Publications of Vitkup Lab

Vitkup Lab at Columbia Univeristy

Selected Publications

Feldman I, Rzhetsky A, Vitkup D. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4323-8. "Network properties of genes harboring inherited disease mutations". [pdf]

Hsiao TL, Vitkup D. PLoS Genet. 2008 Mar 14;4(3):e1000014. "Role of duplicate genes in robustness against deleterious human mutations". [pdf]

Breitling R, Vitkup D, Barrett MP. Nat Rev Microbiol. 2008 Feb;6(2):156-61. "New surveyor tools for charting microbial metabolic maps". [pdf]

Fuhrer T, Chen L, Sauer U, Vitkup D. J Bacteriol. 2007 Nov;189(22):8073-8. "Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli". [pdf]

Chen L, Vitkup D. Trends Biotechnol. 2007 Aug;25(8):343-8. "Distribution of orphan metabolic activities". [pdf]

Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., Church, G. M. BMC Bioinformatics 2006, 7:177, "Identifying metabolic enzymes with multiple types of association evidence".[pdf]

Vitkup, D., Kharchenko, P., Wagner, A. Genome Biology 2006, 7:R39, "Influence of metabolic network structure and function on enzyme evolution".[pdf]

Chen, L., Vitkup, D. 2006, 7:R17, Genome Biology, "Predicting genes for orphan metabolic activities using phylogenetic profiles". [pdf]

Mattos, C., Bellamacina, C. R., Peisach, A., Pererira, A., Vitkup, D. Petsko, G. A., Ringe, D. 2006, 31, Journal of Molecular Biology "Multiple solvent crystal structures probing binding sites, plasticity, and hydration". [pdf]

de Hoon, M., Vitkup, D. 2005 RECOMB "Comparative systems biology of the sporulation initiation networks in prokaryotes". [pdf]

Kharchenko, P., Church, G. M., Vitkup, D. 2005, msb4100023 ,EMBO/Nature Molecular Systems Biology, "Expression dynamics of a cellular metabolic network". [pdf]

Kharchnko, P., Vitkup D., Church, G. M., 2004, 20, I178-I185, Bioinformatics, "Filling gaps in metabolic networks using expression data". [pdf]

Vitkup D, 2004, 3, R313, Genome Biology, "Biological Networks: From physical principles to biological insights". [pdf]

Vitkup D., Sander, C., Church, G. M. 2003, 4,R72, Genome Biology, "The Mutational Spectrum of Human Genetic Disease". [pdf]

Segre, D., Vitkup D., Church, G. M. 2002, 99, 151112-15117, PNAS, "Analysis of optimality in natural and perturbed metabolic networks". [pdf]

Vitkup D, Ringe D., Karplus M., Petsko, G. A. 2002, 46, 345-354, Proteins, "Why protein R-factors are so large : A self-consistent analysis". [pdf]

Vitkup D., Melamud E., Moult J., Sander, C. 2001, 8, 559-566, Nature Structural Biology, "Completeness in Structural Genomics". [pdf]

Vitkup D., Ringe D., Petsko G. A., Karplus, M. Nature Structural Biology, 2000, 7, 34-38, "Solvent Mobility and the protein glass transition". [pdf]

Zhou Y., Vitkup D., Karplus M. Journal of Molecular Biology, 1999, 29, 1371-1375, "Native and surface-molten solids: application of the Lindemann criterion". [pdf]

Vitkup D., Petsko G. A., Karplus M. Nature Structural Biology, 1997, 4, 202-208, "A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin". [pdf]

Vitkup, D. Brandeis University, 1999, Ph. D. thesis. "Protein glass transition and X-ray experiments in silico".

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