Publications

2012

Sharifpoor, S., van Dyk, D., Costanzo, M., Baryshnikova, A., Friesen, H., Douglas, A.C., Youn, J.Y., Vandersluis, B., Myers, C.L., Papp, B., Boone, C., Andrews , B.J.. (2012) Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res.

Papp, B., Notebaart, R.A., Pál, C. (2011) Systems-biology approaches for predicting genomic evolution. Nature Rev. Genet. 12: 591.

Papp, B., Pál, C. (2011) Systems biology of epistasis: shedding light on genetic interaction "hubs". Cell Cycle 10: 2623.

Szappanos, B., Kovács, K., Szamecz, B., Honti, F., Costanzo, F., Baryshnikova, A., Gelius-Dietrich, G., Lercher, M.J., Jelasity, M., Myers, C.L., Andrews, B.J., Boone, C., Oliver, S.G., Pál, C., Papp, B. (2011) An integrated approach to characterize genetic interaction networks in yeast metabolism. Nature Genetics 43: 656 [Supplementary website]

Papp, B., Szappanos, B., Notebaart, R.A. (2011) Use of genome-scale metabolic models in evolutionary systems biology. Methods Mol. Biol. 759: 483.

Yizhak, K., Tuller, T., Papp, B., Eytan, R. (2011) Metabolic modeling of endosymbiont genome reduction on a temporal scale. Mol Sys Biol. 7: 479.

2010

VanderSluis, B., Bellay, J., Musso, G., Costanzo, M., Papp, B., Vizeacoumar, F.J., Baryshnikova, A., Andrews, B., Boone, C., Myers, C.L. (2010) Genetic interactions reveal the evolutionary trajectories of duplicate genes. Mol Sys Biol. 6:  429.

Costanzo et al. (2010) The Genetic Landscape of a Cell. Science 327: 425-431.

2009

Kovacs, K., Hurst, L.D., Papp, B. (2009) Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli. PloS Biol. 7: e1000115.

Papp, B., Teusink, B., Notebaart, R.A. (2009) A critical view of metabolic network adaptations. HFSP J. 3: 24-35.

2008

Kun, A., Papp, B., Szathmary, E. (2008) Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks. Genome Biol. 9: R51.

Notebaart, R.A., Teusink, B., Siezen, R.J., Papp, B. (2008) Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PloS Comp. Biol. 4: 157-163.

2007

Pinney, J.W., Papp, B., Hyland, C., Wambua, L., Westhead, D.R., McConkey, G.A. (2007) Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol 23: 548-554.

Feher, T, Papp B, Pal C, Posfai G (2007) Systematic Genome Reductions: Theoretical and Experimental Approaches. Chemical Reviews 107: 3498-3513

Miskey, C., Papp, B., Mates, L., Sinzelle, L., Keller, H., Izsvak, Z., Ivics, Z. (2007) The Ancient Mariner Sails Again: Transposition of the Human Hsmar1 Element by a Reconstructed Transposase and Activities of the SETMAR Protein on Transposon Ends. Mol. Cell. Biol. 27: 4589-600.

Harrison, R, Papp B, Pal, C, Oliver SG and Delneri D. (2007) Plasticity of genetic interactions in metabolic networks of yeast. PNAS 104: 2307-12.

Bundy, J.G., Papp, B., Harmston, R., Browne, R.A., Clayson, E.M., Burton, N., Reece, R.J., Oliver, S.G., Brindle, K.M. (2007) Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling. Genome Res. 17: 510-19.

2006

Pal C, Papp B. , Lercher M.J. (2006) An integrated view on protein evolution. Nature Rev. Genet. 7: 337-348.

Sopko, R., Papp, B., Oliver, S.G. and Andrews, B.J. (2006) Phenotypic activation to discover biological pathways and kinase substrates. Cell Cycle 5: 1397-402.

Pal C, Papp B, Lercher MJ, Csermely P, Oliver SG and Laurence D. Hurst. (2006) Chance and necessity in the evolution of minimal metabolic networks. Nature 440: 667-670.

Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S.G., Cyert, M., Hughes, T.R., Boone, C. and Andrews, B. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21: 319-30.

2005

Pal C., Papp B. and Lercher M.J. (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nature Genetics 37: 1372-5.

Pal, C., Papp B. and Lercher, M.J. (2005) Horizontal gene transfer depends on gene content of the host. Bioinformatics 21: ii222-223

Lovell, S.C. and Papp, B. (2005) Report. Bioinformatics: from molecules to systems. A Discussion Meeting held at The Royal Society on 4 and 5 April 2005. Journal of The Royal Society Interface (DOI: 10.1098/rsif.2005.0053).

Papp, B. and Oliver, S.G. (2005) Genome-wide analysis of the context-dependence of regulatory networks. Genome Biology 6: 206.

Soti, C., Pal, C., Papp, B. and Csermely, P. (2005) Molecular chaperones as regulatory elements of cellular networks. Current Opinion in Cell Biology 17: 210-215.

2004

Papp, B., Pal, C. and Hurst, L.D. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-4.

2003

Papp, B., Pal, C. and Hurst, L.D. (2003) Dosage sensitivity and the evolution of gene family size in yeast. Nature 424: 194-7.

Papp, B., Pal, C. and Hurst, L.D. (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet. 19: 417-22.

Pal, C., Papp, B. and Hurst, L.D. (2003) Genomic function: Rate of evolution and gene dispensability. Nature 421: 496-7.

2000 - 2001

Pal, C. Papp, B. and Hurst, L.D. (2001) Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol Biol Evol. 18: 2323-6.

Pal, C. Papp, B. and Hurst, L.D. (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.

Pal, C. and Papp, B. (2000) Selfish cells threaten multicellular life. Trends Ecol Evol 15: 351-352.