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).

Publications 1.3k Datasets 392.5k Experiments 772

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From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.

PMID 41810129 · PMC12969317 · Current research in microbial sciences · 2026 · 8 claims · 6 setups

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Dietary variables had the largest effect on microbiota composition among lifestyle factors tested

faecal 16s microbiota 16s volatile faecal
Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.

PMID 41037662 · PMC12877751 · Cancer discovery · 2026 · 8 claims · 7 setups

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ATAC-seq profiling of osteosarcoma patient samples, PDXs, and PDX-CLs reveals two distinct chromatin accessibility subtypes: early osteoblast-derived (EOD) and late osteoblast-derived (LOD)

n=8 pdx-derived pdx osteosarcoma atac-seq bulk h3k27ac
Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

PMID 41159380 · PMC12979040 · Neuro-oncology · 2026 · 8 claims · 8 setups

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A unified UMAP-based transcriptomic landscape built from 888 medulloblastoma and 370 ependymoma tumors reveals distinct clusters corresponding to known and novel molecular subtypes.

medulloblastoma ependymoma healthy shh bulk fusion copy
Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

PMID 41356191 · PMC12680593 · Theranostics · 2026 · 6 claims · 8 setups

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Berberine enhances energy metabolism (oxidative phosphorylation, ATP biosynthesis, fatty acid metabolism) in intestinal epithelial cells of DSS-induced mice, preserving normal physiological function

colon feces serum dss-induced single-cell targeted 16s
YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

PMID 41431390 · PMC13040214 · Cancer prevention research (Philadelphia, Pa.) · 2026 · 7 claims · 8 setups

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YAP1 nuclear localization and mRNA expression significantly increase in luminal epithelial cells (LEp) with increased age and with genetic risk for breast cancer (e.g., BRCA1/2 mutation carriers)

breast hmec post-stasis 184d-p16sh ihc bulk odds
CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

bulk previously round paired transfer-learning cross-species
Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

PMID 41515103 · PMC12787715 · Plants (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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295 AP2/ERF transcription factor genes were identified and classified in the S. scabra genome

scabra representative hmm rna-seq qpcr
Temporal constraints on enhancer usage shape the regulation of limb gene transcription.

PMID 41526337 · PMC12795824 · Nature communications · 2026 · 8 claims · 6 setups

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Putative enhancer repertoires at limb developmental gene loci shift over time, with distinct early-acting, common-acting, and late-acting enhancers.

limb shox2 h3k27ac transgenic bulk
Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial
EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

dbps tfs common ctcf deep comparative feature-ablation
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex.

PMID 24883252 · PMC4034613 · PeerJ · 2014 · 8 claims · 8 setups

Has reproduction · 54

All three allopolyploid species are fixed hybrids combining the genomes of the two putative diploid parents hypothesized on the basis of previous crossing and molecular work.

pooled perennial allopolyploid snp single-end read homoeologue
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

PMID 41540084 · PMC12894745 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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The presence of immune cells in the environment significantly alters CLL cell activation

autologous monoculture non-adherent pbmc bulk flow deconvolution
Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

colorectal colon patients bulk single-cell spatial bulk
IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

PMID 41559031 · PMC12819398 · Cell discovery · 2026 · 8 claims · 8 setups

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Aging reduces hASC self-renewal, lineage plasticity (adipogenic/osteogenic differentiation), and in vivo tissue repair efficacy

i-hascs full-thickness nude hascs edu scratch adipogenic
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
Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell
bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

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bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

tcga gtex stem embryonic paired semi-synthetic single-cell
Haplotype-resolved chromosome-level genome assembly of an autohexaploid oil camellia tree Camellia osmantha.

PMID 41663440 · PMC12996448 · Scientific data · 2026 · 8 claims · 8 setups

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First haplotype-resolved chromosome-level genome assembly generated for a hexaploid oil camellia (C. osmantha 'Yidan')

leaves fresh pacbio root pacbio hi-c whole-genome
CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

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CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex
Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

PMID 41689074 · PMC13005531 · Genome medicine · 2026 · 8 claims · 8 setups

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5,507 lead signals (P<5x10^-9) were identified for seven LFQBs across ancestries, including 210 novel loci

hope biobank combined cross-ancestry gwas cross-ancestry functional-informed

Experiments

From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.

Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.

Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

Temporal constraints on enhancer usage shape the regulation of limb gene transcription.

Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex.

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

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

Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

Haplotype-resolved chromosome-level genome assembly of an autohexaploid oil camellia tree Camellia osmantha.

CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.