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 · 79
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.
PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups
Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction · 30
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.
PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups
Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.
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Has reproduction · 76
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups
The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.
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Has reproduction · 78
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.
PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups
annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
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Has reproduction · 74
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.
PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups
RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).
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Has reproduction · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 83
De novo identification of CD4(+) T cell epitopes.
PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups
SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition