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).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: whole-genome ✕ Assay: classifier ✕ Clear

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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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

genomic encode entire chromosome multi-species hmm-based classifier
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal

Experiments

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

Speeding disease gene discovery by sequence based candidate prioritization.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.