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).
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Has reproduction · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups
Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.
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Has reproduction · 67
Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.
PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups
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).
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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 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.
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Has reproduction · 54
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.
PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups
Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes
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Has reproduction · 91
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
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.
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Has reproduction · 87
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
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)
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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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.
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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
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Has reproduction · 71
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
Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.
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Has reproduction · 73
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
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
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Has reproduction · 75
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups
AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles
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Has reproduction · 42
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
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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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 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 86
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.
PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups
RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.
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Has reproduction · 73
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.
PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups
GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.
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Has reproduction · 61
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.
PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups
Omics Playground is a user-friendly, interactive self-service bioinformatics platform for in-depth analysis, visualization and interpretation of transcriptomics and proteomics data without coding
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 90
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.
PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups
Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.
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Has reproduction · 89
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.
PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups
Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.