• Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.

  PMID 42045691 · PMC13175893 · Nature genetics · 2026 · 6 claims · 7 setups

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  INSPIRE is a deep-learning method that unifies adversarial learning with a GNN-based encoder and integrated NMF to interpretably integrate multiple spatial transcriptomics datasets

  synthetic dorsolateral brain cortex simulated visium spatial

• A Statistical Framework for Measuring Reproducibility and Replicability of High-Throughput Experiments From Multiple Sources.

  PMID 41636474 · PMC12871010 · Statistics in medicine · 2026 · 8 claims · 3 setups

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  nestedIDR, a nested copula mixture model, extends the IDR framework to multi-lab studies by jointly modeling within-lab reproducibility and between-lab replicability

  simulated encode seqc simulation chip-seq rna-seq

• On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

  PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

  simulated serum preprocessed simulation mass high-resolution

• The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

  PMID 39549198 · PMC11979089 · GeroScience · 2025 · 9 claims · 2 setups

  Has reproduction · 54

  The Multi-State Epigenetic Pacemaker (MSEPM) can accurately model multiple methylation-associated factors (e.g., age, sex, cell-type) simultaneously.

  blood simulated methylation simulation

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding

• A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

  PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

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  A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

  pooled sickle centenarian snp pooled gene

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal

• Sensitive detection of somatic mutations in GC-rich cancer gene promoters.

  PMID 42088607 · PMC13136893 · NAR cancer · 2026 · 8 claims · 8 setups

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  Gene promoters, due to high GC content (CpG islands, ~70% of promoters), are systematically undersampled and have poor coverage in whole cancer genomes, causing missed somatic mutation calls

  gm12878 cancer ffpe lines hybrid whole-genome dnase-seq

• Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

  PMID 41746282 · PMC12998610 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  dominoSignal extends the Domino algorithm to enable statistical testing of differential cell-cell signaling between experimental conditions.

  single-cell simulated pdac per-sample single-cell simulation cell-cell

• TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

  PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 43

  TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

  mdr-tb paired-end raw bam whole-genome kraken raw

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• ASTROREPOMICS: A curated transcriptomic database for reproductive biology in space.

  PMID 41940322 · PMC13049440 · iScience · 2026 · 8 claims · 6 setups

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  ASTROREPOMICS integrates 17 rigorously normalized and batch-corrected transcriptomic datasets spanning multiple species and reproductive tissues

  pooled mus rattus pca-based combat differential