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1 News 161 Publications 32 Members

Rewiring of genetic networks in response to DNA damage.

Jaehnig, Ej Bodenmiller, B Kate Licon Copeland, W Shales, M Fiedler, D Dutkowski, J Guénolé, A Van Attikum, H Shokat, Km ...

Published in Science

Although cellular behaviors are dynamic, the networks that govern these behaviors have been mapped primarily as static snapshots. Using an approach called differential epistasis mapping, we have discovered widespread changes in genetic interaction among yeast kinases, phosphatases, and transcription factors as the cell responds to DNA damage. Diffe...

Conserved patterns of protein interaction in multiple species.

Sharan, R Suthram, S Kelley, Rm Kuhn, T Mccuine, S Uetz, P Sittler, T Karp, Rm Trey Ideker

Published in Proceedings of the National Academy of Sciences

To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserve...

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data.

Sharan, R Trey Ideker Kelley, B Shamir, R Karp, Rm

Published in Journal of Computational Biology

Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to the yeast S. cerevisiae and the bacteria H. pylori. Our analysis combines protein interaction data that are available for each of the two species and orthology information based on protein sequence comparison...

Systematic interpretation of genetic interactions using protein networks.

Kelley, R Trey Ideker

Published in Nature Biotechnology

Genetic interaction analysis,in which two mutations have a combined effect not exhibited by either mutation alone, is a powerful and widespread tool for establishing functional linkages between genes. In the yeast Saccharomyces cerevisiae, ongoing screens have generated >4,800 such genetic interaction data. We demonstrate that by combining these da...

Transcriptional regulation of protein complexes within and across species.

Tan, K Shlomi, T Feizi, H Trey Ideker Sharan, R

Published in Proceedings of the National Academy of Sciences

Yeast two-hybrid and coimmunoprecipitation experiments have defined large-scale protein-protein interaction networks for many model species. Separately, systematic chromatin immunoprecipitation experiments have enabled the assembly of large networks of transcriptional regulatory interactions. To investigate the functional interplay between these tw...

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

Kelley, R Feizi, H Trey Ideker

Published in Bioinformatics

Genome-wide association data reveal a global map of genetic interactions among protein complexes.

Hannum, G Srivas, R Guénolé, A Van Attikum, H Krogan, Nj Karp, Rm Trey Ideker

Published in PLoS Genetics

This work demonstrates how gene association studies can be analyzed to map a global landscape of genetic interactions among protein complexes and pathways. Despite the immense potential of gene association studies, they have been challenging to analyze because most traits are complex, involving the combined effect of mutations at many different gen...

A gene ontology inferred from molecular networks.

Dutkowski, J Michael Kramer Surma, Ma Balakrishnan, R Cherry, Jm Krogan, Nj Trey Ideker

Published in Nature Biotechnology

Ontologies have proven very useful for capturing knowledge as a hierarchy of terms and their interrelationships. In biology a major challenge has been to construct ontologies of gene function given incomplete biological knowledge and inconsistencies in how this knowledge is manually curated. Here we show that large networks of gene and protein inte...

A proteome-wide protein interaction map for Campylobacter jejuni.

Parrish, Jr Yu, J Liu, G Hines, Ja Chan, Je Mangiola, Ba Zhang, H Pacifico, S Fotouhi, F Dirita, Vj ...

Published in Genome Biology

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

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