Genomes and Genes
Paul T Shannon
Affiliation: Institute for Systems Biology
- Derivation of genetic interaction networks from quantitative phenotype dataBecky L Drees
Institute for Systems Biology, 1441 N, 34th Street, Seattle, WA 98103, USA
Genome Biol 6:R38. 2005..Mutations formed cliques of significant mutual information in their large-scale patterns of genetic interaction. These local and global interaction patterns reflect the effects of gene perturbations on biological processes and pathways...
- The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novoRichard Bonneau
New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
Genome Biol 7:R36. 2006..Several specific regulatory predictions were experimentally tested and verified...
- Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1Richard Bonneau
Institute for Systems Biology, Seattle, WA 98103 8904, USA
Genome Biol 5:R52. 2004..The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function...
- The Gaggle: an open-source software system for integrating bioinformatics software and data sourcesPaul T Shannon
Institute for Systems Biology, Seattle, WA 98103, USA
BMC Bioinformatics 7:176. 2006..A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing...
- The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applicationsJ Christopher Bare
Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
BMC Bioinformatics 8:456. 2007..Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data...
- RCytoscape: tools for exploratory network analysisPaul T Shannon
Fred Hutchison Cancer Research Institute, Seattle, WA, USA
BMC Bioinformatics 14:217. 2013....
- Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome inductionRamsey A Saleem
Institute for Systems Biology, Seattle, Washington 98103, USA
Mol Cell Proteomics 9:2076-88. 2010..These properties are consistent with a scale-free topology, demonstrating that scale-free properties are conserved in condition-specific networks...