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 · 70
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.
PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups
MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling
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Has reproduction · 96
In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma.
PMID 36650150 · PMC9845242 · Nature communications · 2023 · 8 claims · 9 setups
Alveolar macrophages support lung cancer cell proliferation and contribute to unfavourable outcomes.
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Contributions of proteomics to understanding phagosome maturation.
PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups
Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).
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Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.
PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups
A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers
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Has reproduction · 78
Purinergic adipocyte-macrophage crosstalk promotes degeneration of thermogenic brown adipose tissue.
PMID 41261284 · PMC12715258 · EMBO reports · 2025 · 8 claims · 8 setups
Imbalanced sympathetic/thermogenic activation (via UCP1 deficiency or pharmacological futile thermogenesis) causes BAT inflammation, fibrosis and degeneration
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Has reproduction · 50
In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells.
PMID 32665556 · PMC7360550 · Nature communications · 2020 · 8 claims · 7 setups
Cancer cells in vivo display higher coherent orientation and alignment of MT dynamics along their cell major axis than 2D in vitro cultures, and distinct from 3D collagen gel cultures.
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
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Has reproduction · 69
Fluent genomics with plyranges and tximeta.
PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 2 setups
A simple three-step workflow (import, model, integrate) using R/Bioconductor enables fluent, reproducible genomics data analysis integrating RNA-seq and ATAC-seq.
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Has reproduction · 81
Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups
Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.
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Has reproduction · 76
A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.
PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups
58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date
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Has reproduction · 83
Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups
Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.
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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 · 59
CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.
PMID 39645040 · PMC11745947 · Journal of lipid research · 2025 · 8 claims · 8 setups
Cd14−/− mice exhibit a leaner body shape and are protected from HFD-induced obesity compared to WT mice
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Has reproduction
Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.
PMID 41001759 · PMC12713092 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 6 claims · 8 setups
Human primary GBMs contain both tumor-originated pericytes (T-PCs) and normal-originated pericytes (N-PCs) with distinctive cell-intrinsic features.
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Has reproduction · 90
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups
pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics
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The interleukin 12 p40 gene promoter is primed by interferon gamma in monocytic cells.
PMID 8551218 · PMC2192398 · The Journal of experimental medicine · 1996 · 8 claims · 8 setups
IFN-gamma primes phagocytic cells for LPS-induced transcription of the IL-12 p40 gene rather than directly inducing it
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Transcriptome annotation using tandem SAGE tags.
PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups
A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)
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Bioengineering a humanized acne microenvironment model: proteomics analysis of host responses to Propionibacterium acnes infection in vivo.
PMID 18651708 · PMC2699546 · Proteomics · 2008 · 8 claims · 6 setups
A dermis-based cell-trapped system (DBCTS) with human sebocytes inserted into a subcutaneous tissue chamber creates a humanized acne microenvironment in mice
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Has reproduction · 85
GSDME-mediated pyroptosis promotes the progression and associated inflammation of atherosclerosis.
PMID 36807553 · PMC9938904 · Nature communications · 2023 · 8 claims · 8 setups
GSDME-mediated pyroptosis promotes atherosclerosis progression and its associated inflammation
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Has reproduction · 94
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.
PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups
HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)