Joana Carneiro da Silva, PhD

Apicomplexan Parasites.

Shah Z, Adams M, Moser KA, Shrestha B, Stucke EM, Laufer MK, Serre D, Silva JC, Takala-Harrison S. Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples. Malar J. 2020 Mar 30;19(1):135. doi:10.1186/s12936-020-03195-8. PMID: 32228559.

Tretina K, Haidar M, Madsen-Bouterse SA, Sakura T, Mfarrej S, Fry L, Chaussepied M, Pain A, Knowles DP, Nene VM, Ginsberg D, Daubenberger CA, Bishop RP, Langsley G, Silva JC. Theileria parasites subvert E2F signaling to stimulate leukocyte proliferation. Sci Rep. 2020 Mar 4;10(1):3982. doi:10.1038/s41598-020-60939-x. PMID: 32132598.

Tretina K, Pelle R, Orvis J, Gotia HT, Ifeonu OO, Kumari P, Palmateer NC, Iqbal SBA, Fry LM, Nene VM, Daubenberger CA, Bishop RP, Silva JC. Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. BMC Genomics. 2020 Apr 3;21(1):279. doi: 10.1186/s12864-020-6683-0. PMID:32245418.

Moser KA, EF Drabek, A Dwivedi, J Crabtree, E Stucke, A Dara, Z Shah, M Adams, T Li, P Rodrigues, S Korsen, A Phillippy, A Ouattara, K Lyke, L Sadzewicz, L Tallon, MU Ferreira, M Laufer, M Travassos, S Takala-Harrison, CM Fraser, BKL Sim, SL Hoffman, CV Plowe, JC Silva. Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential. Genome Med. 2020;12(1):6. Published 2020 Jan 8. doi:10.1186/s13073-019-0708-9

Schindler T., Deal AC, Fink M, Guirou E, Mwakasungula SM, Mihayo MG, JongoSA, Chaki PP, Abdullah S, Bieri JR, Moser KA, Silva JC, Hoffman SL, Gamboa D, Tanner M and Daubenberger A. A multiplex qPCR approach for detection of pfhrp2 and pfhrp3 gene deletions in multiple strain infections of Plasmodium falciparum. Sci Rep. 2019 Sep 11;9(1):13107. doi: 10.1038/s41598-019-49389-2. PMID: 31511562.

Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nat Commun.2019 Jun 17;10(1):2665. doi: 10.1038/s41467-019-10121-3. PMID: 31209259.

Tonui T, Corredor-Moreno P, Kanduma E, Njuguna J, Njahira MN, Nyanjom SG, Silva JC, Djikeng A, Pelle R. Transcriptomics reveal potential vaccine antigens and a drastic increase of upregulated genes during Theileria parva development from arthropod to bovine infective stages. PLoS One. 2018;13(10):e0204047. doi: 10.1371/journal.pone.0204047. eCollection 2018. PMID: 30303978.

Mendes AM, Machado M, Gonçalves-Rosa N, Reuling IJ, Foquet L, Marques C, Salman AM, Yang ASP, Moser KA, Dwivedi A, Hermsen CC, Jiménez-Díaz B, Viera S, Santos JM, Albuquerque I, Bhatia SN, Bial J, Angulo-Barturen I, Silva JC, Leroux-Roels G, Janse CJ, Khan SM, Mota MM, Sauerwein RW, Prudêncio M. A Plasmodium berghei sporozoite-based vaccination platform against human malaria. NPJ Vaccines. 2018;3:33. doi: 10.1038/s41541-018-0068-2. eCollection 2018.  PMID: 30155278.

Knowles DP, Kappmeyer LS, Haney D, Herndon DR, Fry LM, Munro JB, Sears K, Ueti MW, Wise LN, Silva M, Schneider DA, Grause J, White SN, Tretina K, Bishop RP, Odongo DO, Pelzel-McCluskey AM, Scoles GA, Mealey RH, Silva JC. Discovery of a novel species, Theileria haneyi sp., infective to equids, highlights exceptional genomic diversity within the genus Theileria: implications for apicomplexan parasite surveillance. Int J Parasitol. 2018 Aug;48(9-10):679-690. doi: 10.1016/j.ijpara.2018.03.010. Epub 2018 Jun 6. PMID: 29885436.

Ouattara A, Tran TM, Doumbo S, Matthew A, Agrawal S, Niangaly A, Nelson-Owens S, Doumtabé D, Tolo Y, Ongoiba A, Takala-Harrison S, Traoré B, Silva JC, Crompton PD, Doumbo OK, Plowe CV. Extent and Dynamics of Polymorphism in the Malaria Vaccine Candidate Plasmodium falciparum Reticulocyte-Binding Protein Homologue-5 in Kalifabougou, Mali. Am J Trop Med Hyg. 2018 Jul;99(1):43-50. doi: 10.4269/ajtmh.17-0737. Epub 2018 May 24. PMID: 29848401.

Nyagwange J, E Tijhaar, N Ternette, K Tretina, JC Silva, R Pelle, V Nene. Characterization of the Theileria parva sporozoite proteome. Int J Parasitol. 2018 Mar;48(3-4):265-273. doi: 10.1016/j.ijpara.2017.09.007. Epub 2017 Dec 16. PMID: 29258832.

Dara A, MA Travassos, M Adams, S Schaffer DeRoo, EF Drábek, S Agrawal, MK Laufer, CV Plowe, JC Silva. A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples. Malar J. 2017 Aug 17;16(1):343. doi: 10.1186/s12936-017-1976-8. PMID: 28818101.

Agrawal S, Moser K, Morton L, Cummings MP, Parihar A, Dwivedi A, Shetty AC, Drabek E, Jacob CG, Henrich P, Parobek CM, Jongsakul K, Chaorattanakawee S, Lon C, Fukuda MM, Saunders DL, Fidock DA, Lin JT, Juliano JJ, Plowe CV, Silva JC, Takala-Harrison S. Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity. J Infect Dis. 2017 Aug 15;216(4):468-476. doi: 10.1093/infdis/jix334. PMID: 28931241

Dara A, Drábek EF, Travassos MA, Moser KA, Delcher AL, Su Q, Hostelley T, Coulibaly D, Daou M, Dembele A, Diarra I, Kone AK, Kouriba B, Laurens MB, Niangaly A, Traore K, Tolo Y, Fraser CM, Thera MA, Djimde AA, Doumbo OK, Plowe CV, Silva JC. New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali. Genome Med. 2017 Mar 28;9(1):30. doi: 10.1186/s13073-017-0422-4. PMID: 28351419.

Epstein JE, Paolino KM, Richie TL, Sedegah M, Singer A, Ruben AJ, Chakravarty  S, Stafford A, Ruck RC, Eappen AG, Li T, Billingsley PF, Manoj A, Silva JC, Moser K, Nielsen R, Tosh D, Cicatelli S, Ganeshan H, Case J, Padilla D, Davidson S, Garver L, Saverino E, Murshedkar T, Gunasekera A, Twomey PS, Reyes S, Moon JE, James ER, Kc N, Li M, Abot E, Belmonte A, Hauns K, Belmonte M, Huang J, Vasquez C, Remich S, Carrington M, Abebe Y, Tillman A, Hickey B, Regules J, Villasante E, Sim BK, Hoffman SL. Protection against Plasmodium falciparum malaria by PfSPZ Vaccine. JCI Insight. 2017 Jan 12;2(1):e89154. PubMed PMID: 28097230.

Silva JC, E Cornillot, C McCracken, S Usmani-Brown, A Dwivedi, OO Ifeonu, J Crabtree, HT Gotia, AZ Virji, C Reynes, J Colinge, V Kumar, L Lawres, JE Pazzi, JV Pablo, C Hung, J Brancato, P Kumari, J Orvis, K Tretina, MC Chibucos, S Ott, L Sadzewicz, N Sengamalay, AC Shetty, Q Su, L Tallon, CM Fraser, R Frutos, DM Molina, P Krause, CB Mamoun. Genome-wide diversity and gene expression profiling of Babesia microtiisolates identify polymorphic genes that mediate host-pathogen interactions. Sci Rep. 2016 Oct 18;6:35284. PMID: 27752055.

Ifeonu OO, R Simon, SM Tennant, AS Sheoran, JC Kissinger, G Widmer, MM Levine, S Tzipori, JC Silva. Cryptosporidium hominis Gene Catalog: A Resource for Selecting Novel Vaccine Candidates Using Reverse Vaccinology. Database (Oxford). 2016 Oct 19;2016. pii: baw137. PubMed PMID: 28095366.

Ifeonu OO, M Chibucos, J Orvis, Q Su, K Elwin, F Guo, H Zhang, L Xiao, M Sun, RM Chalmers, CM Fraser, G Zhu, JC Kissinger, G Widmer, JC Silva. Annotated Draft Genome Sequences of Cryptosporidium meleagridis isolate UKMEL1, Cryptosporidium baileyi isolate TAMU-09Q1, and Cryptosporidium hominis isolates TU502_2012 and UKH1. Pathog Dis. 2016 Oct;74(7). pii: ftw080. PMID: 27519257.

Gotia HT, JB Munro, DP Knowles, CA Daubenberger, RP Bishop, JC Silva. Quantification of the ratio of host-to-parasite DNA in samples from Theileria parva-infected host lymphocyte cell lines. PLoS One. 2016 11(3):e0150401. PMID: 26930209. 

Tretina K, R Pelle and JC Silva. Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva. BMC Genomics. 2016 17(1):128. PMID: 26896950. 

Norling M, Bishop RP, Pelle R, Qi W, Henson S, Drábek 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.

Tretina, K., Gotia HT, Mann D, Silva JC. Theileria-transformed bovine leukocytes have cancer hallmarks. Trends Parasitol. 2015 Jul;31(7):306-14. doi: 10.1016/j.pt.2015.04.001. 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. PMID: 25673078.

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. PMID: 25589738

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. PMID: 25514047.

Takala-HarrisonS, JacobCG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H, Nosten F, Kyaw MP, Nhien NTT, Imwong M, Bethell D, Y S, Lon C, Stuart D. Tyne SD, Saunders DL, Socheat D, Ariey F, Mercereau-Puijalon O, Menard D, Newton PN, Khanthavong M, Hongvanthong B, Starzengruber P, Fuehrer H-P, 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, and Plowe CV. Independent emergence of Plasmodium falciparum artemisinin resistance mutations in Southeast Asia. Journal Infectious Diseases. 2015 Mar 1;211(5):670-9. doi: 10.1093/infdis/jiu491. Epub 2014 Sep 1. PubMed PMID: 25180241.

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. PMID: 24023759.

Takala-Harrison S., T.G. Clark, C.G. Jacob, M.P. Cummings, O. Miotto, A.M. Dondorp, M.M Fukuda, F. Nosten, H. Noedl, M. Imwong, D. Bethell, Y. Se, C. Lon, S. .D Tyner, D. Saunders, D. Socheat, F. Ariey, A. Pyae Phyo, P. Starzengruber, H-P Fuehrer, P. Swoboda, K. Stepniewska, J. Flegg, C. Arze, G.C. Cerqueira, J.C. Silva, S.M. Ricklefs, S.F. Porcella, R.M. Stephens, M. Adams, L.J Kenefic, S. Campino, S. Auburn, B. MacInnis, D.P. Kwiatkowski, X-Z Su, N.J. White, P. Ringwald, C.V. Plowe. 2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. PNAS 110: 240-5. PMID: 23248304.

Kappmeyer L.S., M. Thiagarajan, D.R. Herndon, J.D. Ramsay, E. Caler, A. Djikeng, J.J. Gillespie, A.O.T. Lau, E.H. Roalson, J.C. Silva, M.G. Silva, C.E. Suarez, M.W. Ueti, V.M. Nene, R.H. Mealey, D.P. Knowles and K.A. Brayton. 2012. Comparative genomic analysis and phylogenetic position of Theileria equi. BMC Genomics 13(1):603. PMID: 23137308.

Munro JB and JC Silva. 2011. Ribonucleotide reductase as a drug target for apicomplexan parasites. Curr Issues Mol Biol. 14(1):9-26. PMID: 21791713.

Pelle, R., S.P. Graham, M. Njahira, J. Osaso, R.M. Saya, D.O. Odongo, P.G. Toye, P.R. Spooner, A.J. Musoke, D.M. Mwangi, E.L. Taracha, I.W. Morrison, W.Weir, J.C. Silva, and R.P. Bishop. 2011. 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 6(4): e19015. PMID:21559495.

Silva, J.C., A. Egan, R. Friedman, J.B. Munro, J.M. Carlton, A.L. Hughes. 2011. Genome sequences reveal divergence times of malaria parasite lineages. Parasitology 138:1737-49. PMID: 21118608.

Guo X and JC Silva. 2008. Properties of non-coding DNA and identification of putativecis-regulatory regions in Theileria parva. BMC Genomics 9:582. PMID:19055776.

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.

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.

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 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.

Non-Apicomplexan Parasites and Other Organism

Silva MC, Chibucos M, Munro JB, Su Q, Daugherty S, MM Coelho, JC Silva. Characterization and adaptive evolution of olfactory receptor genes in Cory’s shearwater: evidence for a molecular basis of smell in procellariiform seabirds. Sci Rep 10, 543 (2020) doi:10.1038/s41598-019-56950-6.

Eyun S-i, HY Soh, M Posavi, JB Munro, DST Hughes, SC Murali, J Qu, S Dugan, SL Lee, H Chao, H Dinh, Y Han, HV Doddapaneli, KC Worley, DM Muzny, E-O Park, JC Silva, RA Gibbs, S Richards, CE Lee. Evolutionary History of Chemosensory-Related Gene Families Across the Arthropoda. Mol Biol Evol. 2017 Aug 1;34(8):1838-1862. doi: 10.1093/molbev/msx147. PMID: 28460028.

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. 9(6):e99979. PMID: 24936976.

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, 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. PMID:18404212.

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. Müller, 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. PMID:17218520.

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

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.

Genome Evolution, Genomics Methods

Robinson KM, AS Hawkins, I Santana-Cruz, RS Adkins, AC Shetty, S Nagaraj, L Sadzewicz, LJ Tallon, DA Rasko, CM Fraser, A Mahurkar, JC Silva, JC Dunning-Hotopp. Aligner Optimization Increases Accuracy and Decreases Compute Times in Multi-Species Sequence Data. Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep. PMID: 29114401

Egan A, A Mahurkar, J Crabtree, JH Badger, JM Carlton, JC Silva. 2008. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics 9:524. PMID: 19061522.

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. PMID:18284697.

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., 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.

Silva JC and AS Kondrashov. 2002.Patterns in spontaneous mutation revealed by human-baboon sequence comparison. Trends Genetics 18:544-547. 

Yang H.-P., A.Y. Tanikawa, W.A. Van Voorhies, J.C. Silva, A.S.Kondrashov. 2001. Whole-genome effects of ethyl methanesulfonate-induced mutation on nine quantitative traits in   outbred Drosophila melanogaster. Genetics 157:1257-65.

Transposable Elements

Lopes F.R., J.C. Silva, M. Benchimol, G.G.L. Costa, G.A.G. Pereira and C.M.A. Carareto. 2009. The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements. BMC Genomics 10:330. PMID: 19622157.

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. PMID:15371525.

Carvalho, M.O., J.C. Silva,and ELS Loreto. 2004. Analyses of P-like transposable element sequences from the genome of Anopheles gambiae. Insect Mol. Biol. 13:55-63. 

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. PMID:14632259.

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., 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.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: 3381. PMID:11773243.

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.

1992-1996       Doctoral Research Fellowship, Junta Nacional de Investigação Científica e Tecnológica (JNICT), Portugal

1997-1999       Doctoral Dissertation Improvement Award, National Science Foundation

1997-1998       NSF Research Training Group in the Analysis of Biological Diversification Research Fellowship, The University of Arizona

1998-1999       Robert S. Flinn Foundation Research Fellowship, The University of Arizona

2000-2002       Fogarty International Post-doctoral Fellowship, National Institutes of Health

2011-present    Affiliate Member, Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine

2013                2013 Maryland’s Top 100 Women Award, The Daily Record. Maryland’s Top 100 Women recognizes high-achieving Maryland women who are making an impact through their leadership, community service and mentoring.

2014-2018    Affiliate Faculty, School of Systems Biology, George Mason University

2016                Baltimore City Community College (BCCC), Partnership Award. This award is granted to BCCC community partners who contribute to the success of BCCC programs and the academic development of its students.

2016                Dr. Patricia Sokolove Outstanding Mentor Award. The award was established by the UMB Graduate Student Association (GSA) to honor those who put forth great effort in aiding and mentoring graduate students. 

Institute for Genome Sciences (IGS) - International Livestock Research Institute (ILRI) Partnership: IGS-ILRI Pathogen Genomics

Cryptosporidium hominis Gene Catalog