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 tumor-intrinsic WNT-inhibitory NOTUM program drives immune resistance in microsatellite stable colorectal cancer.

  PMID 42097145 · PMC13198260 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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  A distinct NOTUM/NKD1/APCDD1-high, WNT-inhibitory cancer cell population (WICC) emerges predominantly in advanced-stage MSS CRC

  crc patient-derived ibd mmr-proficient single-cell cell-cycle patient-level

• scSurv: a deep generative model for single-cell survival analysis.

  PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

  simulated tcga melanoma renal scrna-seq bulk single-cell

• singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.

  PMID 41838773 · PMC13008255 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  singIST provides explainable quantitative measures of disease model similarity to a human reference at the pathway, cell type, and gene levels

  skin ear simulated scrna-seq simulation

• A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.

  PMID 41980989 · PMC13253844 · Nature communications · 2026 · 8 claims · 7 setups

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  scDiffusion-X is a multi-modal latent denoising diffusion probabilistic model for single-cell multi-omics data generation, translation, and interpretation.

  openproblem 10x babel miniatlas paired modality augmentation

• Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

  PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

  skin combined annotated scrna-seq single-cell spatial cell2location

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

  PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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  ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

  lines chromosome embryonic transcription chip-seq chromhmm hi-c

• PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

  PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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  PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

  pah scrna-seq pah-former candidate scrna-seq transfer perturbation

• Predictive modeling of molecular activity underlying physical cell-cell interactions.

  PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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  Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

  tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq

• TRAP5 Inhibition Targeting Scar-Associated Macrophages Ameliorates Acute Kidney Injury to Chronic Kidney Disease Transition.

  PMID 41773735 · PMC13159109 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A distinct scar-associated macrophage (SM) subset marked by high Acp5/TRAP5, Ctsk, Mmp9, and Spp1 emerges and predominates during the renal remodeling/CKD phase after AAI-induced AKI

  kidney ckd aai unilateral single-cell velocity pseudotime

• Uropathogenic Escherichia coli invade luminal prostate cells via FimH-PPAP receptor binding.

  PMID 41507584 · PMC12872464 · Nature microbiology · 2026 · 8 claims · 8 setups

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  A 2D mouse stem cell-derived prostate epithelial organoid model was developed that mimics epithelial heterogeneity of the murine prostate

  prostate bladder immunofluorescence single-cell transepithelial

• 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

• Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

  PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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  cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

  discoideum single-cell scrna-seq dissecting

• Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

  PMID 42047819 · PMC13125642 · Cancer immunology, immunotherapy : CII · 2026 · 7 claims · 8 setups

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  A novel ecDNA-related Gene Prognostic Score Model (EGPSM) was constructed using an integrated framework of 101 machine learning algorithm combinations and validated in training, testing, and external cohorts.

  osteosarcoma treatment-naive bulk 143b bulk single-cell cibersort

• scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

  PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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  scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

  single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type

• 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

• Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

  PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

  dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount

• Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

  PMID 41637188 · PMC12932927 · Cell reports · 2026 · 8 claims · 8 setups

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  Combined MPRA enhancer assays, RNA-seq (DE/ATU) analysis, and CRISPR-Cas9 engineering to dissect the function of 94 rare non-coding variants (RNVs) associated with blood traits

  k-562 chrf-288-11 hl-60 thp-1 massively bulk crispr-cas9

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• 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