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 · 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
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
Mitophagy affects tumour development, immune cell infiltration, and prognosis in HPV-associated HNSCC
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Full-text index only
Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.
PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups
48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes
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Has reproduction · 90
A2TEA: Identifying trait-specific evolutionary adaptations.
PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups
A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment
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Has reproduction · 75
Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.
PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 8 setups
The three mouse models (5xFAD, APP/PS1, hAβ-KI) share more DEGs and GOBP terms with LOAD than with EOAD patients
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Full-text index only
SeqExpressionAnalyser: An R Package for Automated End-to-End RNA-Seq Analysis From Reads to Differential Expression.
PMID 41602550 · PMC12833196 · Bioinformatics and biology insights · 2026 · 8 claims · 2 setups
SeqExpressionAnalyser is a novel R package/Shiny web application that provides the first R-based, fully integrated interface for interactive end-to-end RNA-Seq differential gene expression analysis, from FASTQ reads to results.
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Has reproduction · 73
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.
PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups
Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.
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Has reproduction · 100
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.
PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups
A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.
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Has reproduction · 66
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.
PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups
Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level
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Has reproduction · 69
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.
PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups
COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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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 · 8 claims · 6 setups
PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons
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Has reproduction · 71
Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.
PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups
Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.
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Has reproduction · 68
Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.
PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 8 claims · 7 setups
CEP120 and SPDL1 were identified as diagnostic genes for IDD using a random forest model
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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
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Has reproduction · 90
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.
PMID 37948380 · PMC10637681 · PloS one · 2023 · 8 claims · 8 setups
Stemness-related genes ORC1L, KIF20A, and DLGAP5 are upregulated in LUAD and correlate with altered immune cell infiltration (Th2, MDSC, HSC) and reduced patient survival.
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Has reproduction · 73
ASTRA: a comprehensive resource of stress-induced transcriptional activity in human cell lines.
PMID 41263110 · PMC12807686 · Nucleic acids research · 2026 · 8 claims · 6 setups
ASTRA is a curated, open-access database cataloging transcriptomic stress responses in human cell lines across four stress categories (oxidative stress, hypoxia, heat shock, DNA damage/UV)
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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 · 69
COVID-19 vaccination atlas using an integrative systems vaccinology approach.
PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups
mRNA vaccines induce transient but strong immune responses after booster doses
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC