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Dennis M. Vitkup, Ph.D. - Publications

Affiliations: 
Biomedical Informatics Columbia University, New York, NY 
 1999 Brandeis University, Waltham, MA, United States 
Area:
relationship of protein three-dimensional structure to chemical function
Website:
https://www.dbmi.columbia.edu/people/dennis-vitkup/
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Konaté MM, Plata G, Park J, Usmanova DR, Wang H, Vitkup D. Molecular function limits divergent protein evolution on planetary timescales. Elife. 8. PMID 31532392 DOI: 10.7554/Elife.39705  0.375
2019 Konaté MM, Plata G, Park J, Usmanova DR, Wang H, Vitkup D. Author response: Molecular function limits divergent protein evolution on planetary timescales Elife. DOI: 10.7554/Elife.39705.035  0.327
2017 Plata G, Vitkup D. Avoidance of toxic misfolding and protein stability do not explain the sequence constraints of highly expressed proteins. Molecular Biology and Evolution. PMID 29309671 DOI: 10.1093/Molbev/Msx323  0.343
2015 Plata G, Henry CS, Vitkup D. Long-term phenotypic evolution of bacteria Nature. 517: 369-372. PMID 25363780 DOI: 10.1038/Nature13827  0.314
2012 Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D. Global probabilistic annotation of metabolic networks enables enzyme discovery. Nature Chemical Biology. 8: 848-54. PMID 22960854 DOI: 10.1038/Nchembio.1063  0.337
2011 Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron. 70: 898-907. PMID 21658583 DOI: 10.1016/J.Neuron.2011.05.021  0.307
2010 Plata G, Gottesman ME, Vitkup D. The rate of the molecular clock and the cost of gratuitous protein synthesis. Genome Biology. 11: R98. PMID 20920270 DOI: 10.1186/Gb-2010-11-9-R98  0.343
2010 de Hoon MJ, Eichenberger P, Vitkup D. Hierarchical evolution of the bacterial sporulation network. Current Biology : Cb. 20: R735-45. PMID 20833318 DOI: 10.1016/J.Cub.2010.06.031  0.331
2010 Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Molecular Systems Biology. 6: 408. PMID 20823846 DOI: 10.1038/Msb.2010.60  0.324
2010 Hsiao TL, Revelles O, Chen L, Sauer U, Vitkup D. Automatic policing of biochemical annotations using genomic correlations. Nature Chemical Biology. 6: 34-40. PMID 19935659 DOI: 10.1038/Nchembio.266  0.314
2008 Feldman I, Rzhetsky A, Vitkup D. Network properties of genes harboring inherited disease mutations. Proceedings of the National Academy of Sciences of the United States of America. 105: 4323-8. PMID 18326631 DOI: 10.1073/Pnas.0701722105  0.303
2007 Fuhrer T, Chen L, Sauer U, Vitkup D. Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. Journal of Bacteriology. 189: 8073-8. PMID 17873044 DOI: 10.1128/Jb.01027-07  0.311
2006 Vitkup D, Kharchenko P, Wagner A. Influence of metabolic network structure and function on enzyme evolution. Genome Biology. 7: R39. PMID 16684370 DOI: 10.1186/Gb-2006-7-5-R39  0.356
2006 Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. Bmc Bioinformatics. 7: 177. PMID 16571130 DOI: 10.1186/1471-2105-7-177  0.337
2006 Chen L, Vitkup D. Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biology. 7: R17. PMID 16507154 DOI: 10.1186/Gb-2006-7-2-R17  0.315
2006 Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. Multiple solvent crystal structures: probing binding sites, plasticity and hydration. Journal of Molecular Biology. 357: 1471-82. PMID 16488429 DOI: 10.1016/J.Jmb.2006.01.039  0.61
2005 Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Molecular Systems Biology. 1: 2005.0016. PMID 16729051 DOI: 10.1038/Msb4100023  0.316
2002 Vitkup D, Ringe D, Karplus M, Petsko GA. Why protein R-factors are so large: a self-consistent analysis. Proteins. 46: 345-54. PMID 11835510 DOI: 10.1002/Prot.10035  0.601
2000 Vitkup D, Ringe D, Petsko GA, Karplus M. Solvent mobility and the protein 'glass' transition. Nature Structural Biology. 7: 34-8. PMID 10625424 DOI: 10.1038/71231  0.63
1999 Zhou Y, Vitkup D, Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology. 285: 1371-5. PMID 9917381 DOI: 10.1006/Jmbi.1998.2374  0.599
1997 Vitkup D, Petsko GA, Karplus M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nature Structural Biology. 4: 202-8. PMID 9164461 DOI: 10.1038/Nsb0397-202  0.532
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