Instituto Gulbenkian de Ciência

Publications

pre-IGC

  1. BulletLevy, ED, Pereira-Leal, JB, Chothia, C and Teichmann (2006) 3D Complex: a structural classification of protein complexes PLoS Comp. Bio.2(11):e155

  2.         Must read by Faculty of 1000

  3. BulletPereira-Leal, JB, Levy, ED and Teichmann (2006) The evolution and origins of modularity: lessons from protein complexes Phyl. Trans. R. Soc 361(1467):507-17

  4. BulletMosedale G, Niedzwiedz W, Alpi A, Perrina F, Pereira-Leal JB, Johnson M, Langevin F, Pace P, Patel KJ. (2005) The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway.Nature Struct. Mol. Biol. 361(1467):507-17

  5. BulletEl-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N(2005) Comparative genomics of trypanosomatid parasitic protozoa Science 309(5733):404-9

  6. BulletPereira-Leal, JB and Teichmann (2005) Novel specificities emerge by step-wize duplication of functional modules Genome Res. 15(4):552-9

  7. BulletVogel, C, Teichmann, SA and Pereira-Leal, JB (2004)The relationship between domain duplication and recombination J. Mol. Bio. 346(1):355-65

  8. BulletPereira-Leal, JB*, Audit, B*, Peregrin-Alvarez and Ouzounis, CA (2004) An exponential core in the heart of the yeast protein interaction network Mol. Bio. Evo 22(3):421-5

  9. BulletKunin, V*, Pereira-Leal, JB* and Ouzounis, CA (2004) Functional evolution of the yeast protein interaction networks Mol. Bio. Evo21:1171-6

  10.         Must read by Faculty of 1000

  11. BulletPereira-Leal, JB*, Enright, A*. and Ouzounis (2004) Identification of Functional Modules from Protein Interaction networks. Proteins - Structure function and Genetics 54(1): 49-57.

  12. Bulletvon Mering, C, Zdobnov, E, Tsoka, S, Ciccarelli, F, Pereira-Leal, JB, Ouzounis, CA, Bork, P. (2003) Comparative genomics reveals biochemical networks and functional modules. Proc. Natl. Acd. Sci. USA 100(26): 15428-33

  13. BulletOuzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB. (2003) Classification schemes for protein structure and function. Nat. Rev. Genetics 4:508-19

  14. BulletJanssen P, Audit, B, Cases, I, Darzentas, N, Goldovsky, L, Kunin, V, Lopez-Bigas, N, Peregrin-Alvarez, JM,Pereira-Leal, JB, Tsoka, S, and Ouzounis, CA (2003) Beyond 100 Genomes Genome Biol. 4:402

  15. BulletPereira-Leal, JB, Strom, M, Godfrey, RF, and Seabra, MC (2003) Structural determinants of Rab:REP binding: Rab family conserved motifs define a conserved binding surface to REP Biochem. Biophys. Res. Commun. 301: 92-7.

  16. BulletPereira-Leal, JB and Seabra, MC (2002) Evolution of the Rab family of small GTP-binding proteins J. Mol. Bio. 313: 889-901

  17. BulletPereira-Leal, JB, Gomes, AR and Seabra, MC (2002)“ Analysis and preparation of stable complexes between Rab GTPases, Rab Escort Protein and Rab Geranlygeranyl Transferase” in “GTPase Protocols – The Ras Superfamily” ed. Manser, EJ and Leung, T. – Methods in Molecular Biology” – series ed. Walker, JM.

  18. BulletPereira-Leal, JB, Hume, AN, and Seabra, MC (2001) Prenylation of Rab GTPases: molecular mechanisms and involvement in genetic diseases FEBS Lett. 498: 197-200

  19. BulletPereira-Leal, JB and Seabra, MC (2000) The mammalian Rab family of small GTPases: definition of family and subfamily motifs suggests a mechanisms for functional specificity in the Ras superfamily J. Mol. Bio. 301: 1077-1087

submitted

Published @IGC


  1. BulletAlmeida P, Rodo J, Lino A, Pereira-Leal JB (2011) FlowBase: A web-based system to manage flow cytometry data


  1. BulletRodrigues & Pereira-Leal (2011) Extensive innovation in the evolution of transient Rab:effector interactions

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  1. BulletDiekmann Y, Seixas E, Gouw M, Tavares-Cadete F, Seabra MC, Pereira-Leal JB (2011) Thousands of Rab GTPases for the cell biologist. PLoS Comp Bio. in press


  1. BulletSu X, Qiu W, Gupta, Jr. ML, Pereira-Leal JB, Reck-Peterson SL, and Pellman D (2011) Mechanisms underlying the dual-mode regulation of microtubule dynamics by Kip3/kinesin-8 Mol. Cell in press



  4. BulletCarvalho-Santos Z, Azimzadeh J, Pereira-Leal JB & Bettencourt-Dias M (2011) Evolution of Centrioles and derived structures J. Cell Bio. in press



  1. BulletSousa FL, Alves RJ, Pereira-Leal JB, Teixeira M, Pereira MM (2011) A bioinformatics classifier and database for heme-copper oxygen reductases PLoS One. in press


  1. BulletRodrigues ML & Pereira-Leal (2011) Novel Rabs. in ‘Rab GTPases and Membrane Trafficking’ Eds. Guanpu Li & Nava Segev, Bentham Science Publishers



  1. BulletMendonça A, Alves, RJ, Pereira-Leal, JB (2011) Loss of genetic redundancy in reductive genome evolution. PLoS Comp. Bio. 7(2): e1001082



  1. BulletCarvalho-Santos Z, Machado P, Branco P, Tavares-Cadete F, Rodrigues-Martins A, Pereira-Leal JB, Bettencourt-Dias M.(2010) Stepwise Evolution Of Centriole Assembly Mechanisms. J. Cell Sci. 23(Pt 9):1414-26



  1. BulletMoosajee M, Tulloch M, Baron RA, Gregory-Evans CY, Pereira-Leal, JB , and Seabra MC. (2009) Single Rab Escort Protein gene in non-mammalian vertebrates explains early embryonic lethality of a zebrafish model of Choroideremia Invest Ophthalmol Vis Sci. 50(6):3009-16



  1. BulletLevy, ED & Pereira-Leal, JB (2008) Evolution and dynamics of protein interactions and networks Curr. Op. Struct. Bio. 18(3):349-57



  1. BulletPereira-Leal, JB (2008) The Ypt/Rab family and the evolution of trafficking in Fungi Traffic 9(1):27-38



  1. BulletRasteiro, R & Pereira-Leal, JB (2007) Multiple domain insertions in the evolution of the Rab prenylation complex BMC Evol. Bio. 7:140



  1. BulletPereira-Leal, JB, Levy, ED, Kamp. C and Teichmann, SA (2007) The evolution of protein complexes by duplication of homomeric interactions Genome Biol. 8(4):R51



  1. BulletPereira-Leal, JB (2006) Book Review: Modularity in natural complex systems Acta Biotheoretica 54:295-9