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Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

A, Roguev S, Bandyopadhyay M, Zofall K, Zhang T, Fischer Sr, Collins H, Qu M, Shales Ho, Park J, Hayles ...

Published in Science

An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring the phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction map focused on various aspects of chromosome function, including transcription regulation and DNA repair/replication. The E-MAP u...

Forging new ties between E. coli genes. PDF available through Get Fulltext Research

Ideker, Trey

Published in Cell

A recent study in Nature (Isalan et al., 2008) has examined the effects of systematically adding new transcriptional interactions in the bacterium Escherichia coli. Surprisingly, the majority of the engineered connections have no effect on growth, and in some cases the new connections enhance fitness. These findings reveal insights into the robustn...

eQED: an efficient method for interpreting eQTL associations using protein networks. PDF available through Get Fulltext Research

Suthram, Silpa Beyer, Andreas Karp, Richard M Eldar, Yonina Ideker, Trey

Published in Molecular systems biology

Analysis of expression quantitative trait loci (eQTLs) is an emerging technique in which individuals are genotyped across a panel of genetic markers and, simultaneously, phenotyped using DNA microarrays. Because of the spacing of markers and linkage disequilibrium, each marker may be near many genes making it difficult to finely map which of these ...

Network-based classification of breast cancer metastasis

Chuang, Hy Lee, E Liu, Yt Lee, D Trey Ideker

Published in journal of Molecular Engineering and Systems Biology

Protein Networks and Analysis of Global Gene Expression From DNA to Proteins: The Multiple Levels of Regulation , The Bi...

Trey Ideker

Data collection and analysis in systems biology

Trey Ideker Proteomics, Bioinformatics Dunn, M J Jorde, L B Little, P F R Subramaniam, S

Published in ” Wiley Encyclopedia of Genetics Genomics

Visualization and Integration of Protein Interaction Networks”, in Protein-Protein Interactions Second Edition: A Molecu...

Trey Ideker Tan, K Uetz, P

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

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

Hybridization and Post-Hybridization Washing

Trey Ideker Grimmond, S Ibarra, S

Visualization and Integration of Protein-Protein Interactions

Uetz, P Schwikowski, B Trey Ideker

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