2018

Abbas AH, Silva Pereira S, D’Archivio S, Wickstead B, Morrison LJ, Hall N, Hertz-Fowler C, Darby AC, Jackson AP. 2018. The structure of a conserved telomeric region associated with variant antigen loci in the blood parasite Trypanosoma congolense. Genome Biology and Evolution, 10(9):2458-2473. doi: 10.1093/gbe/evy186.

Silva Pereira S, Casas-Sánchez A, Haines LR, Ogugo M, Absolomon K, Sanders M, Kemp S, Acosta-Serrano Á, Noyes H, Berriman M, Jackson AP. 2018. Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs. Genome Research 28(9):1383-1394. doi: 10.1101/gr.234146.118.

Silva Pereira S, Jackson AP. 2018. UDP-glycosyltransferase genes in trypanosomatid genomes have diversified independently to meet the distinct developmental needs of parasite adaptations. BMC Evolutionary Biology 18(1):31. doi: 10.1186/s12862-018-1149-6.

2016

Fougère A, Jackson AP, Paraskevi Bechtsi D, Braks JA, Annoura T, Fonager J, Spaccapelo R, Ramesar J, Chevalley-Maurel S, Klop O, van der Laan AM, Tanke HJ, Kocken CH, Pasini EM, Khan SM, Böhme U, van Ooij C, Otto TD, Janse CJ, Franke-Fayard B. 2016. Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole. PLoS Pathogens, 12(11):e1005917. doi: 10.1371/journal.ppat.1005917.

Jackson AP. 2016. Gene family phylogeny and the evolution of parasite cell surfaces. Molecular and Biochemical Parasitology, doi: 10.1016/j.molbiopara.2016.03.007.

Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F, Schlacht A, Hartley C, Sanders M, Wastling JM, Dacks JB, Acosta-Serrano A, Field MC, Ginger ML, Berriman M. 2016. Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Current Biology, 26: 1-12.

2015

Jackson AP, Goyard S, Xia D, Bernardo FJ, Sanders M, Wastling JM, Minoprio P, Berriman M. 2015. Global gene expression profiling through the complete life cycle of Trypanosoma vivax. PLoS Neglected Tropical Diseases, 9(8):e0003975.

Jackson AP. 2015. Genome evolution in trypanosomatid parasites. Parasitology, 142: S40-56.

2014

Carnes J, Anupama A, Balmer O, Jackson AP,  Lewis M, Brown R, Cestari I, Desquesnes M, Gendrin C, Hertz-Fowler C, Imamura H, Ivens A, Kořený L, Lai DH, MacLeod A, McDermott SM, Merritt C, Monnerat S, Moon W, Myler P, Phan I, Ramasamy G, Sivam D, Lun ZR, Lukeš J, Stuart K, Schnaufer A. 2015. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty. PLoS Neglected Tropical Diseases 9(1):e3404.

Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D, Echaide IE, Farber M, Gahlot S, Gamble J, Gupta D, Gupta Y, Jackson L, Malandrin L, Malas TB, Moussa E, Nair M, Reid AJ, Sanders M, Sharma J, Tracey A, Quail MA, Weir W, Wastling JM, Hall N, Willadsen P, Lingelbach K , Shiels B, Tait A, Berriman M, Allred DR, Pain A. 2014. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of host-parasite interaction. Nucleic Acids Research, 42(11):7113-31.

OttoTD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, Religa AA, RobertsonL, Sanders M, Ogun SA, Cunningham D, Erhart A, Billker O, Khan SM, Stunnenberg HG, Langhorne J, Holder AA, Waters AP, Newbold CI, Pain A, Berriman M, Janse CJ. 2014. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biology, 12(1):86.

2013

Jackson AP, Allison HC, Barry JD, Field MC, Hertz-Fowler C, Berriman M. 2013. A cell-surface phylome for African trypanosomes. PLoS Neglected Tropical Diseases, 7(3): e2121.

2012

Lawton J, Brugat T, Yan YX, Reid AJ, Böhme U, Otto TD, Pain A, Jackson AP, Berriman M, Cunningham D, Preiser P, Langhorne J. 2012. Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics, 13:125.

Jackson  AP, Berry A , Aslett M , Allison HC , Burton P , Vavrova-Anderson J , Brown R, Browne H , Corton N , Hauser H , Gamble J , Gilderthorp R , Marcello L, McQuillan J, Otto TD , Quail MA , Sanders MJ , van Tonder A , Ginger ML , Field MC , Barry JD , Hertz-Fowler C and Berriman M. 2012. Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proceedings of the National Academy of Sciences of the USA, 109 (9): 3416-3421.

2010

Depledge DP, MacLean LM, Hodgkinson MR, Smith BA, Jackson AP, Ma S, Uliana SR and Smith DF. 2010. Leishmania-specific surface antigens show sub-genus sequence variation and immune recognition. PLoS Neglected Tropical Diseases, 4 (9): e829.

Jackson AP. 2010. Evolution of the amastin surface glycoprotein family in trypanosomatid parasites. Molecular Biology and Evolution, 27: 33-45.

2009

Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA, Quail MA, Chukualim B, Capewell P, MacLeod A, Melville SE, Gibson W, Barry JD, Berriman M, Hertz-Fowler C. 2010. The genome sequence of Trypanosoma brucei gambiense: the causative agent of chronic sleeping sickness. PLoS Neglected Tropical Diseases, 4. e658.

Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D, Harris D, Aslett M, Barrell JF, Butler G, Citiulo F, Coleman DC, de Groot PWJ, Goodwin TJ, Quail MA, McQuillan J, Munro CA, Pain A, Poulter RT, Rajandream MA, Renauld H, Spiering MJ, Tivey A, Gow NAR, Barrell B, Sullivan DJ and Berriman M. 2009. Comparative genomics of the fungal pathogens Candida dubliniensis and C. albicans. Genome Research 19 (12): 2231-2244.

Jackson AP, Thomas GH, Parkhill J, Thomson NR. 2009. Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics. 10:584.

2008

Hertz-Fowler C,  Figueiredo LM,  Quail MA,  Becker M,  Jackson AP,  Bason N,  Brooks K,  Churcher C,  Fahkro S,  Goodhead I,  Heath P,  Kartvelishvili M,  Mungall K,  Harris D,  Hauser H,  Sanders M,  Saunders D,  Seeger K,  Sharp S,  Taylor JE,  Walker D,  White B,  Young R,  Cross GA,  Rudenko G,  Barry JD,  Louis EJ, and Berriman M. 2008. Telomeric expression sites are highly conserved in Trypanosoma brucei.  PLoS One, 3. e3527.

Jackson AP, Quail MA and Berriman M. 2008. Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans. BMC Genomics, 9: 594.

Pain A,  Bohme U,  Berry AE,  Mungall K,  Finn RD, Jackson AP,  Mourier T,  Mistry J,  Pasini EM,  Aslett MA,  Balasubrammaniam S,  Borgwardt K,  Brooks K,  Carret C,  Carver TJ,  Cherevach I,  Chillingworth T, Clark TG,  Galinski MR,  Hall N,  Harris D,  Hauser H,  Ivens A,  Janssen CS,  Keane T,  Larke N,  Lapp S,  Marti M,  Moule S,  Meyer IM,  Ormond D,  Peters N,  Sanders M,  Sanders S,  Sargeant TJ,  Simmonds M,  Smith F,  Squares R,  Thurston S,  Tivey AR,  Walker D,  White B,  Zuiderwijk E,  Churcher C,  Quail MA,  Cowman AF,  Turner CM,  Rajandream MA,  Kocken CH,  Thomas AW,  Newbold CI,  Barrell BG and Berriman M. 2008. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature, 455. pp. 799-803.

2007

Jackson AP. 2007. Origins of amino acid transporter loci in trypanosomatid parasites. BMC Evolutionary Biology, 7: 26.

Jackson AP. 2007. Evolutionary consequences of a large duplication event in Trypanosoma brucei: Chromosomes 4 and 8 are partial duplicons. BMC Genomics, 8: 432.

Jackson AP. 2007. Tandem gene arrays of Trypanosoma brucei: Comparative phylogenomic analysis of duplicate sequence variation. BMC Evolutionary Biology, 7: 54.

2006

Jackson AP, Vaughan S and Gull, K. 2006. Comparative genomics and concerted evolution of beta-tubulin paralogs in Leishmania spp. BMC genomics, 7: 137.

Jackson AP, Vaughan S and Gull, K. 2006. Evolution of tubulin gene arrays in Trypanosomatid parasites: genomic restructuring in Leishmania. BMC genomics, 7: 261.

2005

Jackson AP. 2005. The Effect of Paralogous Lineages on the Application of Reconciliation Analysis by Cophylogeny Mapping. Systematic Biology, 4 (1): 127-145.

2004

Jackson AP. 2004. A reconciliation analysis of host switching in plant-fungal symbioses. Evolution, 58: 1909-1923.

Jackson AP. 2004. Cophylogeny of the Ficus microcosm. Biological reviews of the Cambridge Philosophical Society, 79 (4): 751-68.

2003

Jackson AP, Charleston MA. 2004. A cophylogenetic perspective of RNA-virus evolution. Molecular Biology and Evolution, 21 (1): 45-57.