Publications

Cryptosporidium  publications co-authored by the Silva Group

Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates
Ifeonu OO, Simon R, Tennant SM, Sheoran AS, Daly MC, Felix V, Kissinger JC, Widmer G, Levine MM, Tzipori S, Silva JC.
Database. 2016 Sep; 2016:1-13. doi: 10.1093/database/baw137. PMCID: PMC5070614

Annotated draft genome sequences of three species of Cryptosporidium: C. meleagridis isolate UKMEL1 , C. baileyi isolate TAMU-09Q1, and C. hominis isolates TU502_2012 and UKH1
Ifeonu OO, Chibucos MC, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers RM, Fraser CM, Zhu G, Kissinger JC, Widmer G, Silva JC.
Pathog Dis. 2016 Oct;74(7). pii: ftw080. Epub 2016 Aug 12. PMID: 27519257

"Genomics"
Harb OS, Boehme U, Crouch K, Ifeonu OO, Roos DS, Silva JC, Silva-Franco F, Svärd S, Tretina K, Weedal G.
In: Molecular Parasitology: Protozoan Parasites and their Molecules
J. Walochnik and M. Duchêne, Editors. 2016, Springer-Verlag: Vienna. p. 3-49

Other publications on Apicomplexa organisms, co-authored by the Silva Group

New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.
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.
Genome Med. 2017 Mar 28;9(1):30. doi: 10.1186/s13073-017-0422-4. PubMed PMID: 28351419.

A novel mutation in the Plasmodium falciparum chloroquine resistance transporter is associated with piperaquine resistance.
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.
J Infect Dis. 2017 Aug 15; 216(4):468-476

A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples.
Dara A, MA Travassos, M Adams, S Schaffer DeRoo, EF Drábek, S Agrawal, MK Laufer, CV Plowe, JC Silva.
Malar J. 2017 Aug 17;16(1):343. doi: 10.1186/s12936-017-1976-8. PubMed PMID: 28818101; PubMed Central PMCID: PMC5561619.

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions
Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C.
Sci Rep. 2016 Oct 18;6:35284. doi: 10.1038/srep35284. PMID: 27752055

Quantification of the ratio of host-to-parasite DNA in samples from Theileria parva-infected host lymphocyte cell lines.
Gotia HT, JB Munro, DP Knowles, CA Daubenberger, RP Bishop, JC Silva.
PLoS One. 2016 Mar 1;11(3):e0150401. doi: 10.1371/journal.pone.0150401. eCollection 2016. PMID: 26930209.

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva.
Tretina K, R Pelle and JC Silva.
BMC Genomics. 2016 Feb 20;17:128. doi: 10.1186/s12864-016-2444-5. PMID: 26896950.

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.
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.
BMC Genomics. 2015 Sep 24;16(1):729. doi: 10.1186/s12864-015-1910-9. PMID: 26403690.

Theileria-transformed bovine leukocytes have cancer hallmarks.
Tretina, K., Gotia HT, Mann D, Silva JC.
Trends Parasitol. 2015 Jul;31(7):306-14. doi: 10.1016/j.pt.2015.04.001. Epub 2015 May 4. Review. PMID: 25951781.

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.
Obara I, Ulrike S, Musoke T, Spooner PR, Jabbar A, Odongo D, Kemp S, Silva JC, Bishop RP.
Parasitol Res. 2015 May;114(5):1729-37. doi: 10.1007/s00436-015-4358-6. Epub 2015 Feb 13. PMID: 25673078.

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

Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.
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.
Infect Genet Evol. 2015 Mar;30:318-22. doi: 10.1016/j.meegid.2014.12.010. Epub 2014 Dec 13. PMID: 25514047.

Independent emergence of Plasmodium falciparum artemisinin resistance mutations in Southeast Asia.
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 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.
J Infect Dis. 2015 Mar 1;211(5):670-9. doi: 10.1093/infdis/jiu491. Epub 2014 Sep 1. PMID: 25180241.

A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites.
Munro JB, Jacob C, Silva JC.
J Mol Evol. 2013. 77(3):92-106. PMID: 24046025.

Whole genome mapping and re-organization of the nuclear and mitochondrial genomes of Babesia microti isolates.
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.
PLoS One. 2013 Sep 4;8(9):e72657. PMID: 24023759.

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia.
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.
PNAS 2013. 110: 240-5. PMID: 23248304.

Comparative genomic analysis and phylogenetic position of Theileria equi.
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.
BMC Genomics. 2012 13(1):603. PMID: 23137308.

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

Two Theileria parva CD8 T cell antigen genes are more variable in buffalo than cattle parasites, but differ in pattern of sequence diversity.
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.
PLoS ONE. 2011 6(4): e19015. PMID: 21559495.

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

Properties of non-coding DNA and identification of putative cis-regulatory regions in Theileria parva.
Guo, X. and J.C. Silva.
BMC Genomics. 2008. 9:582. PMID: 19055776.

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.
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.
Nature. 2008 Oct 9;455(7214):757-63. doi: 10.1038/nature07327. PMID: 18843361.

The genome of model malaria parasites, and comparative genomics.
Carlton, J.M., J.C. Silva, and N. Hall.
Curr. Issues Mol. Biol. 2005. 7: 23-37.

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.
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.
Science. 2005 Jul 1;309(5731):134-7. PMID: 15994558.

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.
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.
Nature. 2002 Oct 3;419(6906):512-9. PMID: 12368865.