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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Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.
PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups
Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.
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Aligned cross-modal integration and regulatory heterogeneity characterization of single-cell multiomic data with deep contrastive learning.
PMID 41588477 · PMC12833949 · Genome medicine · 2026 · 8 claims · 4 setups
scMDCF outperforms existing state-of-the-art scMulti-omics integration and clustering models across various types of scMulti-omics datasets, including robustness against batch effects
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Has reproduction · 75
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.
PMID 38860884 · PMC11261899 · Microbial genomics · 2024 · 7 claims · 4 setups
No standardized attributes or mechanisms existed for tagging poor-quality or purpose-specific pathogen sequence datasets prior to this work
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Has reproduction · 32
Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods.
PMID 34307679 · PMC8272456 · BioMed research international · 2021 · 7 claims · 2 setups
A pipeline combining Boruta and mRMR feature selection with incremental feature selection (IFS) was used to identify COVID-19-specific transcriptomic biomarkers from blood gene expression data.
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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 · 8 claims · 7 setups
COVID-19 and HLH share a transcriptional overlap of 239 unique common differentially expressed genes (DEGs), 237 of which are up-regulated
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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 · 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 · 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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Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.
PMID 41923360 · PMC13070649 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups
umi-pipeline-nf is a portable, fully containerized, modular Nextflow DSL2 workflow that generates single-molecule consensus sequences from UMI-tagged nanopore amplicon data and scales linearly from single samples to large cohorts.