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).
-
Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
-
Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups
GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance
-
Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups
TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene
-
Has reproduction
Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.
PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 7 setups
CD4+ T cells and B cells independently and significantly contribute to MS GWAS heritability enrichment, distinct from a merely shared immune regulatory landscape.
-
Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups
A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence
-
Has reproduction · 51
Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.
PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups
A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients
-
Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups
Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution
-
Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups
AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)
-
Has reproduction · 100
Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.
PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 8 setups
The study presents comprehensive serum exosome miRNA transcriptome data from four independent Japanese cohorts of PD patients and controls.
-
Has reproduction · 68
Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.
PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups
RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)
-
Has reproduction · 76
Estimation of peptide elongation times from ribosome profiling spectra.
PMID 33885812 · PMC8136808 · Nucleic acids research · 2021 · 7 claims · 4 setups
A maximum likelihood statistical model using 915 context-defining parameters can neutralize technical biases (e.g. RNase cleavage preferences) in Ribo-Seq data and estimate peptide elongation times at single-codon resolution.
-
Has reproduction · 83
Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.
PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups
Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD
-
Has reproduction · 73
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
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.
-
Has reproduction · 19
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.
PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 7 setups
Glioblastoma, ischemic stroke, and moyamoya disease share molecular biomarkers and pathways indicating a pathological interconnection
-
Has reproduction · 62
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.
PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups
A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform
-
Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
-
Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs
-
Has reproduction · 81
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.
PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups
USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression
-
Has reproduction · 100
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.
PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 7 claims · 7 setups
A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.
-
Has reproduction · 59
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.
PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering