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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Identification of protein–protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity… Expand
Interaction network containing conserved and essential protein complexes in Escherichia coli
Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported.… Expand
Draft Genome of the Filarial Nematode Parasite Brugia malayi
Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial… Expand
The phylogenetic extent of metabolic enzymes and pathways.
The evolution of metabolic enzymes and pathways has been a subject of intense study for more than half a century. Yet, so far, previous studies have focused on a small number of enzyme families or… Expand
Bacteriome.org—an integrated protein interaction database for E. coli
- Chong Su, J. M. Peregrín-Alvarez, +4 authors J. Parkinson
- Computer Science, Biology
- Nucleic Acids Res.
- 16 October 2007
We present Bacteriome.org, a resource that combines locally generated interaction and evolutionary datasets with a previously generated knowledgebase, to provide an integrated view of the Escherichia coli interactome. Expand
An exponential core in the heart of the yeast protein interaction network.
- J. Pereira-Leal, B. Audit, J. M. Peregrín-Alvarez, C. Ouzounis
- Biology, Medicine
- Molecular biology and evolution
- 1 March 2005
Protein interactions in the budding yeast have been shown to form a scale-free network, a feature of other organized networks such as bacterial and archaeal metabolism and the World Wide Web. Here,… Expand
The origins of apicomplexan sequence innovation.
- James Wasmuth, J. Daub, J. M. Peregrín-Alvarez, Constance A M Finney, J. Parkinson
- Biology, Medicine
- Genome research
- 1 July 2009
The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and… Expand
The conservation and evolutionary modularity of metabolism
BackgroundCellular metabolism is a fundamental biological system consisting of myriads of enzymatic reactions that together fulfill the basic requirements of life. The recent availability of vast… Expand
The Modular Organization of Protein Interactions in Escherichia coli
- J. M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, J. Parkinson
- Biology, Computer Science
- PLoS Comput. Biol.
- 1 October 2009
Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins (∼45% of its proteome). Expand
The global landscape of sequence diversity
BackgroundSystematic comparisons between genomic sequence datasets have revealed a wide spectrum of sequence specificity from sequences that are highly conserved to those that are specific to… Expand