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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C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.
PMID 19997494 · PMC2778949 · PLoS pathogens · 2009 · 8 claims · 8 setups
The C-terminal helix of apoL1 is entirely responsible for its interaction with SRA
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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 · 53
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups
spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.
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Has reproduction · 69
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.
PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups
Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis
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From linear genome sequence to three-dimensional organization of the cell nucleus.
PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups
Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR
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Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.
PMID 19638617 · PMC2889494 · Science signaling · 2009 · 8 claims · 6 setups
Pathway reconstruction can be modeled as a prize-collecting Steiner tree problem, balancing penalties for excluding terminal nodes against costs for including edges, controlled by a parameter β.
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Systems biology and the host response to viral infection.
PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups
Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets
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Has reproduction · 85
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.
PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups
Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.
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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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Cohesin regulates alternative splicing.
PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups
Cohesin regulates alternative splicing independently of its effects on transcription.
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Has reproduction · 74
Genetic architecture of natural variation of cardiac performance from flies to humans.
PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups
Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines
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Protein kinase A-dependent biophysical phenotype for V227F-KCNJ2 mutation in catecholaminergic polymorphic ventricular tachycardia.
PMID 19843922 · PMC2766080 · Circulation. Arrhythmia and electrophysiology · 2009 · 7 claims · 7 setups
Homomeric Kir2.1-V227F channels have significantly reduced I K1 (inward reduced ~40%; outward reduced 85-99% at -40 to -60mV) compared to WT
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups
An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.
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Has reproduction · 68
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.