- 1992, B.Sc., Biology, University of Lisbon, Faculty of Sciences, Portugal
- 2000, Ph.D., Genetics, The University of Arizona, USA (Major advisor: Margaret Kidwell)
- 2000-2002, Fogarty Postdoctoral Fellow, National Center for Biotechnology Information (NCBI), National Institutes of Health, USA (Advisor: Alex Kondrashov)
- 2002-2005, Staff Scientist, The Institute for Genomic Research (TIGR), USA
- 2006-2007, Assistant Investigator, The Institute for Genomic Research (TIGR), USA
My research interests are centered on the evolutionary forces and genetic mechanisms that shape genome evolution, and focus on three main topics: (1) the processes that affect gene content and nucleotide composition, (2) the evolution, and detection, of antigens pathogen genomes, and (3) the evolution of host-parasite interactions. To address these questions I use a combination of population genetics and molecular evolution approaches. Bioinformatics and genomics tools allow me to apply these approaches to large data sets, bringing into play the power of comparative genomics.
My research is primarily process-oriented, but the study of single-celled eukaryotic parasites in the phylum Apicomplexa is a central component of my research program. Many species of Apicomplexa have tremendous medical, agricultural, and economic significance. Some of the infectious diseases they cause include malaria, babesiosis, cryptosporidiosis, and toxoplasmosis in humans, and babesiosis, theileriosis and East Coast fever in cattle. Apicomplexan organisms have complex life cycles, often requiring multiple hosts and complex environmental cues. For some, humans are the primary (or the sole) vertebrate host. Due to these constraints, apicomplexans are often not amenable to lab culture and in silico analyses provide a powerful approach to explore their evolution, pathogenesis and epidemiology. Due to their relatively small and gene-dense genome sizes, apicomplexans are also an ideal system in which to address fundamental question regarding the evolution of eukaryotic genomes.
Apicomplexans as a Model System for Disease and Evolutionary Genomics
Principal Investigator(s): Carneiro da Silva, Joana
The phylum Apicomplexa consists of over 4,000 described species, all of which, with a few exceptions, are pathogenetic, obligate, intracellular parasites, Each year they lead to the death of millions of people, are responsible for productivity losses of millions of dollars and the diseases they cause result in dire socio-economic prospects for many communities, especially in developing countries.
Current projects in the lab include the study of gene and genome variability in Theileria, and the identification and characterization of antigens from genomic data in several apicomplexan species, the evolution of population variation in response to vaccine or drug treatment, and the evolution of genome nucleotide composition in Plasmodium.
Evolution and Function of Species Interactions in an Aquatic Host-Parasite System
Principal Investigator(s): Carneiro da Silva, Joana and Lee, Carol E. (University of Wisconsin)
Copepods form the largest biomass of metazoans in the world’s oceans, and often dominate zooplankton assemblages in nearshore environments. Concentrations of bacteria associated with copepods tend to be several orders of magnitude higher than in comparable volumes of water. Given their abundance these bacteria, termed the copepod microbiome, have the potential to play a fundamental role in biogeochemical processes in many aquatic ecosystems.
Software Development: IDEA - Interactive Display for Evolutionary Analyses
Principal Investigator(s): Carneiro da Silva, Joana
IDEA (Interactive Display for Evolutionary Analyses) provides a graphical interface for PAML (Phylogenetic Analysis by Maximum Likelihood, Ziheng Yang, 1997), a suite of programs for conducting molecular evolution analyses on nucleotide and amino acid data. IDEA allows you to run either of the PAML programs codeml or baseml on a single dataset or on multiple datasets simultaneously, monitor run status and visualize the results interactively.
Fedorova, N. D.N. Khaldi, V.S. Joardar, R. Maiti, P. Amedeo, M.J. Anderson, J. Crabtree, J.C. Silva, J.H. Badger, A. Albarraq, S. Angiuoli, H. Bussey, P. Bowyer, P.J. Cotty, P.S. Dyer, A. Egan, K. Galens, C.M. Fraser-Liggett, B.J. Haas, J.M. Inman, R. Kent, S. Lemieux, I. Malavazi, J. Orvis, T. Roemer, C.M. Ronning, J.P. Sundaram, G. Sutton, G. Turner, J.C. Venter, O.R. White, B.R. Whitty, P. Youngman, K.H. Wolfe, G.H. Goldman, J.R. Wortman, B. Jiang, D.W. Denning, W.C. Nierman. 2008. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics 4:e1000046.
Lin, H., S. Ouyang, A. Egan, K. Nobuta, B.J. Haas, W. Zhu, X. Gu, J.C. Silva, B.C. Meyers, and C.R. Buell. 2008. Characterization of paralogous protein families in rice. BMC Plant Biology 8: 18.
Carlton, J.M., J. Adams, J.C. Silva, S.L. Bidwell, H. Lorenzi, E. Caler, D. LaCount, S.V. Date, J. Crabtree, S.V. Angiuoli, E.F. Merino, P. Amedeo, Q. Cheng, R. Chettier, R.M.R. Coulson, B.S. Crabb, H.A. del Portillo, K. Essien, T.V. Feldblyum, C. Fernandez-Becerra, S. Fields, P.R. Gilson, A.H. Gueye, X. Guo, R. Hughes, S. Kang’a, T.W.A. Kooij, M.l Korsinczky, C. Kurschner, E.V.-S. Meyer, V.Nene, I. Paulsen, O. White, S.A. Ralph, Q. Ren, T.J. Sargeant, S. Sahasrabudhe, S. Salzberg, L.W. Schoenfeld, C.J. Stoeckert, S.A. Sullivan, M. Vignali, M.M. Yamamoto, S.L. Hoffman, J.R. Wortman, M.J. Gardner, M. Galinski, J.W. Barnwell and C.M. Fraser-Liggett. Comparative genomics of the neglected human parasite Plasmodium vivax illuminates malaria parasite biology. Nature 455:757-763.
Guo, X. and J.C. Silva. 2008. Properties of non-coding DNA and identification of putative cis-regulatory regions in Theileria parva. BMC Genomics 9:582 [Epub ahead of print].
Egan, A., A. Mahurka, J. Crabtree, J.H. Badger, J.M. Carlton, J.C. Silva. 2008. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics 9:524 [Epub ahead of print].
Carlton, J.M., R.P. Hirt, J.C. Silva, A.L. Delcher, M. Schatz, Q. Zhao, J.R. Wortman, S.L. Bidwell, U.C.M. Alsmark, S. Besteiro, T. Sicheritz-Ponten, C.J. Noel, J.B. Dacks, P.G. Foster, C. Simillion, Y. Van de Peer, D. Miranda-Saavedra, G.J. Barton, G.D. Westrop, S. Mueller, D. Dessi, P.L. Fiori, Q. Ren, I. Paulsen, H. Zhang, F.D. Bastida-Corcuera, A. Simoes-Barbosa, M.T. Brown, R.D. Hayes, M. Mukherjee, C.Y. Okumura, R. Schneider, A.J. Smith, S. Vanacova, M. Villalvazo, B.J. Haas, M. Pertea, T. Feldblyum, T.R. Utterback, C.-L. Shu, K. Osoegawa, P.J. de Jong, I. Hrdy, L. Horvathova, Z. Zubacova, P. Dolezal, S.-B. Malik, J.M. Logsdon, Jr., K. Henze, A. Gupta, C.C. Wang, R.L. Dunne, J.A. Upcroft, P. Upcroft, O. White, S.L. Salzberg, P. Tang, C.-H. Chiu, Y.-S. Lee, T.M. Embley, G.H. Coombs, J.C. Mottram, J. Tachezy, C.M. Fraser-Liggett and P.J. Johnson 2007. Draft Genome Sequence of the Sexually-Transmitted Pathogen Trichomonas vaginalis. Science 315: 207-212.
Eisen, J.A., Coyne, R.S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J.R., Badger, J.H., Ren, Q., Amedeo, P., Jones, K.M., Tallon, L.J., Delcher, A.L., Salzberg, S.L., Silva, J.C., Haas, B.J., Majoros, W.H., Farzad, M., Carlton, J.M., Smith, R.K., Garg, J., Pearlman, R.E., Karrer, K.M., Sun, L., Manning, G., Elde, N.C., Turkewitz, A.P., Asai, D.J., Wilkes, D.E., Wang, Y., Cai, H., Collins, K., Stewart, B.A., Lee, S.R., Wilamowska, K., Weinberg, Z., Ruzzo, W.L., Wloga, D., Gaertig, J., Frankel, J., Tsao, C.C., Gorovsky, M.A., Keeling, P.J., Waller, R.F., Patron, N.J., Cherry, J.M., Stover, N.A., Krieger, C.J., Del Toro, C., Ryder, H.F., Williamson, S.C., Barbeau, R.A., Hamilton, E.P., Orias, E. (2006) Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4(9):e286.
Lin, H., W. Zhu, J.C. Silva, X. Gu and R. Buell. 2006. Intron turnover of segmentally duplicated genes in rice. Genome Biology: 7: R4.
Silva, J.C., F. Bastida, S.L. Bidwell, P.J. Johnson and J.M. Carlton 2005. A potentially functional mariner transposable element in the protist Trichomonas vaginals. Mol. Biol. Evol. 22: 126-134.
El-Sayed N.M., P.J. Myler, G. Blandin, M. Berriman, J. Crabtree, G, Aggarwal, E. Caler, H. Renauld, E.A. Worthey C. Hertz-Fowler, E. Ghedin, C. Peacock, D.C. Bartholomeu, B. J. Haas, A.N. Tran, J.R. Wortman, U.C. Alsmark, S. Angiuoli, A. Anupama, J. Badger, F. Bringaud, E. Cadag, J.M. Carlton, G.C. Cerqueira, T. Creasy, A.L. Delcher, A. Djikeng, T.M. Embley, C. Hauser, A.C. Ivens, S.K. Kummerfeld, J.B. Pereira-Leal, D. Nilsson, J. Peterson, S.L. Salzberg, J. Shallom, J.C. Silva, J. Sundaram, S. Westenberger, O. White, S.E. Meilville, J.E. Donelson, B. Andersson, K.D. Stuart, N. Hall. 2005. Comparative genomics of the trypanosomatid parasitic protozoa. Science 309: 404-409.
Gardner M.J., R. Bishop, T. Shah, E.P. de Villiers, J.M. Carlton, N. Hall, Q. Ren, I.T. Paulsen, A. Pain, M. Berriman, R.J. Wilson, S. Sato, S.A. Ralph, D.J. Mann, Z. Xiong, S.J. Shallom, J. Weidman, L. Jiang, J. Lynn, B. Weaver, A. Shoaibi, A.R. Domingo, D. Wasawo, J. Crabtree, J.R. Wortman, B. Haas, S.V. Angiuoli, T.H. Creasy, C. Lu, B. Suh, J.C. Silva, T.R. Utterback, T.V. Feldblyum, M. Pertea, J. Allen, W.C. Nierman, E.L. Taracha, S.L. Salzberg, O.R. White, H.A. Fitzhugh, S. Morzaria, J.C. Venter, C.M. Fraser, V. Nene. 2005. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309: 134-137.
Carlton, J.M., J.C. Silva, and N. Hall 2005. The genome of model malaria parasites, and comparative genomics. Curr. Issues Mol. Biol. 7: 23-37.
Silva, J.C. and M.G. Kidwell 2004. Evolution of P elements in natural populations of Drosophila willistoni and D. sturtevanti. Genetics 168: 1323-1335.
Silva, J.C., E.L. Loreto and J.B. Clark 2004. Factors that affect horizontal transfer of transposable elements. Curr. Issues Mol. Biol. 6:57-72.
Carvalho, M.O., J.C. Silva, and E.L. Loreto. 2004. Analyses of P-like transposable element sequences from the genome of Anopheles gambiae. Insect Mol. Biol. 13:55-63.
Silva, J.C., S.A. Shabalina, D.G. Harris, J. Spouge and A.S. Kondrashov 2003. Conserved transposable elements in intergenic regions: recruitment of MIR- and L2-derived sequences in the mouse and human genomes. Genet. Res. 82:1-18.
Carlton, J.M., S.V. Angiuoli, B.B. Suh, T.W. Kooij, M. Pertea, J.C. Silva, M.D. Ermolaeva, J.E. Allen, J.D. Selengut, H.L. Koo, J.D. Peterson, M. Pop, D.S. Kosack, M.F. Shumway, S.L. Bidwell, S.J. Shallom, S.E. van Aken, S.B. Riedmuller T.V. Feldblyum, J.K. Cho, J. Quackenbush, M. Sedegah, A. Shoaibi, L.M. Cummings, L. Florens, J.R. Yates, J.D. Raine, R.E. Sinden, M.A. Harris, D.A. Cunningham, P.R. Preiser, L.W. Bergman, A.B. Vaidya, L.H. van Lin, C.J. Janse, A.P. Waters, H.O. Smith, O.R. White, S.L. Salzberg, J.C. Venter, C.M. Fraser, S.L. Hoffman, M.J. Gardner, D.J. Carucci. 2002. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419:512-519.
Silva, J.C. and A.S. Kondrashov 2002.Patterns in spontaneous mutation revealed by human-baboon sequence comparison. Trends in Genetics 18:544-547.
Loreto, E.L.S., L.B. da Silva, A. Zaha, J.C. Silva, V.L.S. Valente and M.G. Kidwell 2001. Drosophila mediopunctata P elements: a new example of horizontal transfer. Journal of Heredity, 92: 375-381.
Yang H.-P., Tanikawa A.Y., W.A. Van Voorhies, Silva JC, A.S.Kondrashov 2001. Whole-genome effects of ethyl methanesulfonate-induced mutation on nine quantitative traits in outbred Drosophila melanogaster. Genetics 157:1257-65.
Silva, J.C., and M.G. Kidwell. 2000. Horizontal transfer and selection in P transposable elements. Mol. Biol. Evol. 17: 1542-1557.
Carareto, C.M.A., W. Kim, M.F. Wojciechowski, P.M. O'Grady, A.V. Prokchorova, J.C. Silva and M.G. Kidwell 1997. Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system. Genetica 101:13-33.
Carlton, J.M., J.C. Silva, and N. Hall. 2004. The genome of model malaria parasites, and comparative genomics. In Genomes and the Molecular Cell Biology of Malaria Parasites (A. Waters and C. Janse, eds.) Horizon Scientific Press.
Clark, J.B., J.C. Silva and M.G. Kidwell 2002. Evidence for horizontal transfer of P transposable elements. In Horizontal Gene Transfer, 2nd edition (Syvanen, M. and Kado, eds.), pp 161-171. Academic Press, San Diego, CA.