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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Analysis of sequence conservation at nucleotide resolution.
PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups
SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups
Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.
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Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.
PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups
Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.
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Vertebrate gene finding from multiple-species alignments using a two-level strategy.
PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups
DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism