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 1.8k

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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
Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus
Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

PMID 41472934 · PMC12745711 · Iranian journal of biotechnology · 2026 · 8 claims · 7 setups

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IL-1β can substitute for PAMPs in inducing DC maturation via a non-canonical pathway distinct from classical TLR-mediated activation

monocyte-derived dendritic bulk principal pathway
A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

PMID 41481381 · PMC13155955 · Blood · 2026 · 8 claims · 4 setups

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A 24-gene HSPC-derived weighted-sum expression score (MPN24) is prognostic for overall survival in myelofibrosis

peripheral lin-cd34+ pb-mncs pm-c1 bulk single-cell nanostring
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
Oxidative stress and GPX2 control pancreatic vs. non-pancreatic cell fate in human endoderm.

PMID 41484137 · PMC12881361 · Nature communications · 2026 · 8 claims · 8 setups

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GPX2 is a critical regulator of human posterior foregut differentiation, with oxidative stress acting as a key determinant of pancreatic vs. non-pancreatic cell fate

hpsc-derived hpsc fetal bulk immunofluorescence flow
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
Single-cell resolution of an open chromatin signature in persister tumor cells.

PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

non-malignant same epithelial tumor single-nucleus mitochondrial copy-number
De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

PMID 41492091 · PMC12948678 · Nature cancer · 2026 · 8 claims · 8 setups

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FGF4 supplementation during organoid patterning specifically induces pontine/rostral hindbrain brainstem identity

hes brainstem day developing bulk immunofluorescence scrna-seq
Deep-learning prediction of gene expression from personal genomes.

PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

gtex rosmap same monocyte paired mutagenesis chromhmm
Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

snscc bulk single-nucleus bulk single-nucleus methylation
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
Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.

PMID 41501500 · PMC12881478 · Communications biology · 2026 · 8 claims · 8 setups

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The white adipocyte transcriptional program is tightly linked to promoter-level modulation of H3K27ac and chromatin accessibility.

adipose asc-derived white ascs bulk atac-seq chip-seq
Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

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MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

bulk single-cell tcga glioma gsva aucell machine
Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

PMID 41503159 · PMC12770975 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

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Eight prominent imputation methods (MAGIC, SAVER, scVI, DCA, scBiG, kNN-smoothing, scImpute, ALRA) were systematically evaluated for their ability to recover the true non-zero expression fraction using simulated and real-world scRNA-seq data

basal tracheal airway k562 simulated scrna-seq imputation
Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

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RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

tcga cell-line same gtex bulk whole-exome whole-genome
Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB.

PMID 41505470 · PMC12810902 · PLoS genetics · 2026 · 8 claims · 6 setups

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1,25D treatment induces widespread transcriptional and chromatin accessibility changes in colonic organoids

colonic bulk atac-seq gene
Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.

PMID 41507177 · PMC12783615 · Nature communications · 2026 · 8 claims · 8 setups

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Silent SPIs display spurious antisense transcription originating from H-NS-free regions

salmonella facs hi-c chip
Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

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A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent
Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

liver hepg2 293t serum bulk single-cell oil

Experiments

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

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

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

Oxidative stress and GPX2 control pancreatic vs. non-pancreatic cell fate in human endoderm.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

Single-cell resolution of an open chromatin signature in persister tumor cells.

De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

Deep-learning prediction of gene expression from personal genomes.

Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

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

Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.

Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB.

Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.

Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.