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).

• Persistence of alveolar fibroblast-derived ADAMTS4+ cells in a preclinical model of delayed pulmonary fibrosis resolution.

  PMID 42103706 · PMC13156320 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Lipofibroblasts (LIFs/AF1) differentiate into myofibroblasts during fibrogenesis, with the reverse (MyoFB-to-LIF) trajectory occurring during fibrosis resolution

  aged live facs-sorted scrna-seq h&e masson's rnascope

• 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

  Full-text index only

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

  faecal 16s microbiota 16s volatile faecal

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

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

  Full-text index only

  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

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

  Full-text index only

  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• p53 mutations occur in clinical, but not latent, human prostate carcinoma.

  PMID 7737911 · PMC5920585 · Japanese journal of cancer research : Gann · 1995 · 5 claims · 4 setups

  Full-text index only

  p53 point mutations occur in clinical prostate cancer but not in latent (subclinical) prostate carcinoma

  prostate sscp rflp direct

• Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

  PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

  Has reproduction · 80

  The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

  mpm mesomics whole-genome bulk methylation

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

  Full-text index only

  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• Multimodal learning reveals plants' hidden sensory integration logic.

  PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

  tomato multimodal transcriptomics metabolomics

• Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

  PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

  Full-text index only

  Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

  dorsolateral brain postmortem cortex h3k9ac bulk proteomics

• Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.

  PMID 42026624 · PMC13238118 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  SEAGALL combines a geometry-regularised autoencoder (GRAE) to embed cells and build a cell-cell graph with a graph attention network (GAT) classifier and GNNExplainer-based XAI to identify features driving cell type/phenotype.

  count same scchip-seq ten count latent classification

• DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

  PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups

  Has reproduction · 40

  DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.

  simulated real-world simulation scrna-seq-based

• Genetic subtraction reveals divergent pathways and targets in anxiety-related and anxiety-independent TMD.

  PMID 41796324 · PMC13081294 · The journal of headache and pain · 2026 · 8 claims · 8 setups

  Full-text index only

  Anxiety shows significant genetic correlation with TMD (rg=0.4417, p=1.98x10^-19)

  european tmd gwas gtex gwas gwas-by-subtraction bayesian

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

  PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 8 claims · 8 setups

  Has reproduction · 90

  Phage Mimer is the first described lytic ssDNA (Microviridae) phage targeting Pectobacterium

  phage conserved gpg cscl-gradient-purified whole-genome comparative intergenomic

• Bioavailable Nutrients (N and P) and Precipitation Patterns Drive Cyanobacterial Blooms in Missisquoi Bay, Lake Champlain.

  PMID 34683418 · PMC8537112 · Microorganisms · 2021 · 8 claims · 8 setups

  Has reproduction · 67

  High concentrations of N and P were typically measured in April and May, before blooms occurred.

  water filtered lugol's-iodine-preserved 16s 16s nutrient situ

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

  Full-text index only

  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• A unified framework for correcting batch effects and integrating multi-omics data.

  PMID 41786846 · PMC13079841 · Scientific reports · 2026 · 7 claims · 6 setups

  Full-text index only

  MoDAmix, a four-stage domain adaptation framework (pre-training, single-omics adversarial adaptation, multi-omics adversarial alignment, semi-supervised class alignment), unifies batch correction across multiple omics layers.

  brain aml same single-cell bulk k-means

• MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

  PMID 41811907 · PMC12998955 · PLoS computational biology · 2026 · 8 claims · 7 setups

  Full-text index only

  MultiPert reliably predicts both perturbed gene expression and protein abundance profiles from single-cell multi-omics data

  thp-1 kidney gse156478 computational zinb-vae autoencoder eccite-seq