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Items: 37

1.

Avoidance of toxic misfolding and protein stability do not explain the sequence constraints of highly expressed proteins.

Plata G, Vitkup D.

Mol Biol Evol. 2017 Dec 21. doi: 10.1093/molbev/msx323. [Epub ahead of print]

PMID:
29309671
2.

Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers.

Mayers JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM, Muir A, Chin CR, Freinkman E, Jacks T, Wolpin BM, Vitkup D, Vander Heiden MG.

Science. 2016 Sep 9;353(6304):1161-5. doi: 10.1126/science.aaf5171.

3.

Genotype to phenotype relationships in autism spectrum disorders.

Chang J, Gilman SR, Chiang AH, Sanders SJ, Vitkup D.

Nat Neurosci. 2015 Feb;18(2):191-8. doi: 10.1038/nn.3907. Epub 2014 Dec 22.

4.

Long-term phenotypic evolution of bacteria.

Plata G, Henry CS, Vitkup D.

Nature. 2015 Jan 15;517(7534):369-72. doi: 10.1038/nature13827. Epub 2014 Oct 26.

PMID:
25363780
5.

Genetic robustness and functional evolution of gene duplicates.

Plata G, Vitkup D.

Nucleic Acids Res. 2014 Feb;42(4):2405-14. doi: 10.1093/nar/gkt1200. Epub 2013 Nov 27.

6.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

7.

Heterogeneity of tumor-induced gene expression changes in the human metabolic network.

Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D.

Nat Biotechnol. 2013 Jun;31(6):522-9. doi: 10.1038/nbt.2530. Epub 2013 Apr 21.

8.

Properties of cell death models calibrated and compared using Bayesian approaches.

Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK.

Mol Syst Biol. 2013;9:644. doi: 10.1038/msb.2012.69.

9.

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.

Gilman SR, Chang J, Xu B, Bawa TS, Gogos JA, Karayiorgou M, Vitkup D.

Nat Neurosci. 2012 Dec;15(12):1723-8. doi: 10.1038/nn.3261. Epub 2012 Nov 11.

10.

Global probabilistic annotation of metabolic networks enables enzyme discovery.

Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D.

Nat Chem Biol. 2012 Oct;8(10):848-54.

11.

Verification of systems biology research in the age of collaborative competition.

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
12.

Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.

Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D.

Neuron. 2011 Jun 9;70(5):898-907. doi: 10.1016/j.neuron.2011.05.021.

13.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21.

14.

The rate of the molecular clock and the cost of gratuitous protein synthesis.

Plata G, Gottesman ME, Vitkup D.

Genome Biol. 2010;11(9):R98. doi: 10.1186/gb-2010-11-9-r98. Epub 2010 Sep 29.

15.

Hierarchical evolution of the bacterial sporulation network.

de Hoon MJ, Eichenberger P, Vitkup D.

Curr Biol. 2010 Sep 14;20(17):R735-45. doi: 10.1016/j.cub.2010.06.031. Review.

16.

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.

Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D.

Mol Syst Biol. 2010 Sep 7;6:408. doi: 10.1038/msb.2010.60.

17.

Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis.

Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick RM.

Proc Natl Acad Sci U S A. 2010 May 4;107(18):8486-91. doi: 10.1073/pnas.1002499107. Epub 2010 Apr 19.

18.

Automatic policing of biochemical annotations using genomic correlations.

Hsiao TL, Revelles O, Chen L, Sauer U, Vitkup D.

Nat Chem Biol. 2010 Jan;6(1):34-40. doi: 10.1038/nchembio.266. Epub 2009 Nov 22.

19.

Role of duplicate genes in robustness against deleterious human mutations.

Hsiao TL, Vitkup D.

PLoS Genet. 2008 Mar 14;4(3):e1000014. doi: 10.1371/journal.pgen.1000014.

20.

Network properties of genes harboring inherited disease mutations.

Feldman I, Rzhetsky A, Vitkup D.

Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4323-8. doi: 10.1073/pnas.0701722105. Epub 2008 Mar 7.

21.

New surveyor tools for charting microbial metabolic maps.

Breitling R, Vitkup D, Barrett MP.

Nat Rev Microbiol. 2008 Feb;6(2):156-61. Review.

PMID:
18026122
22.
23.

Distribution of orphan metabolic activities.

Chen L, Vitkup D.

Trends Biotechnol. 2007 Aug;25(8):343-8. Epub 2007 Jun 18.

PMID:
17580095
24.

Expression dynamics of a cellular metabolic network.

Kharchenko P, Church GM, Vitkup D.

Mol Syst Biol. 2005;1:2005.0016. Epub 2005 Aug 2.

25.

Influence of metabolic network structure and function on enzyme evolution.

Vitkup D, Kharchenko P, Wagner A.

Genome Biol. 2006;7(5):R39. Epub 2006 May 9.

26.

Identifying metabolic enzymes with multiple types of association evidence.

Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM.

BMC Bioinformatics. 2006 Mar 29;7:177.

27.

Predicting genes for orphan metabolic activities using phylogenetic profiles.

Chen L, Vitkup D.

Genome Biol. 2006;7(2):R17. Epub 2006 Feb 15.

28.

Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D.

J Mol Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30.

PMID:
16488429
29.

Filling gaps in a metabolic network using expression information.

Kharchenko P, Vitkup D, Church GM.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i178-85.

PMID:
15262797
30.

Biological networks: from physical principles to biological insights.

Vitkup D.

Genome Biol. 2004;5(3):313. Epub 2004 Feb 16. No abstract available.

31.

The amino-acid mutational spectrum of human genetic disease.

Vitkup D, Sander C, Church GM.

Genome Biol. 2003;4(11):R72. Epub 2003 Oct 30.

32.

Analysis of optimality in natural and perturbed metabolic networks.

Segrè D, Vitkup D, Church GM.

Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):15112-7. Epub 2002 Nov 1.

33.

Why protein R-factors are so large: a self-consistent analysis.

Vitkup D, Ringe D, Karplus M, Petsko GA.

Proteins. 2002 Mar 1;46(4):345-54.

PMID:
11835510
34.

Completeness in structural genomics.

Vitkup D, Melamud E, Moult J, Sander C.

Nat Struct Biol. 2001 Jun;8(6):559-66.

PMID:
11373627
35.

Solvent mobility and the protein 'glass' transition.

Vitkup D, Ringe D, Petsko GA, Karplus M.

Nat Struct Biol. 2000 Jan;7(1):34-8.

PMID:
10625424
36.
37.

A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin.

Vitkup D, Petsko GA, Karplus M.

Nat Struct Biol. 1997 Mar;4(3):202-8.

PMID:
9164461

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