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).

• DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

  PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

  Full-text index only

  DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

  heart cortex visual brain spatial cell-type

• LIMPACAT: Multi-omics attention transformer for immune prediction in liver cancer using whole-slide imaging.

  PMID 41511965 · PMC12788640 · PloS one · 2026 · 8 claims · 6 setups

  Full-text index only

  LIMPACAT, a multiple instance learning attention transformer, predicts immune cell levels relevant to HCC prognosis directly from whole-slide images

  hcc simulated pbmc tcga-lihc scrna-seq type deconvolution

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• The gene expression landscape of disease genes.

  PMID 41664080 · PMC12983648 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  In tissues and cell types with established disease relevance, disease genes show higher and more specific gene expression than control genes

  gtex pubmed tabula archs4 differential magma anderson-darling

• ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

  PMID 41243977 · PMC12807738 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  ATACdb 2.0 expands data scale, adding mouse chromatin accessibility data and substantially expanding human samples, plus pseudo-bulk ATAC-seq profiles built from scATAC-seq data to increase cell type diversity

  geo scatac-ref bulk scatac-seq h3k27ac

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• Single nuclei and spatial profiling of sacrococcygeal teratomas reveals cellular composition and X inactivation heterogeneity.

  PMID 41565739 · PMC12949016 · NPJ precision oncology · 2026 · 7 claims · 4 setups

  Full-text index only

  snRNA-seq and spatial transcriptomics of eight SCTs identify five broad cell lineages (neuroectoderm, epithelia, stroma, endothelia, immune) resolved into 26 transcriptionally distinct subtypes

  postnatal prenatal aggregated single-nucleus single-cell spatial

• Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

  PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

  Full-text index only

  Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

  substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell

• Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

  PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

  Has reproduction

  Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

  nasal aggregated genes differentially whole-genome methylation tiling

• Transcription and potential functions of a novel XIST isoform in male peripheral glia.

  PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

  Full-text index only

  XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

  heart skeletal atlas peripheral scrna-seq aggregated scatac-seq

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

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

  Full-text index only

  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

• isoSeQL: comparing long-read isoforms across multiple datasets.

  PMID 41452740 · PMC12790818 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  isoSeQL enables comparison of long-read isoform profiles across multiple datasets by consolidating SQANTI3-annotated samples into a unified SQLite database with consistent isoform IDs

  gencode simulated gm12878 peripheral intron simulated long-read

• Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

  PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

  Full-text index only

  Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

  breast real colon tcga paired pseudobulk bulk