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 · 68
Bayesian transcriptome assembly.
PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups
Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.
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Has reproduction · 97
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups
CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly
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Full-text index only
Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
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Full-text index only
Automated recognition of retroviral sequences in genomic data--RetroTector.
PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups
RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences