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enoLOGOS: a versatile web tool for energy normalized sequence logos.

Workman, Ct Yin, Y Corcoran, Dl Trey Ideker Stormo, Gd Benos, Pv

Published in Nucleic Acids Research

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information c...

PathBLAST: a tool for alignment of protein interaction networks.

Kelley, Bp Yuan, B Lewitter, F Sharan, R Stockwell, Br Trey Ideker

Published in Nucleic Acids Research

PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic method searches for high-scoring alignments between pairs of protein interaction paths, for which proteins of the first path are paired with putative o...

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.

Hsiao, A Trey Ideker Olefsky, Jm Subramaniam, S

Published in Nucleic Acids Research

Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Bayesian statistical methods for ...

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species.

Lee, Kiyoung Chuang, Han-Yu Beyer, Andreas Sung, Min-Kyung Huh, Won-Ki Lee, Bonghee Ideker, Trey

Published in Nucleic acids research

The function of a protein is intimately tied to its subcellular localization. Although localizations have been measured for many yeast proteins through systematic GFP fusions, similar studies in other branches of life are still forthcoming. In the interim, various machine-learning methods have been proposed to predict localization using physical ch...

CellCircuits: a database of protein network models.

Mak, Hc Daly, M Gruebel, B Trey Ideker

Published in Nucleic Acids Research

CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways. CellCircuits captures the output from an increasing number of approaches that screen molecular interaction networks to iden...

NeXO Web: the NeXO ontology database and visualization platform.

Dutkowski, J Keiichiro Ono Michael Kramer Michael Yu Pratt, D Barry Demchak Trey Ideker

Published in Nucleic Acids Research

The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hie...

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