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Publications

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75. Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity

Máté Manczinger, Balázs Koncz, Gergő Mihály Balogh, Benjamin Tamás Papp, Leó Asztalos, Lajos Kemény, Balázs Papp, Csaba Pál
Nature Cancer, 2021

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74. Suboptimal global transcriptional response increases the harmful effects of loss-of-function mutations

Károly Kovács, Zoltán Farkas, Djordje Bajić, Dorottya Kalapis, Andrea Daraba, Karola Almási, Bálint Kintses, Zoltán Bódi, Richard A Notebaart, Juan F Poyatos, Patrick Kemmeren, Frank C P Holstege, Csaba Pál, Balázs Papp
Molecular Biology and Evolution (-), 2020

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73. Limited Evolutionary Conservation of the Phenotypic Effects of Antibiotic Resistance Mutations

Gábor Apjok, Gábor Boross, Ákos Nyerges, Gergely Fekete, Viktória Lázár, Balázs Papp, Csaba Pál, Bálint Csörgő
Molecular Biology and Evolution (36/8), 2019

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72. Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach

Viktor Vernyik, Ildikó Karcagi, Edit Tímár, István Nagy, Ádám Györkei, Balázs Papp, Zsuzsanna Györfy, György Pósfai
Journal/Proc./Book:
Scientific Reports (10/1), 2020

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71. Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion

Anett Dunai, Réka Spohn, Zoltán Farkas, Viktória Lázár, Ádám Györkei, Gábor Apjok, Gábor Boross, Balázs Szappanos, Gábor Grézal, Anikó Faragó, László Bodai, Balázs Papp, Csaba Pál
eLife (-), 2019

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70. Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

Zsolt Merényi, Arun N Prasanna, Zheng Wang, Károly Kovács, Botond Hegedüs, Balázs Bálint, Balázs Papp, Jeffrey P Townsend, László G Nagy
Molecular Biology and Evolution (-), 2019
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69. Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach.

Vernyik, V., Karcagi, I., Tímár, E., Nagy, I., Györkei, Á., Papp, B., Györfy, Z., Pósfai, G. Scientific Reports 2020 Apr 30;10(1):7345.

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68. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi.

Merényi, Z., Prasanna, AN., Wang, Z., Kovács, K., Hegedüs, B., Bálint, B., Papp, B., Townsend, JP., Nagy, LG. Mol Biol Evol. 2020 Aug 1;37(8):2228-2240.

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67. Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action.

Kintses, B., Jangir, PK., Fekete, G., Számel, M., Méhi, O., Spohn, R., Daruka, L., Martins, A., Hosseinnia, A., Gagarinova, A., Kim, S., Phanse, S., Csörgő, B., Györkei, Á., Ari, E., Lázár, V., Nagy, I., Babu, M., Pál, C., Papp, B.  Nat Commun. 2019 Dec 16;10(1):5731.

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66. Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance.

Spohn, R., Daruka, L., Lázár, V., Martins, A., Vidovics, F., Grézal, G., Méhi, O., Kintses, B., Számel, M., Jangir, PK., Csörgő, B., Györkei, Á., Bódi, Z., Faragó, A., Bodai, L., Földesi, I., Kata, D., Maróti, G., Pap, B., Wirth, R., Papp, B., Pál, C.  Nat Commun. 2019 Oct 4;10(1):4538.

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65. Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion.

Dunai, A., Spohn, R., Farkas, Z., Lázár, V., Györkei, Á., Apjok, G., Boross, G., Szappanos, B., Grézal, G., Faragó, A., Bodai, L., Papp, B., Pál, C.  Elife. 2019 Aug 16;8:e47088.

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64. Limited evolutionary conservation of the phenotypic effects of antibiotic resistance mutations.

Apjok, G., Boross, G., Nyerges, Á., Fekete, G., Lázár, V., Papp, B., Pál, C., Csörgő, B.  Biol. Evol.

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63. Enzyme promiscuity shapes adaptation to novel growth substrates.

Guzmán, GI.,Sandberg, TE., LaCroix, RA., Nyerges, Á., Papp, H., de Raad, M., King, ZA., Hefner, Y.,Northen, TR., Notebaart, RA., Pál, C., Palsson, BO., Papp, B., Feist, AM.  Syst. Biol. (2019)15:e8462

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62. Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations.

Manczinger, M., Boross, G., Kemény, L., Müller, V., Lenz, TL., Papp, B.*, Pál, C.*  PLoS Biol. 17(1): e3000131

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61. Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota. 

Kintses, B.,Méhi, O., Ari, E., Számel, M., Györkei, Á., Jangir, PK., Nagy, I., Pál, F., Fekete, G., Tengölics, R.,Nyerges, Á., Likó, I., Bálint, A., Molnár, T., Bálint, B., Vásárhelyi, BM., Bustamante, M., Papp, B.*, Pál, C.*
Nat Microbiol 4, pages 447–458 (2019)

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60. Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance.

Nyerges, Á.,Csörgő, B., Draskovits, G., Kintses, B., Szili, P., Ferenc, G., Révész, T., Ari, E., Nagy, I., Bálint, B.,Vásárhelyi, BM., Bihari, P., Számel, M., Balogh, D., Papp, H., Kalapis, D., Papp, B., Pál, C.
PNAS 115 (25) E5726-E5735

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59. Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides

Lázár, V., Martins, A., Spohn, R., Daruka, L., Grézal, G., Fekete, G., Számel, M., Jangir, P.K., Kintses, B., Csörgő, B., Nyerges, Á, Györkei, Á., Kincses, A., Dér, A., Walter ,F.R., Deli , M.A., Urbán, E., Hegedűs, Z., Olajos G., Méhi, O., Bálint, B., Nagy, I., Martinek, T. A., Papp B.*, Pál C.*
Microbiol

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58. High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds

Zampieri, M., Szappanos, B., Maria Virginia Buchieri, Trauner, A., Piazza, I., Picotti, P., Gagneux, S., Borrell, S., Gicquel, B., Lelievre, J., Balazs Papp, Uwe Sauer
Science Translational Medicine 21 Feb 2018: Vol. 10, Issue 429, eaal3973

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57. Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Natan, E., Endoh, T., Haim-Vilmovsky, L., Flock, T., Chalancon, G., Hopper, J.T.S, Kintses, B., Horvath, P., Daruka, L., Fekete, G., Pál, C., Papp, B., Oszi, E., Magyar, Z., Marsh, J.A., Elcock, A.H., Babu, M.M., Robinson, C.V., Sugimoto ,N., Teichmann, S. A
Nature Structural & Molecular Biology 25, 279–288

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56. Hsp70-associated chaperones have a critical role in buffering protein production costs.

Farkas, Z., Kalapis, D., Bódi, Z., Szamecz, B., Daraba, A., Almási, K., Kovács, K., Boross, G., Pál, F., Horvath, P., Balassa, T., Molnar, Cs., Pettkó-Szandtner, A., Klement, É., Rutkai, E., Szvetnik, A., Papp, B., Pál, C.
Elife 2018 Jan 29;7.

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55. Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells.

Marín de Mas, I.,Aguilar, E., Zodda, E., Balcells, C., Marin, S., Dallmann, G., Thomson, TM., Papp, B.*,Cascante, M.*
PLoS Comput. Biol. January 2, 2018

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54. Underground metabolism: network-level perspective and biotechnological potential.

Notebaart, RA., Kintses, B., Feist, AM., Papp, B. Curr. Opin. Biotechnol. 49, 108-114

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53. Evolution of complex adaptations in molecular systems.

Pál, Cs.,Papp, B.
Nature Ecology & Evolution 1, 1084–1092

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52. Phenotypic heterogeneity promotes adaptive evolution

Bódi, Z., Farkas, Z., Nevozhay, D., Kalapis, D., Lázár, V., Csörgő, B., Nyerges, Á., Szamecz, B., Fekete, G., Papp, B., Araújo, H., Oliveira, J.L., Moura, G., Santos, M.A.S., Székely, T. Balázsi, G., Pál, C. PLoS Biol 15(5): e2000644.

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51. Erroneous energy-generating cycles in published genome scale metabolic networks: identification and removal.

Fritzemeier, J.C., Hartleb, D., Szappanos, B., Papp, B., Lercher, M.J. PLoS Comput Biol 13(4): e1005494

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50. No evidence that protein noise-induced epigenetic epistasis constrains gene expression evolution.

Boross, G.,Papp, B. Molecular Biology and Evolution. (2017) 34 (2): 380-390.

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49. Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach.

Marín de Mas, I.,Fanchon, E., Papp, B., Roca, J., Cascante, M.
Bioinformatics 33:95-103

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48. Antibiotics: New recipe for targeting resistance.

Papp, B.,Lázár, V.
Nature Chemical Biology 12, 891–892 (2016) doi:10.1038/nchembio.2215

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47. Adaptive evolution of complex innovations through stepwise metabolic niche expansion

Szappanos B.,Fritzemeier, J., Csörgő, B., Lázár, V., Xiaowen Lu,, Fekete, G., Bálint, B., Herczeg, R., Nagy, I.,Notebaart, R A., Lercher, M J., Pál, C.*, Papp, B.*
Nature Communications 7: 11607

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46. Indispensability of horizontally transferred genes and its impact on bacterial genome streamlining.

Karcagi, I.,Draskovits, G., Umenhoffer, K., Fekete, G., Kovács, K., Méhi, O., Balikó, G, Szappanos, B., Györfy, Z.,Fehér, T, Bogos, B., Blattner, F.R., Pál, C.*, Pósfai, G.*, Papp, B.*
Mol Biol Evol 33: 1257-1269.

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45. Collateral sensitivity of antibiotic-resistant microbes

Pál, C, Papp, B, Lázár, V,
Trends in Microbiology 23: 401-407

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44. Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance.

Méhi, O, Bogos, B, Csörgő, B, Pál, F, Nyerges, Á, Papp, B, Pál, C,
Mol Biol Evol 31: 2793-2804

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43. Network-level architecture and the evolutionary potential of underground metabolism.

Notebaart, RA,Szappanos, B, Kintses, B, Pál, F, Györkei, Á, Bogos, B, Lázár, V, Spohn, R, Csörgő, B,Wagner, A, Ruppin, E, Pál, C*, Papp, B*
PNAS 111: 11762–11767

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42. The genomic landscape of compensatory evolution.

Szamecz, B,Boross, G, Kalapis, D, Kovács, K, Fekete, G, Farkas, Z, Lázár, V, Hrtyan, M, Kemmeren, P,Groot Koerkamp MJA, Rutkai, E, Holstege, FCP, Papp, B*, Pál, C*
PLoS Biol 12(8): e1001935

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41. Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network.

Lázár, V,Nagy, I, Spohn, R, Csörgő, B, Györkei, A, Nyerges, Á, Horváth, B, Vörös, A, Busa-Fekete, R, Hrtyan, M,Bogos, B, Méhi, O, Fekete, G, Szappanos, B, Kégl, B, Papp, B* 
Nature Communications 5: 4352

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40. Antagonism between bacteriostatic and bactericidal antibiotics is prevalent.

Ocampo, PS,Lázár, V, Papp, B, Arnoldini, M, Abel Zur Wiesch, P, Busa-Fekete, R, Fekete, G, Pál, C,Ackermann, M, Bonhoeffer, S
Antimicrob Agents Chemotherapy 2014 May 27. pii: AAC.02463-14.

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39. The dawn of evolutionary genome engineering

Csaba Pál, Balázs Papp, Pósfai, G
Nature Reviews Genetics 15: 504-512

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38. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

Benjamin VanderSluis,David C Hess, Colin Pesyna, Elias W Krumholz, Tahin Syed, Balázs Szappanos,Corey Nislow, Balázs Papp, Olga G Troyanskaya, Chad L Myers, Amy A Caudy
Genome Biology 2014, 15:R64

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37. Cancer cell metabolism as new targets for novel designed therapies.

Marín de Mas, I., Aguilar, E., Jayaraman, A., Polat, I.H., Martín-Bernabé, A., Bharat, R., Foguet, C., Milà, E., Papp, B., Centelles, J.J., Cascante, M.  Future Med Chem. 6:1791-810

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36. Bacterial evolution of antibiotic hypersensitivity

Lázár, V, Singh, G P, Spohn, R, Nagy, I, Horváth, B, Hrtyan, M, Busa-Fekete, R, Bogos, B, Méhi, O, Csörgő, B, Pósfai, G, Fekete, G, Szappanos, B, Kégl, B, Papp, B*, Pál, C* Molecular Systems Biology 9:700

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34. Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks.

Abrusán G, Szilágyi A, Zhang Y, Papp, B Nucleic Acids Research 41:3190-200.

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33. ModuLand Plug-in for Cytoscape: Determination of Hierarchical Layers of Overlapping Network Modules and Community Centrality.

Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B., Csermely, P. Bioinformatics 28: 2202

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32. Competition between Transposable Elements and Mutator Genes in Bacteria

Fehér, T., Bogos, B., Méhi, O., Fekete, G., Csörgő, B., Kovács, K., Pósfai, G., Papp, B., Hurst, L.D., Pál, C. Mol Biol Evol 29: 3153

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31. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs.

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. Genome Res 22: 791

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30. Systems-biology approaches for predicting genomic evolution.

Papp, B., Notebaart, R.A., Pál, C. Nature Rev. Genet. 12: 591.

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28.  Use of genome-scale metabolic models in evolutionary systems biology.

Papp, B., Szappanos, B., Notebaart, R.A.Methods Mol. Biol. 759: 483.

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27. Metabolic modeling of endosymbiont genome reduction on a temporal scale.

Yizhak, K., Tuller, T., Papp, B., Eytan, R. Mol Sys Biol. 7: 479.

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26. An integrated approach to characterize genetic interaction networks in yeast metabolism.

Szappanos, B., Kovács, K., Szamecz, B., Honti, F., Costanzo, M., 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. Nature Genetics 43: 656

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25. Genetic interactions reveal the evolutionary trajectories of duplicate genes.

VanderSluis, B., Bellay, J., Musso, G., Costanzo, M., Papp, B., Vizeacoumar, F.J., Baryshnikova, A., Andrews, B., Boone, C., Myers, C.L.  Mol Sys Biol. 6: 429.

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24. The Genetic Landscape of a Cell.

 Costanzo et al. Science 327: 425-431.

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22. A critical view of metabolic network adaptations.

Papp, B., Teusink, B., Notebaart, R.A.  HFSP J. 3: 24-35.

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20. Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

Notebaart, R.A., Teusink, B., Siezen, R.J., Papp, B. PloS Comp. Biol. 4: 157-163.

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19. Metabolic reconstruction and analysis for parasite genomes.

Pinney, J.W., Papp, B., Hyland, C., Wambua, L., Westhead, D.R., McConkey, G.A. Trends Parasitol 23: 548-554.

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18. Systematic Genome Reductions: Theoretical and Experimental Approaches.

Feher, T., Papp, B., Pal, C., Posfai, G. Chemical Reviews 107: 3498-3513

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17. The Ancient Mariner Sails Again: Transposition of the Human Hsmar1 Element by a Reconstructed Transposase and Activities of the SETMAR Protein on Transposon Ends.

Miskey, C., Papp,, Mates, L., Sinzelle, L., Keller, H., Izsvak, Z., Ivics, Z. Mol. Cell. Biol. 27: 4589-600.

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16. Plasticity of genetic interactions in metabolic networks of yeast.

Harrison, R.*, Papp, B.*, Pal, C., Oliver SG., Delneri D. PNAS 104: 2307-12.

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15. Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling.

Bundy, J.G., Papp, B., Harmston, R., Browne, R.A., Clayson, E.M., Burton, N., Reece, R.J, Oliver, S.G., Brindle, K.M. Genome Res. 17: 510-19.

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14. An integrated view on protein evolution.

Pal, C., Papp, B., Lercher M.J.  Nature Rev. Genet. 7: 337-348.

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13. Phenotypic activation to discover biological pathways and kinase substrates.

Sopko, R., Papp, B., Oliver, S.G., Andrews, B.J. Cell Cycle 5: 1397-402.

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12. Chance and necessity in the evolution of minimal metabolic networks.

Pal, C.*, Papp, B.*, Lercher, MJ., Csermely, P., Oliver, SG., Laurence, D. Hurst. Nature 440: 667-670.

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11. Mapping pathways and phenotypes by systematic gene overexpression.

Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S.G., Cyert, M., Hughes, T.R., Boone, C., Andrews, B. Mol. Cell 21: 319-30.

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10. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

Pal, C., Papp, B., Lercher M.J.  Nature Genetics 37: 1372-5.

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9. Horizontal gene transfer depends on gene content of the host.

Pal, C., Papp, B., Lercher M.J. Bioinformatics 21: ii222-223

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7. Genome-wide analysis of the context-dependence of regulatory networks.

Papp, B., Oliver, S.G. Genome Biology 6: 206.
 

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6. Molecular chaperones as regulatory elements of cellular networks.

Soti, C., Pal, C., Papp, B., Csermely, P. Current Opinion in Cell Biology 17: 210-215.

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4. Dosage sensitivity and the evolution of gene family size in yeast.

Papp, B., Pal, C., Hurst, L.D. Nature 424: 194-7.

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3. Evolution of cis-regulatory elements in duplicated genes of yeast.

Papp, B., Pal, C., Hurst, L.D. Trends Genet. 19: 417-22.

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2. Genomic function: Rate of evolution and gene dispensability.

Pal, C., Papp, B., Hurst, L.D.  Nature 421: 496-7.

 
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