Search on Ideker Lab - UC San Diego's publications - page 1

PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

M, Smoot K, Ono T, Ideker S, Maere

Published in Bioinformatics

cyNeo4j: connecting Neo4j and Cytoscape.

Summer, G Kelder, T Keiichiro Ono Radonjic, M Heymans, S Barry Demchak

Published in Bioinformatics

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

Ourfali, O Shlomi, T Trey Ideker Ruppin, E Sharan, R

Published in Bioinformatics

NetworkBLAST: comparative analysis of protein networks.

Kalaev, M Smoot, M Trey Ideker Sharan, R

Published in Bioinformatics

Discovering regulatory and signalling circuits in molecular interaction networks.

Trey Ideker Ozier, O Schwikowski, B Siegel, Af

Published in Bioinformatics

Inferring gene ontologies from pairwise similarity data.

Kramer, Michael Dutkowski, Janusz Yu, Michael Bafna, Vineet Ideker, Trey

Published in Bioinformatics (Oxford, England)

While the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hier...

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.

Kelley, R Feizi, H Trey Ideker

Published in Bioinformatics

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.

Pentchev, K Keiichiro Ono Herwig, R Trey Ideker Kamburov, A

Published in Bioinformatics

Bioinformatics in the human interactome project.

Trey Ideker Valencia, A

Published in Bioinformatics

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological ...

Cannistraci, Cv Ravasi, T Montevecchi, Fm Trey Ideker Alessio, M

Published in Bioinformatics