Oltvai Lab - Publications

Review Articles

  1. Z. N. Oltvai and A.-L. Barabási
    Life's complexity pyramid
    Science 298, 763-764 (2002) [ PDF ]

  2. A.-L. Barabási and Z. N. Oltvai
    Network Biology: Understanding the Cell's Functional Organization
    Nature Reviews Genetics 5, 101-113 (2004) [ PDF ]

  3. G. Balázsi and Z. N. Oltvai
    Sensing your surroundings: How transcription-regulatory networks of the cell discern environmental signals
    Science STKE 5, pe20 (2005) [ PDF ]

  4. Illés J. Farkas, Qasim K. Beg and Zoltán N. Oltvai
    Exploring Transcriptional Regulatory Networks in the Worm
    Cell 125, 1032-1034 (2006) [ PDF ]

  5. R. Albert and Z.N. Oltvai
    Shaping specificity in signaling networks. Nature Genetics 39, 286-287 (2007) [ PDF ]

  6. Tegner, J., Compte, A., Auffray, C., An, G., Cedersund, G., Clermont, G., Gutkin, B., Oltvai, Z.N., Stephan, K.E., Thomas, R., Villoslada, P. (2009) Computational disease modeling - fact or fiction? BMC Systems Biol., 3, 56 [ PDF ]

Research Papers

  1. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási
    The large-scale organization of metabolic networks
    Nature 407, 651-654 (2000). [ PDF ]

  2. H. Jeong, S. Mason, A.-L. Barabási and Z. N. Oltvai
    Lethality and centrality in protein networks
    Nature 411, 41-42 (2001). [ PDF ]

  3. J. Podani, Z. N. Oltvai, H. Jeong, B. Tombor, A.-L. Barabási and E. Szathmáry
    Comparable system-level organization of Archaea and Eukaryotes
    Nature Genetics 29, 54-56 (2001). [ PDF ]

  4. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A.-L. Barabási
    Hierarchical organization of modularity in metabolic networks
    Science 297, 1551-1555 (2002). [ PDF ]

  5. I. J. Farkas, H. Jeong, T. Vicsek, A.-L. Barabási, and Z.N. Oltvai
    The topology of transcription regulatory network in the yeast, Saccharomyces cerevisiae
    Physica A 318, 601-612 (2003). [ PDF ]

  6. H. Jeong, Z. N. Oltvai, and A.-L. Barabási
    Prediction of protein essentiality based on genomic data
    ComplexUs 1, 19-28 (2003). [ PDF ]

  7. G. Balázsi, K. A. Kay, A.-L. Barabási and Z. N. Oltvai
    Spurious spatial periodicity of co-expression in microarray data due to printing design
    Nucleic Acids Res. 31, 4425-4433 (2003). [ PDF ]

  8. S. Y. Gerdes, M. Scholle, J.W. Campbell, G. Balazsi, E. Ravasz, et al.
    Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
    Journal of Bacteriology 185, 5673-5684 (2003). [ PDF ]

  9. S. Wuchty, Z. N. Oltvai and A.-L. Barabási
    Evolutionary conservation of motif constituents in the yeast protein interaction network
    Nature Genetics 35, 176-179 (2003). [ PDF ]

  10. Z. Dezso, Z. N. Oltvai, and A.-L. Barabási
    Bioinformatics analysis of experimentally determined protein complexes in the yeast saccharomyces cerevisiae
    Genome Research 13, 2450-2454 (2003). [ PDF ]

  11. R. Dobrin, Q.K. Beg, A.-L. Barabási, and Z. N. Oltvai
    Aggregation of topological motifs in the E. coli transcriptional regulatory network
    BMC Bioinformatics 5: 10 (2004). [ PDF ]

  12. E. Almaas, B. Kovacs, T. Vicsek, Z. N. Oltvai and A.-L. Barabási
    Global organization of metabolic fluxes in the bacterium Escherichia coli
    Nature 427, 839-843 (2004). [ PDF ]

  13. S. Y. Yook, Z. N. Oltvai and A.-L. Barabási
    Functional and topological characterization of protein interaction networks
    Proteomics 4, 928-942 (2004). [ PDF ]

  14. X. Tong, J.W. Campbell, G. Balazsi, K.A. Kay, B.L. Wanner, et al.,
    Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays
    Biochem. Biophys. Res. Comm. 322, 347-54 (2004). [ PDF ]

  15. A. Vazquez, R. Dobrin, D. Sergi, J.-P. Eckmann, Z. N. Oltvai, and A.-L. Barabási
    The topological relationship between the large-scale attributes and local interactions patterns of complex networks
    Proceedings of the Nat'l Academy of Sciences 101, 17940-17945 (2004). [ PDF ]

  16. G. Balázsi, A.-L. Barabási, and Z. N. Oltvai
    Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
    Proceedings of the Nat'l Academy of Sciences 102: 7841-7846. (2005) [ PDF ]

  17. Eivind Almaas, Zoltán N. Oltvai, Albert-L Barabási
    The Activity Reaction Core and Plasticity of Metabolic Networks
    PLoS Computational Biology, Vol 1, Issue 7, e68 (2005) [ PDF ]

  18. I.J. Farkas, C. Wu, C. Chennubhotla, I. Bahar, Z.N. Oltvai
    Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics 7:478 (2006) [ PDF ]

  19. Q. K. Beg, A. Vazquez, J. Ernst, M. A. de Menezes, Z. Bar-Joseph, A.-L. Barabási, and Z. N. Oltvai
    Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. PNAS 104: 12663-12668 (2007) [ PDF ]

  20. Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-L Barabási, László G Boros and Zoltán N Oltvai
    Impact of the solvent capacity constraint on E. coli metabolism. BMC Systems Biology 2008, 2:7 [ PDF ]

  21. Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph
    A Semi-Supervised Method for Predicting Transcription Factor¨CGene Interactions in Escherichia coli PLoS Computational Biology 4(3): e1000044 [ PDF ]

  22. D.-S. Lee, J. Park, K. A. Kay, N. A. Christakis, Z. N. Oltvai, and A.-L. Barabási
    The implications of human metabolic network topology for disease comorbidity PNAS July 22, 2008 . vol. 105 . no. 29 [ PDF ]

  23. Alexei Vazquez, Marcio A. de Menezes, Albert-La´ szlo´ Baraba´ si, Zoltan N. Oltvai
    Impact of Limited Solvent Capacity on Metabolic Rate, Enzyme Activities, and Metabolite Concentrations of S. cerevisiae Glycolysis PLoS Computational Biology October 2008, Volume 4, Issue 10, e1000195 [ PDF ]

  24. Lee, D.-S., Burd, H., Liu, J., Almaas, E., Wiest, O., Barabasi, A.-L., Oltvai, Z.N., and Kapatral, V. (2009) Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel anti-microbial drug targets. J. Bacteriol., 191, 4015-24 [ PDF ]

  25. Shen Y, Liu J, Estiu G, Isin B, Ahn YY, Lee DS, Barabási AL, Kapatral V, Wiest O, Oltvai ZN. (2010) Blueprint for antimicrobial hit discovery targeting metabolic networks. Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1082-7. Epub 2010 Jan 5. [ PDF ]

  26. Vazquez A, Liu J, Zhou Y, Oltvai ZN. (2010) Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited. BMC Syst Biol. 2010 May 6;4:58. [ PDF ]

  27. S. T. Henriksen, J. Liu, G. Estiu, Z. N. Oltvai, O. Wiest (2010) Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays. Bioorganic & Medicinal Chemistry 2010, Vol. 18, Pp5148-5156 [ PDF ]

  28. Hai-Son Le, Zoltan N. Oltvai and Ziv Bar-Joseph (2010) Cross-species queries of large gene expression databases. BIOINFORMATICS Vol. 26 no. 19 2010, pages 2416–2423 [ PDF ]

  29. Vazquez A, Oltvai ZN(2011) Molecular Crowding Defines a Common Origin for the Warburg Effect in Proliferating Cells and the Lactate Threshold in Muscle Physiology. PLoS One 2011 Apr 29;6(4):e19538. [ PDF ]

  30. Vazquez A, Markert EK, Oltvai ZN. (2011) Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation. PLoS One 2011;6(11):e25881. Epub 2011 Nov 2. [ PDF ]