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).

• Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

  PMID 41530870 · PMC12888741 · Genome medicine · 2026 · 8 claims · 8 setups

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  MAAS integrates chromatin accessibility, CNVs, and SNVs from scATAC-seq data to identify functional tumor cell subpopulations

  tumor pediatric b-cell glioblastoma scatac-seq bulk gene

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

  PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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  13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

  13-lined retina 13lgs retinal single-cell scrna-seq chromvar

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

  PMID 41540108 · PMC13004696 · Nature medicine · 2026 · 7 claims · 7 setups

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  GPRC5D antigenic drift/mutational events occurred in 68.4% of relapsed cases following anti-GPRC5D TCE therapy (13/19 evaluable patients)

  cd138+ pbmcs cohort bulk single-cell targeted

• Partially shared multi-modal embedding learns holistic representation of cell state.

  PMID 41741805 · PMC13021527 · Nature computational science · 2026 · 8 claims · 5 setups

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  APOLLO automatically learns partial information sharing between multiple data modalities using an autoencoder with a partially overlapping latent space trained via latent optimization.

  simulated paired single simulation scrna-seq multiplexed

• A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.

  PMID 41663439 · PMC12996591 · Nature communications · 2026 · 7 claims · 7 setups

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  Aggregating peaks from 624 high-quality bulk ATAC-seq datasets defines ~1.4 million observed consensus peaks (cPeaks) covering ~30% of the genome.

  bulk scatac-seq cnn gm12878 bulk scatac-seq deep

• Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

  PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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  The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

  first-trimester decidual spots dnk 10x h&e type

• Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

  PMID 41673768 · PMC12998334 · Journal of experimental & clinical cancer research : CR · 2026 · 6 claims · 8 setups

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  Organoids derived from malignant effusions of PDAC patients reproducibly generate peritoneal metastases after orthotopic implantation into the pancreas of immunodeficient mice

  pdac organoids frozen pdox orthotopic single-nucleus single-cell

• Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.

  PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups

  Has reproduction · 82

  Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.

  dlx5 progenitors sections cortical scrna-seq trackerseq flashtag

• Rtf1-dependent transcriptional pausing regulates cardiogenesis.

  PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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  Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

  zebrafish embryo embryonic mescs crispr situ shrna