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Joana  Carneiro da Silva

Joana Carneiro da Silva Ph.D.

Academic Title: Associate Professor
Primary Appointment: Microbiology and Immunology
Additional Title(s): Associate Professor, Institute for Genome Sciences; Associate Member, Institute for Global Health, Division of Malaria Research, University of Maryland School of Medicine; Affiliate Faculty, School of Systems Biology, George Mason University
Location: BioPark II, 645
Phone: (410) 706-6721
Phone: (410) 706-6755
Fax: (410) 706-6756
Lab: 410-706-6721

Personal History:

Joana Carneiro da Silva is an Associate Professor of Microbiology and Immunology in the Institute for Genome Sciences, at the University of Maryland School of Medicine. Her research focuses on single-celled eukaryotic parasites, with particular emphasis on organisms in the phylum Apicomplexa. These include the causative agents of malaria in humans (genus Plasmodium), theileriosis and East Coast fever in cattle (genus Theileria), human and bovine babesiosis (genus Babesia), and cryptosporidiosis in vertebrates, including humans (genus Cryptosporidium).

  • 1992, B.Sc., Biology, University of Lisbon, Faculty of Sciences, Portugal
  • 2000, Ph.D., Genetics, The University of Arizona, USA (Margaret Kidwell, Advisor)
  • 2000-2002, Fogarty Postdoctoral Fellow, National Center for Biotechnology Information (NCBI), National Institutes of Health, USA (Alex Kondrashov, Advisor)
  • 2002-2005, Staff Scientist, The Institute for Genomic Research (TIGR), USA
  • 2006-2007, Assistant Investigator, The Institute for Genomic Research (TIGR), USA
  • 2007-2015, Assistant Professor, University of Maryland School of Medicine
  • 2015-present, Associate Professor, University of Maryland School of Medicine

Research Interests:

I am an evolutionary geneticist by training. In my research, I apply genomic sciences to translational research of infectious diseases. My group uses population, evolutionary and comparative genomics to understand the biology of species, and to uncover their defining traits. These traits can in turn be used to identify new drug or vaccine targets. Our genome-wide studies also address topics in drug resistance, vaccine evasion and vaccine design.

My research is funded by NSF, NIH, USDA and the Bill and Melinda Gates Foundation.

Research Highlights:

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, nearly all of which 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 Plasmodium and Theileria, the identification and characterization of antigens from genomic data in several apicomplexan species, the evolution of population variation in response to vaccination 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.


Selected Publications:

Norling M, Bishop RP, Pelle R, Qi W, Henson S, Drabek EF, Tretina K, Odongo D, Mwaura S, Njoroge T, Bongcam-Rudloff E, Daubenberger CA, Silva JC. The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence. BMC Genomics. 2015 Sep 24;16(1):729. doi: 10.1186/s12864-015-1910-9. PMID: 26403690; Central PMCID: PMC4583173.

Tretina K, Gotia HT, Mann DJ, Silva JC. Theileria-transformed bovine leukocytes have cancer hallmarks. Trends Parasitol. 2015 Jul;31(7):306-14. doi: 10.1016/ Epub 2015 May 4. Review. PMID: 25951781.

Obara I, Ulrike S, Musoke T, Spooner PR, Jabbar A, Odongo D, Kemp S, Silva JC, Bishop RP. Molecular evolution of a central region containing B cell epitopes in the gene encoding the p67 sporozoite antigen within a field population of Theileria parva. Parasitol Res. 2015 May;114(5):1729-37. doi: 10.1007/s00436-015-4358-6. Epub 2015 Feb 13. PMID: 25673078; Central PMCID: PMC4412645.

Silva JC, Egan A, Arze C, Spouge JL, Harris DG. A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts. Mol Biol Evol. 2015 May;32(5):1354-64. doi: 10.1093/molbev/msv005. Epub 2015 Jan 13. PMID: 25589738; Central PMCID: PMC4408405.

Brown TS, Jacob CG, Silva JC, Takala-Harrison S, Djimdé A, Dondorp AM, Fukuda M, Noedl H, Nyunt MM, Kyaw MP, Mayxay M, Hien TT, Plowe CV, Cummings MP. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype. Infect Genet Evol. 2015 Mar;30:318-22. doi: 10.1016/j.meegid.2014.12.010. Epub 2014 Dec 13. PMID: 25514047; Central PMCID: PMC4316729.

Takala-Harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H, Nosten F, Kyaw MP, Nhien NT, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Ariey F, Mercereau-Puijalon O, Menard D, Newton PN, Khanthavong M, Hongvanthong B, Starzengruber P, Fuehrer HP, Swoboda P, Khan WA, Phyo AP, Nyunt MM, Nyunt MH, Brown TS, Adams M, Pepin CS, Bailey J, Tan JC, Ferdig MT, Clark TG, Miotto O, MacInnis B, Kwiatkowski DP, White NJ, Ringwald P, Plowe CV. Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. J Infect Dis. 2015 Mar 1;211(5):670-9. doi: 10.1093/infdis/jiu491. Epub 2014 Sep 1. PMID: 25180241; Central PMCID: PMC4334802.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014. PMID: 24936976; Central PMCID: PMC4061050.

Munro JB, Jacob CG, Silva JC. A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites. J Mol Evol. 2013 Sep;77(3):92-106. doi: 10.1007/s00239-013-9583-y. Epub 2013 Sep 18. PMID: 24046025; Central PMCID: PMC3824934.

Cornillot E, Dassouli A, Garg A, Pachikara N, Randazzo S, Depoix D, Carcy B, Delbecq S, Frutos R, Silva JC, Sutton R, Krause PJ, Mamoun CB. Whole genome mapping and re-organization of the nuclear and mitochondrial genomes of Babesia microti isolates. PLoS One. 2013 Sep 4;8(9):e72657. doi: 10.1371/journal.pone.0072657. eCollection 2013. PMID: 24023759; Central PMCID: PMC3762879.

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Socheat D, Ariey F, Phyo AP, Starzengruber P, Fuehrer HP, Swoboda P, Stepniewska K, Flegg J, Arze C, Cerqueira GC, Silva JC, Ricklefs SM, Porcella SF, Stephens RM, Adams M, Kenefic LJ, Campino S, Auburn S, MacInnis B, Kwiatkowski DP, Su XZ, White NJ, Ringwald P, Plowe CV. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):240-5. doi: 10.1073/pnas.1211205110. Epub 2012 Dec 17. PMID: 23248304; Central PMCID: PMC3538248.

Kappmeyer LS, Thiagarajan M, Herndon DR, Ramsay JD, Caler E, Djikeng A, Gillespie JJ, Lau AO, Roalson EH, Silva JC, Silva MG, Suarez CE, Ueti MW, Nene VM, Mealey RH, Knowles DP, Brayton KA. Comparative genomic analysis and phylogenetic position of Theileria equi. BMC Genomics. 2012 Nov 9;13:603. doi: 10.1186/1471-2164-13-603. PMID: 23137308; Central PMCID: PMC3505731.

Munro JB, Silva JC. Ribonucleotide reductase as a target to control apicomplexan diseases. Curr Issues Mol Biol. 2012;14(1):9-26. Epub 2011 Jul 26. Review. PMID: 21791713.

Pelle R, Graham SP, Njahira MN, Osaso J, Saya RM, Odongo DO, Toye PG, Spooner PR, Musoke AJ, Mwangi DM, Taracha EL, Morrison WI, Weir W, Silva JC, Bishop RP. Two Theileria parva CD8 T cell antigen genes are more variable in buffalo than cattle parasites, but differ in pattern of sequence diversity. PLoS One. 2011 Apr 29;6(4):e19015. doi: 10.1371/journal.pone.0019015. PMID: 21559495; Central PMCID: PMC3084734.

Silva JC, Egan A, Friedman R, Munro JB, Carlton JM, Hughes AL. Genome sequences reveal divergence times of malaria parasite lineages. Parasitology. 2011 Nov;138(13):1737-49. doi: 10.1017/S0031182010001575. Epub 2010 Dec 1. PMID: 21118608; Central PMCID: PMC3081533.

Lopes FR, Silva JC, Benchimol M, Costa GG, Pereira GA, Carareto CM. The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements. BMC Genomics. 2009 Jul 21;10:330. doi: 10.1186/1471-2164-10-330. PMID: 19622157; Central PMCID: PMC2725143.

Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics. 2008 Dec 8;9:524. doi: 10.1186/1471-2105-9-524. PMID: 19061522; Central PMCID: PMC2655098.

Guo X, Silva JC. Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva. BMC Genomics. 2008 Dec 3;9:582. doi: 10.1186/1471-2164-9-582. PMID: 19055776; Central PMCID: PMC2612703.

Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008 Oct 9;455(7214):757-63. doi: 10.1038/nature07327. PMID: 18843361; Central PMCID: PMC2651158.

Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008 Apr 11;4(4):e1000046. doi: 10.1371/journal.pgen.1000046. PMID: 18404212; Central PMCID: PMC2289846.

Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR. Characterization of paralogous protein families in rice. BMC Plant Biol. 2008 Feb 19;8:18. doi: 10.1186/1471-2229-8-18. PMID: 18284697; Central PMCID: PMC2275729.

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007 Jan 12;315(5809):207-12. PMID: 17218520; Central PMCID: PMC2080659.

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006 Sep;4(9):e286. PMID: 16933976; Central PMCID: PMC1557398.

Lin H, Zhu W, Silva JC, Gu X, Buell CR. Intron gain and loss in segmentally duplicated genes in rice. Genome Biol. 2006;7(5):R41. Epub 2006 May 23. PMID: 16719932; Central PMCID: PMC1779517.

El-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. Comparative genomics of trypanosomatid parasitic protozoa. Science. 2005 Jul 15;309(5733):404-9. PMID: 16020724.

Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science. 2005 Jul 1;309(5731):134-7. PMID: 15994558.

Carlton J, Silva J, Hall N. The genome of model malaria parasites, and comparative genomics. Curr Issues Mol Biol. 2005 Jan;7(1):23-37. Review. PMID: 15580778.

Silva JC, Kidwell MG. Evolution of P elements in natural populations of Drosophila willistoni and D. sturtevanti. Genetics. 2004 Nov;168(3):1323-35. PMID: 15579688; Central PMCID: PMC1448778.

Silva JC, Bastida F, Bidwell SL, Johnson PJ, Carlton JM. A potentially functional mariner transposable element in the protist Trichomonas vaginalis. Mol Biol Evol. 2005 Jan;22(1):126-34. Epub 2004 Sep 15. PMID: 15371525; Central PMCID: PMC1406841.

Oliveira de Carvalho M, Silva JC, Loreto EL. Analyses of P-like transposable element sequences from the genome of Anopheles gambiae. Insect Mol Biol. 2004 Feb;13(1):55-63. PMID: 14728667.

30: Silva JC, Loreto EL, Clark JB. Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol. 2004 Jan;6(1):57-71. Review. PMID: 14632259.

Silva JC, Shabalina SA, Harris DG, Spouge JL, Kondrashovi AS. Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet Res. 2003 Aug;82(1):1-18. PMID: 14621267.

Silva JC, Kondrashov AS. Patterns in spontaneous mutation revealed by human-baboon sequence comparison. Trends Genet. 2002 Nov;18(11):544-7. PMID: 12414177.

Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002 Oct 3;419(6906):512-9. PMID: 12368865.

Loreto EL, Valente VL, Zaha A, Silva JC, Kidwell MG. Drosophila mediopunctata P elements: a new example of horizontal transfer. J Hered. 2001 Sep-Oct;92(5):375-81. PMID: 11773243.

Yang HP, Tanikawa AY, Van Voorhies WA, Silva JC, Kondrashov AS. Whole-genome effects of ethyl methanesulfonate-induced mutation on nine quantitative traits in outbred Drosophila melanogaster. Genetics. 2001 Mar;157(3):1257-65. PMID: 11238409; Central PMCID: PMC1461548.

Silva JC, Kidwell MG. Horizontal transfer and selection in the evolution of P elements. Mol Biol Evol. 2000 Oct;17(10):1542-57. PMID: 11018160.

Carareto CM, Kim W, Wojciechowski MF, O'Grady P, Prokchorova AV, Silva JC, Kidwell MG. Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system. Genetica. 1997;101(1):13-33. PMID: 9465407.