Publications of Vitkup Lab

Vitkup Lab at Columbia Univeristy

Selected Publications

Ji B, Sheth R, Dixit P, Wang H, Vitkup D bioRxiv. 2018 Aug 15; doi:10.1101/310649 "Quantifying spatiotemporal dynamics and noise in absolute microbiota abundances using replicate sampling". [pdf]

Ji B, Sheth R, Dixit P, Vitkup D bioRxiv. 2018 Jul 18; doi:10.1101/370676 "Macroecological relationships in the dynamics of gut microbiota". [pdf]

Konate M, Plata G, Park J, Wang H.H, Vitkup D bioRxiv. 2017 Oct 05; doi:10.1101/158774 "Molecular function limits divergent protein evolution on planetary timescales". [pdf]

Lyashenko E, Niepel M, Dixit P, Lim S, Sorger P Vitkup D bioRxiv. 2017 Jul 02; doi:10.1101/158774 "Receptor-Based Mechanism of Relative Sensing in Mammalian Signaling Networks". [pdf]

Dixit P, Lyashenko E, Niepel M, Vitkup D bioRxiv. 2017 May 12; doi:10.1101/137513 "Maximum Entropy Framework For Inference Of Cell Population Heterogeneity In Signaling Networks". [pdf]

Plata G, Vitkup D bioRxiv. 2017 Jul 27; doi:10.1101/168963 "Avoidance of toxic misfolding does not explain the sequence constraints of highly expressed proteins across organisms". [pdf]

Mayers J, et al. Science. 2016 Sep 09; doi:10.1126/science.aaf5171 "Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers". [pdf]

Chang J, Gilman SR, Chiang AH, Sanders SJ, Vitkup D. Nat Neuroscience. 2014 Dec 22; doi:10.1038/nn.3907. "Genotype to phenotype relationships in autism spectrum disorders". [pdf]

Plata G, Henry C, Vitkup D. Nature. 2014 Oct 26; doi:10.1038/nature13827. "Long-term phenotypic evolution of bacteria". [pdf]

Plata G, Vitkup D. Nucleic Acids Res. 2013 Nov 27; doi:10.1093/nar/gkt1200. "Genetic robustness and functional evolution of gene duplicates". [pdf]

Hu j, Locasale J, Bielas J, O'Sullivan J, Sheahan K, Cantley L, Vander Heiden M, Vitkup D. Nat Biotech. 2013 Feb 12; doi:10.1038/nbt.2530. "Heterogeneity of tumor-induced gene expression changes in the human metabolic network". [pdf]

Eydgahi H, Chen W, Muhlich J, Vitkup D, Tsitsiklis J, Sorger P. Mol Syst Biol. 2013 Feb 5; 9:644; doi:10.1038/msb.2012.69. "Properties of cell death models calibrated and compared using Bayesian approaches". [pdf]

Gilman SR, Chang J, Xu B, Bawa TS, Gogos J, Karayiorgou M, Vitkup D. Nat Neurosci. 2012 Nov; doi:10.1038/nn.3261. "Diverse types of genetic variation converge on functional gene networks involved in schizophrenia". [pdf]

Plata G, Fuhrer T, Hsiao, TL, Sauer U, Vitkup D. Nat Chem Biol. 2012 Oct; 8(10):848-854. "Global probabilistic annotation of metabolic networks enables enzyme discovery". [pdf]

Meyer P. et al., Vitkup D, Stolovitzky G. Nat Biotechnol. 2011 Sep 8; 29(9):811-815. "Verification of systems biology research in the age of collaborative competition". [pdf]

Roberts R, et al. Nucleic Acids Research. 2011 July; 39(13). "COMBREX: a project to accelerate the functional annotation of prokaryotic genomes". [pdf]

Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D Neuron. 2011 June 9;70, 898-907. "Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses". [pdf]

Plata G, Gottesman M, Vitkup D. Genome Biol. 2010 Sep 29;11(9):R98. "The rate of the molecular clock and the cost of gratuitous protein synthesis". [pdf]

de Hoon M, Eichenberger P, Vitkup D. Current Biology. 2010 Sep 14;20(17):R735-45. "Hierarchical evolution of the bacterial sporulation network". [pdf]

Plata G, Hsiao TL, Olszewski K, Llinas M, Vitkup D. Mol Syst Biol. 2010 Sep 7;6:408. "Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network". [pdf]

Chastanet A, Vitkup D, Yuanc GC, Norman T, Liud JS, Losick RM. Proc Natl Acad Sci U S A. 2010 April 19; 107(18)8486-8491. "Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis". [pdf]

Hsiao TL, Revelles O, Chen L, Sauer U, Vitkup D. Nat Chem Biol. 2009 Nov 22. "Automatic policing of biochemical annotations using genomic correlations". [pdf]

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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