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 · 60
Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.
PMID 35494238 · PMC9046238 · iScience · 2022 · 8 claims · 6 setups
A customized bootstrapping/random-forest divide-and-conquer clustering pipeline integrating three scRNA-seq datasets robustly resolves cell states despite high cell-to-cell similarity within compartments
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Has reproduction · 64
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.
PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups
Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.
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Has reproduction · 91
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.
PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups
175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data
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Has reproduction · 20
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.
PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups
AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats
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Has reproduction · 83
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.
PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 5 claims · 8 setups
A near-complete metagenome-assembled genome (MAG) of Dolichospermum lemmermannii (FEM_B0920) was recovered from a Lake Garda bloom and clarified the species' taxonomic position within the genus Dolichospermum and the ADA group.
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Has reproduction · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 71
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.
PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups
An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.
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Has reproduction · 74
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.
PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups
RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).
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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
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WebGestalt: an integrated system for exploring gene sets in various biological contexts.
PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups
WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.
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Has reproduction · 80
Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.
PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups
928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase
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Has reproduction · 67
Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.
PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups
Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups
A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 87
Covalent binding of thioredoxin to TXNIP is required for diet-induced insulin resistance in the liver.
PMID 40345590 · PMC12180993 · The Journal of biological chemistry · 2025 · 8 claims · 9 setups
TXNIP Cysteine 247 is required for high-fat diet-induced hepatic and whole-body insulin resistance in mice
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Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 7 claims · 6 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified across three independent GEO datasets in EOC vs normal ovarian tissue.
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Has reproduction · 85
Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.
PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.
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Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups
A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.
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Has reproduction · 67
Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development.
PMID 33679890 · PMC7933673 · Frontiers in genetics · 2021 · 8 claims · 7 setups
Immune cell infiltration and abnormal gene expression are closely related to vitiligo pathogenesis