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 329

Assay: kegg ✕ Clear

Physiological and transcriptomic analyses reveal that exogenous silicon alleviate the response of tomato to salt stress.

PMID 41930998 · PMC13051611 · Plant signaling & behavior · 2026 · 8 claims · 7 setups

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Exogenous silicon alleviates NaCl-induced inhibition of tomato seedling growth (plant height, shoot/root fresh weight)

tomato growth chlorophyll mda
Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

PMID 41933362 · PMC13173987 · BioData mining · 2026 · 8 claims · 7 setups

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Single-cell analysis of integrated ovarian cancer datasets identifies 9 distinct mononuclear phagocyte clusters (MPC1-MPC9), of which MPC3, MPC5, and MPC7 are hypermetabolic

ovarian mpc annotated tcga-oc single-cell gene pseudotime
Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

PMID 41935313 · PMC13188593 · Animal microbiome · 2026 · 8 claims · 8 setups

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Genome-wide CNV scanning of dairy vs non-dairy goats identified 62,860 CNVs, with 115 under strong selection (top 1% Fst/Vst).

goat gmecs lps-induced whole-genome immunofluorescence lentiviral
Stimulation to secrete insulin induces pancreatic β-cell dysfunction through Tfe3 activation.

PMID 41940345 · PMC13049674 · iScience · 2026 · 8 claims · 8 setups

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Continuous glucose supplementation in mice induces Tfe3 nuclear accumulation in islet β-cells, associated with Mafa downregulation and impaired glucose tolerance

c57bl pancreas min6 intraperitoneal immunofluorescence insulin
De novo transcriptome assembly and annotation of Penaeus monodon hemocytes under WSSV infection and STAT knockdown.

PMID 41942475 · PMC13233909 · Scientific data · 2026 · 8 claims · 7 setups

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A validated de novo hemocyte transcriptome assembly and 12-library RNA-seq dataset for P. monodon under WSSV infection and PmSTAT knockdown is provided as a public resource.

penaeus monodon assembled predicted bulk novo busco
Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.

PMID 41946881 · PMC13057473 · Communications biology · 2026 · 8 claims · 7 setups

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Bivalent domains have higher GC content and stronger evolutionary conservation than monovalent regions

embryonic mesc random bivalent chip-seq rna-seq k-mer-based
Dietary conjugated linoleic acid enhances resistance to Salmonella infection by promoting PPARγ-mediated metabolic reprogramming and effector function in CD8⁺ T cells.

PMID 41964110 · PMC13078244 · Gut microbes · 2026 · 8 claims · 12 setups

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Dietary CLA supplementation enhances host resistance to Salmonella Typhimurium infection

ileal mice serum culture 16s untargeted bulk
Sphingosine-1-Phosphate-derived 2-Hexadecenal is a central mediator of ocular neovascularization by inhibiting Sphingosine-1-Phosphate receptor 5.

PMID 41980976 · PMC13079744 · Nature communications · 2026 · 8 claims · 8 setups

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Loss of ALDH3B1 impairs 2-HD detoxification and causes retinal vascular abnormalities in zebrafish without affecting trunk vasculature

zebrafish crispr quantitative immunoblot
A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

PMID 42014663 · PMC13230468 · Discover oncology · 2026 · 8 claims · 8 setups

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A 23-gene PARPi-sensor transcriptomic model stratifies ovarian cancer patients into high- and low-risk groups with significantly different overall survival, validated in TCGA and ICGC cohorts

pdx tcga prognostic tcia bulk non-negative univariate
Estimating in silico causal effects of DNA methylation on gene expression through genetic anchors in airway epithelium in asthma.

PMID 42018614 · PMC13101850 · Science advances · 2026 · 8 claims · 8 setups

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DNA methylation is a plausible causal driver of gene expression in the majority (73%) of tested eQTM pairs, more often than the reverse direction (28%)

nasal genes snps types eqtm eqtl causal
Bulk RNA-seq datasets analysis integration identifies robust drought-responsive genes and functional networks in Eucalyptus grandis.

PMID 42038403 · PMC13106539 · Frontiers in bioinformatics · 2026 · 7 claims · 7 setups

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Meta-analysis integration of three independent RNA-seq drought studies identifies 472 robust differentially expressed genes (274 up, 198 down) that remain significant across the full meta-analysis and all leave-one-out Jackknife iterations

grandis computational consistently bulk differential leave-one-out
Transcriptome analysis reveals DNA repair-related clues associated with divergent leaf nuclear DNA diversity in Leymus chinensis.

PMID 42040274 · PMC13106374 · Frontiers in plant science · 2026 · 7 claims · 6 setups

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LC-ZK2 exhibits fewer polymorphic sites and lower nucleotide/haplotype diversity than LC-W across three nuclear loci (MCM7, PsaE, PsaL), indicating more restricted leaf-scale sequence heterogeneity

leaf pcr novo qrt-pcr
Polyploidy-driven expansion and regulatory diversification of the Kelch repeat F-box gene family in sweetpotato.

PMID 42050392 · PMC13262408 · BMC genomics · 2026 · 8 claims · 8 setups

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KFB family size does not scale linearly with ploidy, reflecting lineage-specific gene retention and loss rather than genome multiplication alone

proteomes kfb four pairwise blastp physicochemical chromosomal
Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

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TAGs are linked to HGSOC progression and yield a candidate prognostic model

hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat
A causal glycerophospholipid-IL-18R1-CD9 axis connects lipid metabolism and T-cell activation in atopic dermatitis.

PMID 42061907 · PMC13132603 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

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1-palmitoyl-2-arachidonoyl-GPC (PA-GPC) is a protective metabolite against AD that acts primarily by downregulating IL-18R1

gwas skin training keratinocyte linkage two-sample bayesian
Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

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γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

crc γδt epithelial c4_cxcl13 single-cell differential pseudotime
A Cross-Species Single-Cell Atlas Reveals Conserved Regulatory Networks and Candidate Hearing Loss Genes in the Cochlea.

PMID 42074555 · PMC13115875 · Genes · 2026 · 8 claims · 8 setups

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A cross-species single-cell/single-nucleus RNA-seq atlas of human fetal and mouse postnatal cochlea identifies 19 conserved major cell types

cochlea fetal top scrna-seq snrna-seq cell-cell
Olfactory epithelium organoid models identify Ddit3 as a potential therapeutic target against inflammation-related olfactory sensory neuronal loss and functional deficit.

PMID 42088417 · PMC13137857 · International journal of biological sciences · 2026 · 8 claims · 8 setups

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Three inflammatory OE organoid models (LPS instillation, TNFα treatment, doxycycline induction) were established and mimic impaired cell proliferation and neuronal genesis seen in olfactory inflammation

organoid organoids ddit3 olfactory organoid bulk aav-shrna
A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

PMID 42111187 · PMC13157187 · iScience · 2026 · 8 claims · 8 setups

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cfDNAanalyzer integrates feature extraction, feature processing/selection, and machine learning model building into a single one-command-line toolkit for cfDNA genomic sequencing data

balanced breast healthy multi-cancer cfdna machine computational
Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.

PMID 42112332 · PMC13149443 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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A 6-gene (RGS20, ADA, AICDA, SLC12A5, RUFY4, CDK5RAP3) prognostic risk model was constructed for ccRCC from ammonia death-related genes

tcga-kirc gse159115 clinical bulk univariate gsea

Experiments

Physiological and transcriptomic analyses reveal that exogenous silicon alleviate the response of tomato to salt stress.

Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

Stimulation to secrete insulin induces pancreatic β-cell dysfunction through Tfe3 activation.

De novo transcriptome assembly and annotation of Penaeus monodon hemocytes under WSSV infection and STAT knockdown.

Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.

Dietary conjugated linoleic acid enhances resistance to Salmonella infection by promoting PPARγ-mediated metabolic reprogramming and effector function in CD8⁺ T cells.

Sphingosine-1-Phosphate-derived 2-Hexadecenal is a central mediator of ocular neovascularization by inhibiting Sphingosine-1-Phosphate receptor 5.

A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

Estimating in silico causal effects of DNA methylation on gene expression through genetic anchors in airway epithelium in asthma.

Bulk RNA-seq datasets analysis integration identifies robust drought-responsive genes and functional networks in Eucalyptus grandis.

Transcriptome analysis reveals DNA repair-related clues associated with divergent leaf nuclear DNA diversity in Leymus chinensis.

Polyploidy-driven expansion and regulatory diversification of the Kelch repeat F-box gene family in sweetpotato.

Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

A causal glycerophospholipid-IL-18R1-CD9 axis connects lipid metabolism and T-cell activation in atopic dermatitis.

Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

A Cross-Species Single-Cell Atlas Reveals Conserved Regulatory Networks and Candidate Hearing Loss Genes in the Cochlea.

Olfactory epithelium organoid models identify Ddit3 as a potential therapeutic target against inflammation-related olfactory sensory neuronal loss and functional deficit.

A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.