New surveyor tools for charting microbial metabolic maps (2008)
Breitling, Rainer, Vitkup, Dennis, Barrett, Michael P.
The computational reconstruction and analysis of cellular models of microbial metabolism is one of the great success stories of systems biology. The extent and quality of metabolic network...
Influence of metabolic network structure and function on enzyme evolution (2006)
Vitkup, Dennis, Kharchenko, Peter, Wagner, Andreas
Abstract Background Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks...
Identifying metabolic enzymes with multiple types of association evidence (2006)
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Abstract Background Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational...
Predicting genes for orphan metabolic activities using phylogenetic profiles (2006)
Abstract Homology-based methods fail to assign genes to many metabolic activities present in sequenced organisms. To suggest genes for these orphan activities we developed a novel method that...
Biological networks: from physical principles to biological insights (2004)
A report on the Fourth Georgia Tech and UGA International Conference on Bioinformatics 'Biological Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.
The amino-acid mutational spectrum of human genetic disease (2003)
Vitkup, Dennis, Sander, Chris, Church, George M
Abstract Background Nonsynonymous mutations in the coding regions of human genes are responsible for phenotypic differences between humans and for susceptibility to genetic disease. Computational...
Nature of protein glass transition and x-ray experiments in silico /--Dennis Vitkup. (1999)
"UMI:9959660."
Analysis of optimality in natural and perturbed metabolic networks
Segrè, Daniel, Vitkup, Dennis, Church, George M.
An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that...
The amino-acid mutational spectrum of human genetic disease
Vitkup, Dennis, Sander, Chris, Church, George M
The human disease spectrum is compared to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.
Biological networks: from physical principles to biological insights
A report on the Fourth Georgia Tech and UGA. International Conference on Bioinformatics 'Biological. Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.
Predicting genes for orphan metabolic activities using phylogenetic profiles
A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and Escherichia coli.
Identifying metabolic enzymes with multiple types of association evidence
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Analysis of optimality in natural and perturbed metabolic networks
Segrè, Daniel, Vitkup, Dennis, Church, George M.
An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that...
The amino-acid mutational spectrum of human genetic disease
Vitkup, Dennis, Sander, Chris, Church, George M
The human disease spectrum is compared to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.
Biological networks: from physical principles to biological insights
A report on the Fourth Georgia Tech and UGA. International Conference on Bioinformatics 'Biological. Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.
Predicting genes for orphan metabolic activities using phylogenetic profiles
A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and Escherichia coli.
Identifying metabolic enzymes with multiple types of association evidence
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Influence of metabolic network structure and function on enzyme evolution
Vitkup, Dennis, Kharchenko, Peter, Wagner, Andreas
An analysis of evolutionary constraints, gene duplication and essentiability in the yeast metabolic network demonstrates that the structure and function of a metabolic network shapes the evolution of...
Expression dynamics of a cellular metabolic network
Kharchenko, Peter, Church, George M, Vitkup, Dennis
Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our...
Fuhrer, Tobias, Chen, Lifeng, Sauer, Uwe, Vitkup, Dennis
Although NAD+-dependent succinate semialdehyde dehydrogenase activity was first described in Escherichia coli more than 25 years ago, the responsible gene has remained elusive so far. As an...
Role of Duplicate Genes in Robustness against Deleterious Human Mutations
Hsiao, Tzu-Lin, Vitkup, Dennis
It is now widely recognized that robustness is an inherent property of biological systems [1],[2],[3]. The contribution of close sequence homologs to genetic robustness against null mutations has...
Network properties of genes harboring inherited disease mutations
Feldman, Igor, Rzhetsky, Andrey, Vitkup, Dennis
By analyzing, in parallel, large literature-derived and high-throughput experimental datasets we investigate genes harboring human inherited disease mutations in the context of molecular interaction...