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).

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

  PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 73

  Mitophagy affects tumour development, immune cell infiltration, and prognosis in HPV-associated HNSCC

  hnscc hpv-positive combined rna-seq microarray qrt-pcr

• TriticeaeExpDB: a centralized transcriptomic resource for Triticeae research.

  PMID 41656232 · PMC12983667 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  TriticeaeExpDB integrates and uniformly reprocesses >10,000 (11,016) RNA-seq samples from 528 BioProjects/studies across 17 Triticeae species

  triticeae rna-seq user-selected user-supplied bulk biological differential

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• Plasma protein biomarkers predictive of progression to active tuberculosis among close contacts of patients with tuberculosis.

  PMID 41852731 · PMC12992532 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  TB progressors show broad downregulation of plasma proteins related to immune regulation, cell adhesion, and nucleotide metabolism compared to non-progressors and healthy controls

  plasma daps common six-protein olink differential kegg

• Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.

  PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 6 setups

  Has reproduction · 78

  A 120-gene transcriptomic fingerprint encoding defective decidualization is present in decidua of women who developed sPE in a prior pregnancy

  endometrial proteins bulk rt-qpcr immunofluorescence

• Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

  PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups

  Has reproduction · 93

  Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species

  testis ovary house differentially bulk gene protein-protein

• Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.

  PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Has reproduction · 67

  Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.

  kyse150 bulk rna-seq-based differential

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

  PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

  pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality

• 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

  Full-text index only

  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

• 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

• Reconstruction of the lifeways of Central European Late Bronze Age communities using ancient DNA, isotope and osteoarchaeological analyses.

  PMID 41735297 · PMC12932679 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  Late Bronze Age individuals from Central Germany (Kuckenburg/Esperstedt) show genetic continuity with the preceding Early Bronze Age Únětice population.

  skeletal ancient newly shotgun principal admixture

• A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.

  PMID 41888124 · PMC13022412 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  TranScale is a set of 100 biomimetic RNA spike-in standards with SI-traceable certified copy-number concentrations (via isotope dilution mass spectrometry) that anchor RNA-seq measurements to an absolute scale.

  transcale biological isotope rt-dpcr bulk

• Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.

  PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 47

  Carcinoma cell profiles are distinct for each patient, while diverse microenvironmental (nonmalignant) subsets are shared across different patients.

  tumour single differentially seurat-identified single-cell differential gene

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal

• 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

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups

  Has reproduction

  A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.

  tcga-blca gse32894 deep transfer machine