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 · 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
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.
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Has reproduction · 74
Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.
PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups
AE networks trained on the 266 shared DEGs reveal a comorbidity (positive correlation) relationship between Alzheimer's disease and lung cancer, rather than the inverse relationship suggested by prior epidemiological studies.
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups
Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs
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Has reproduction · 60
Core transcriptional signatures of phase change in the migratory locust.
PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups
PhaseCore genes, identified via AC-PCA across developmental, tissue, and time-course datasets, predict locust phase status (gregarious vs. solitary) with over 87.5% accuracy
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Has reproduction · 55
Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.
PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups
Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls
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Has reproduction · 81
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.
PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL
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Has reproduction · 40
PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.
PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups
NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.
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Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 8 claims · 8 setups
CP and PDAC share a co-expression gene network identifiable via WGCNA on independent GEO datasets
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Has reproduction · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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Has reproduction · 75
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.
PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups
The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.
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Has reproduction · 77
Representing and querying disease networks using graph databases.
PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups
Graph databases are well suited for representing biological information because it is typically highly connected, semi-structured and unpredictable, unlike relational databases which require rigid schemas.
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Has reproduction · 100
Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.
PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups
A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.
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Has reproduction · 54
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.
PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups
In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.
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Has reproduction · 100
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.
PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups
iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Has reproduction · 62
Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).
PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups
TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR