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).

• Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

  PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups

  Has reproduction · 42

  PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.

  paad degs bulk consensus tumor

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

  PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 5 setups

  Has reproduction · 75

  Stage-stratified molecular subclassification of Ta and T1 tumors provides greater biological understanding and more clinically meaningful information than subtypes derived from all NMIBCs combined.

  stage tumors copy genome-wide whole-exome

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

  normal er+ epithelial malignant single-cell spatial copy

• Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

  PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

  generic simulated hiv-1 stochastic dynamic regression

• Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.

  PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups

  Has reproduction · 30

  BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors

  tur matched nmibc relapsed whole-exome sequencing immune

• 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

  PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.

  aml bulk mutation copy

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

  patient-derived tumor single paired single-nucleus infercnv aracne-ap

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

  Full-text index only

  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

  PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

  Has reproduction · 91

  DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.

  solid muscle-invasive ccrcc for bulk single-cell scrna-seq

• Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

  PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

  Has reproduction · 71

  A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

  luad tumor a549 single-cell infercnv pseudotime

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.

  bca meta-geo tcga-blca tcga bulk rna-seq somatic

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

  PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 67

  TNBC can be classified into three molecular subtypes (clusters 1, 2, 3) based on cellular senescence-related pathways, with distinct prognoses (cluster 1 best, then 2, then 3).

  tnbc tcga-tnbc mda-mb-468 single-cell bulk copy

• Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.

  PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups

  Has reproduction · 48

  Breast cancer samples can be divided into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on expression of m6A-related genes, with consistent proportions across datasets

  tcga-brca gse96058 gse25066 bulk gene survival

• Accurate chromatin marks peak calling with Omnipeak.

  PMID 41521664 · PMC12784980 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Has reproduction · 77

  Omnipeak is a universal unsupervised peak-calling algorithm based on a constrained three-state hidden Markov model (zero, noise, signal states)

  gm12878 roadmap abf immgen chip-seq ultra-low-input atac-seq

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Malaria research in the post-genomic era.

  PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

  falciparum plasmodium malaria hela comparative two-hybrid proteomics