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).

• A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

  PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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  Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

  dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial

• 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

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

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  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution.

  PMID 41980945 · PMC13250166 · Nature communications · 2026 · 8 claims · 8 setups

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  Hi-Compass predicts cell-type-specific Hi-C contact maps using only ATAC-seq as cell-type-specific input, plus DNA sequence and a generalized CTCF binding profile

  gm12878 curated bulk training hi-c ctcf matched

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial