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).

• Developing a comprehensive database and search tool for single-cell ATAC-seq data.

  PMID 41545440 · PMC12816011 · Scientific reports · 2026 · 5 claims · 6 setups

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  scATAC.Explorer is a curated database containing 39 publicly available scATAC-seq datasets in a consistent format

  hematopoietic drosophila cancer scatac-seq sci-atac-seq sci-car

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see

• Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

  PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

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  SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

  pbmc bone skin embryos scrna-seq scnmt-seq asap-seq

• 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

• BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.

  PMID 41632825 · PMC12904586 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  BiCLUM consistently outperforms or matches existing integration methods across multiple RNA+ATAC and RNA+protein datasets in visualization and quantitative benchmarks

  pbmc kidney bmmc bmcite scrna-seq cite-seq

• Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset.

  PMID 41807428 · PMC13103403 · Scientific data · 2026 · 8 claims · 4 setups

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  A paired scRNA-seq and scATAC-seq dataset was generated from NPCs differentiated over Days 0, 7, 13, and 20 under baseline and Aβ 1-42 exposure conditions

  hipsc-derived hippocampal scrna-seq scatac-seq flow

• Interpretable and integrative analysis of single-cell multiomics with scMKL.

  PMID 40770488 · PMC12328712 · Communications biology · 2025 · 7 claims · 7 setups

  Has reproduction · 65

  scMKL outperforms SVM, EasyMKL, MLP, and XGBoost in classification accuracy (AUROC) across multiple single-cell cancer datasets

  mcf-7 t-47d small prostate 10x scrna-seq sciatac-seq

• CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

  PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

  pbmc fetal pancreas gse149683 matched unmatched cross-protocol

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

  PMID 41556506 · PMC12818872 · eLife · 2026 · 8 claims · 8 setups

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  Mouse TM contains three molecularly distinct, reproducible cell subtypes (TM1, TM2, TM3) identified by scRNA-seq and validated by IF/ISH

  limbal lmx1b scrna-seq snatac-seq immunofluorescence

• OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

  PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

  simulated classical degs naive simulated bulk real

• Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.

  PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification

  escs naive facs-isolated freshly bulk atac-seq chip-seq

• 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

• Dissecting gene regulatory networks governing human cortical cell fate.

  PMID 41565813 · PMC12999477 · Nature · 2026 · 8 claims · 6 setups

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  ZNF219, a previously uncharacterized transcription factor, represses neural differentiation in human cortical radial glia

  cortical rhesus single-cell scrna-seq immunocytochemistry

• 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

• 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

• 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

• 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

• 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