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).
-
Full-text index only
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.
PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups
Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.
-
Full-text index only
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups
An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set
-
Full-text index only
Bases and spaces: resources on the web for accessing the draft human genome.
PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups
By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.
-
Full-text index only
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.
PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups
Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.