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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An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups
The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions
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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 · 8 claims · 8 setups
CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.
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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 · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.
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Has reproduction · 69
Fluent genomics with plyranges and tximeta.
PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 3 setups
A three-step fluent genomics workflow (import, model, integrate) using plyranges and tximeta provides a coherent, reproducible framework for integrating RNA-seq and ATAC-seq data within the Bioconductor ecosystem.
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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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Use of functional genomics to understand influenza-host interactions.
PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups
Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques
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Has reproduction · 69
Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups
Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis
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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.
PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups
The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988