DasSarma, Shiladitya Kennedy, Sean P. Berquist, Brian Victor Ng, Wailap Baliga, Nitin S. Spudich, John L. Krebs, Mark P. Eisen, Jonathan A. Johnson, Carl H. Hood, Leroy
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Published in
Photosynthesis Research
Halobacterium species display a variety of responses to light, including phototrophic growth, phototactic behavior, and photoprotective mechanisms. The complete genome sequence of Halobacterium species NRC-1 (Proc Natl Acad Sci USA 97: 12176–12181, 2000), coupled with the availability of a battery of methods for its analysis makes this an ideal mod...
Bockmayr, Alexander Courtois, Arnaud
Hybrid concurrent constraint programming can be used to model biological systems. It is a promising alternative to existing modeling approaches in systems biology.
Bockmayr, Alexander Courtois, Arnaud
Systems biology is a new area in biology that aims at achieving a systems-level understanding of biological systems. While current genome projects provide a huge amount of data on genes or proteins, lots of research is still necessary to understand how the different parts of a biological system interact in order to perform complex biological functi...
Forst, Christian V.
Published in
Molecular Biology Reports
Network Genomics studies genomics and proteomics foundations of cellular networks in biological systems. It complements systems biology in providing information on elements, their interaction and their functional interplay in cellular networks. The relationship between genomic and proteomic high-throughput technologies and computational methods are...
De Moor, Bart Marchal, Kathleen Mathys, Janick Moreau, Yves
In this paper, we discuss data sets that are being generated by microarray technology, which makes it possible to measure in parallel the activity or expression of thousands of genes simultaneously. We discuss the basics of the technology, horn to preprocess the data, curd how classical and newly developed algorithms corn be used to generate insigh...
Müller, M.R. Kersten, A.H.
Nutrigenomics is the application of high-throughput genomics tools in nutrition research. Applied wisely, it will promote an increased understanding of how nutrition influences metabolic pathways and homeostatic control, how this regulation is disturbed in the early phase of a diet-related disease and to what extent individual sensitizing genotypes...
Misra, J. Alevizos, I. Bullen, J. Blueher, S. Mantzoros, C. Stephanopoulos, Gregory
A methodology for the construction of predictive empirical models of physiological characteristics from microarray data is presented. The method, applied here to the study of the development of diabetes and insulin resistance, can be further expanded to other cases and to also include a variety of other data, such as protein expression, or metaboli...
Isaacs, Farren J. Hasty, Jeff Cantor, Charles R. Collins, J. J.
Published in
Proceedings of the National Academy of Sciences of the United States of America
The deduction of phenotypic cellular responses from the structure and behavior of complex gene regulatory networks is one of the defining challenges of systems biology. This goal will require a quantitative understanding of the modular components that constitute such networks. We pursued an integrated approach, combining theory and experiment, to a...
Stetter, M. Deco, G. Dejori, M.
Published in
Artificial Intelligence Review
The perhaps most important signaling network in living cells is constitutedby the interactions of proteins with the genome – the regulatory geneticnetwork of the cell. From a system-level point of view, the variousinteractions and control loops, which form a genetic network, represent thebasis upon which the vast complexity and flexibility of life ...
Peri, Suraj Navarro, J.Daniel Amanchy, Ramars Kristiansen, Troels Z. Jonnalagadda, Chandra Kiran Surendranath, Vineeth Niranjan, Vidya Muthusamy, Babylakshmi Gandhi, T.K.B. Gronborg, Mads
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Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellula...
