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 · 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 · 100
Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.
PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups
The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types
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Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 3 setups
PSPred-ALE, a deep learning predictor using a self-adaptive learning embedding algorithm, automatically extracts contextual sequence features and identifies SARS-CoV-2 phosphorylation sites without feature engineering.
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Has reproduction · 95
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.
PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups
Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 5 setups
A network-based approach integrating RNA-seq and cell-shape imaging data identifies data-derived signaling networks specific to cell-shape regulation in breast cancer.
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Has reproduction · 89
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.
PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups
SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.
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Has reproduction · 80
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.
PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 7 claims · 8 setups
C3 PLP2+ Tumor Epithelial Progenitor Cells are a key subpopulation that drives differentiation and progression of cervical carcinoma
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Has reproduction · 50
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.
PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups
Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.
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Has reproduction · 65
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.
PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups
UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.
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Has reproduction · 78
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.
PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups
A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 73
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.
PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups
N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Has reproduction · 96
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.
PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups
An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups
A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.
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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 · 79
Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.
PMID 34911933 · PMC8674326 · Nature communications · 2021 · 7 claims · 4 setups
Shared chromatin accessibility features among low-grade (Gleason pattern 3) prostate cancer cells are lost in high-grade (Gleason pattern 4) tumours.
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Has reproduction · 67
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups
An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data