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Network genomics.

Trey Ideker

Published in Ernst Schering Research Foundation workshop

Network genomics is an emerging area of bioengineering which models the influence of genes (hence, genomics) in the context of a larger biomolecular system or network. A biomolecular network is a comprehensive collection of molecules and molecular interactions that regulate cellular function. Molecular interactions include physical binding events b...

Biological network exploration with Cytoscape 3.

Barry Demchak Bader, Gd Su, G Morris, Jh

Published in Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]

Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental dat...

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders.

Novarino, G Fenstermaker, Ag Zaki, Ms Hofree, M Silhavy, Jl Heiberg, Ad Abdellateef, M Rosti, B Scott, E Mansour, L ...

Published in Science

Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in co...

Ideker is corresponding author) Integration of Biological Networks and Gene Expression Data using Cytoscape

Cline, Ms Smoot, M Cerami, E Kuchinsky, A Landys, N Workman, C Christmas, R Avila-Campilo, I Creech, M Gross, B ...

Published in Nature Protocols

A systems approach to mapping DNA damage response pathways.

Workman, Ct Mak, Hc Mccuine, S Tagne, Jb Agarwal, M Ozier, O Begley, Tj Samson, Ld Trey Ideker

Published in Science

Failure of cells to respond to DNA damage is a primary event associated with mutagenesis and environmental toxicity. To map the transcriptional network controlling the damage response, we measured genomewide binding locations for 30 damage-related transcription factors (TFs) after exposure of yeast to methyl-methanesulfonate (MMS). The resulting 52...

Protein networks as logic functions in development and cancer.

Dutkowski, J Trey Ideker

Published in PLoS Computational Biology

Many biological and clinical outcomes are based not on single proteins, but on modules of proteins embedded in protein networks. A fundamental question is how the proteins within each module contribute to the overall module activity. Here, we study the modules underlying three representative biological programs related to tissue development, breast...

Boosting signal-to-noise in complex biology: prior knowledge is power.

Trey Ideker Dutkowski, J Hood, L

Published in Cell

A major difficulty in the analysis of complex biological systems is dealing with the low signal-to-noise inherent to nearly all large biological datasets. We discuss powerful bioinformatic concepts for boosting signal-to-noise through external knowledge incorporated in processing units we call filters and integrators. These concepts are illustrated...

Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.

Trey Ideker Thorsson, V Siegel, Af Hood, Le

Published in Journal of Computational Biology

Although two-color fluorescent DNA microarrays are now standard equipment in many molecular biology laboratories, methods for identifying differentially expressed genes in microarray data are still evolving. Here, we report a refined test for differentially expressed genes which does not rely on gene expression ratios but directly compares a series...

Integrating phenotypic and expression profiles to map arsenic-response networks.

Haugen, Ac Kelley, R Collins, Jb Tucker, Cj Deng, C Afshari, Ca Brown, Jm Trey Ideker Van Houten, B

Published in Genome Biology

Bioinformatics in the human interactome project.

Trey Ideker Valencia, A

Published in Bioinformatics

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