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).
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Has reproduction · 75
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.
PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups
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.
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Learning collective multicellular dynamics with an interacting mean field neural SDE model.
PMID 41564117 · PMC12854464 · PLoS computational biology · 2026 · 7 claims · 5 setups
scIMF models multicellular dynamics as interacting diffusion processes using a McKean-Vlasov SDE solved via Neural SDE, with a Transformer-based cell-wise attention mechanism approximating the distribution-dependent drift term
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VIST: variational inference for single cell time series.
PMID 41535949 · PMC12892444 · Genome biology · 2026 · 8 claims · 6 setups
VIST is a VAE-based method that decomposes single-cell gene expression into time-dependent and time-independent latent components
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Has reproduction · 53
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups
spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data