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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Full-text index only
Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.
PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups
145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Genetic variation of SARS coronavirus in Beijing Hospital.
PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups
113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain
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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 · 82
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.
PMID 34019643 · PMC8218201 · Nucleic acids research · 2021 · 8 claims · 5 setups
eVITTA is a web-based toolbox with three modules (easyGEO, easyGSEA, easyVizR) that analyze, interpret, and compare transcriptome data from published NCBI GEO studies or new experiments
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Full-text index only
SARS--beginning to understand a new virus.
PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups
A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS
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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 · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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Has reproduction · 87
Single-cell RNA-sequencing highlights a curtailed NK cell function in convalescent COVID-19 pregnant women.
PMID 40661959 · PMC12257036 · Frontiers in immunology · 2025 · 7 claims · 5 setups
NK cells show a sustained reduction during active SARS-CoV-2 infection and persisting after recovery in pregnant women
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Has reproduction · 100
Betacoronavirus-specific alternate splicing.
PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups
Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.
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Has reproduction · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups
The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation
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Has reproduction · 84
The SARS-CoV-2 subgenome landscape and its novel regulatory features.
PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups
Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events
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Has reproduction · 85
Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models.
PMID 35186014 · PMC8855158 · Frontiers in genetics · 2021 · 8 claims · 2 setups
A hierarchical Bayesian factor model using treatment-dependent latent factor loadings can construct gene co-expression networks from scRNA-seq data and identify differences in network structure between two (or more) biological conditions.
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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
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.
PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups
The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells
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Has reproduction · 84
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.
PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups
ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.
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Has reproduction · 90
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)
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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 · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.