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).

• Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.

  PMID 41984780 · PMC13082667 · PLoS computational biology · 2026 · 7 claims · 4 setups

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  IGNITE is an unsupervised framework that infers directed, weighted, and signed GRNs directly from unperturbed scRNA-seq data using the inverse problem for a kinetic Ising model.

  pluripotent scrna-seq gene perturbation

• A comparative analysis of blastoid models through single-cell transcriptomics.

  PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 60

  EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

  blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov

• Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.

  PMID 41860983 · PMC13021174 · PLoS computational biology · 2026 · 8 claims · 8 setups

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  VeloVAE significantly outperforms previous RNA velocity methods in data fit, accuracy of inferred differentiation directions, and transcription rate estimation.

  pancreas developing induced embryo scrna-seq

• Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

  PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

  Has reproduction

  The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

  ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional

• Learning collective multicellular dynamics with an interacting mean field neural SDE model.

  PMID 41564117 · PMC12854464 · PLoS computational biology · 2026 · 7 claims · 5 setups

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  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

  zebrafish embryonic pancreatic temporal umap cell-wise

• Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

  PMID 41857393 · PMC13061643 · Nature neuroscience · 2026 · 8 claims · 6 setups

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  Adult spinal-cord-derived human oligodendroglia and astrocytes, but not microglia, show primed chromatin signatures at HOX loci and a putative SOX10 enhancer.

  postmortem induced lentiviral cns single-nucleus nanocut&tag high-resolution

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• Toward stem cell systems biology: from molecules to networks and landscapes.

  PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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  Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

  stem embryonic promyelocytic genome-wide serial chip-chip