Trey Ideker

Integrative systems biology

Published in Nature Genetics

Network-based classification of breast cancer metastasis

Published in journal of Molecular Engineering and Systems Biology

Data collection and analysis in systems biology

Published in ” Wiley Encyclopedia of Genetics Genomics

Visualization and Integration of Protein-Protein Interactions

Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Co...

Published in Journal of Endourology

A systems approach to mapping DNA damage response pathways.

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...

Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping.

Published in Molecular Cell

DNA repair and checkpoint pathways protect against carcinogen-induced toxicity. Here, we describe additional, equally protective pathways discovered by interrogating 4,733 yeast proteins for their ability to diminish toxicity induced by four known carcinogens. A computational mapping strategy for global phenotypic data was developed to build a syst...

Conserved pathways within bacteria and yeast as revealed by global protein network alignment.

Published in Proceedings of the National Academy of Sciences

We implement a strategy for aligning two protein-protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and complexes. Using this approach we show that the protein-protein interaction networks of two distantly related species, Saccharomyces cerevisiae and Helicobact...

The cancer cell map initiative: defining the hallmark networks of cancer.

Published in Molecular Cell

Progress in DNA sequencing has revealed the startling complexity of cancer genomes, which typically carry thousands of somatic mutations. However, it remains unclear which are the key driver mutations or dependencies in a given cancer and how these influence pathogenesis and response to therapy. Although tumors of similar types and clinical outcome...

The Cytoscape app article collection.

Published in F1000Research

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another resource to help res...

Integrating physical and genetic maps: from genomes to interaction networks.

Published in Nature Reviews Genetics

Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual interaction measurements into contiguous pathway model...

Network genomics.

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...

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

Published in F1000Research

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape t...

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Published in Nature Methods

Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources...

Network-based stratification of tumor mutations.

Published in Nature Methods

Many forms of cancer have multiple subtypes with different causes and clinical outcomes. Somatic tumor genome sequences provide a rich new source of data for uncovering these subtypes but have proven difficult to compare, as two tumors rarely share the same mutations. Here we introduce network-based stratification (NBS), a method to integrate somat...

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease.

Published in Journal of the American Society of Nephrology

Diabetic kidney disease is the leading cause of ESRD, but few biomarkers of diabetic kidney disease are available. This study used gas chromatography-mass spectrometry to quantify 94 urine metabolites in screening and validation cohorts of patients with diabetes mellitus (DM) and CKD(DM+CKD), in patients with DM without CKD (DM-CKD), and in healthy...

Evolutionary trends and functional anatomy of the human expanded autophagy network.

Published in Autophagy

All eukaryotic cells utilize autophagy for protein and organelle turnover, thus assuring subcellular quality control, homeostasis, and survival. In order to address recent advances in identification of human autophagy associated genes, and to describe autophagy on a system-wide level, we established an autophagy-centered gene interaction network by...

A human MAP kinase interactome.

Published in Nature Methods

Mitogen-activated protein kinase (MAPK) pathways form the backbone of signal transduction in the mammalian cell. Here we applied a systematic experimental and computational approach to map 2,269 interactions between human MAPK-related proteins and other cellular machinery and to assemble these data into functional modules. Multiple lines of evidenc...

Dynamic reprogramming of transcription factors to and from the subtelomere.

Published in Genome Research

Transcription factors are most commonly thought of as proteins that regulate expression of specific genes, independently of the order of those genes along the chromosome. By screening genome-wide chromatin immunoprecipitation (ChIP) profiles in yeast, we find that more than 10% of DNA-binding transcription factors concentrate at the subtelomeric re...

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

Published in Bioinformatics