Education Profile

  • ​​​​Post-doctoral fellow, Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, UK, 2001
  • Ph.D., University of Cambridge, UK, 1996

Research Interests

The primary focus of the Pathogen Genomics Laboratory is to use high-throughput sequencing and other functional genomic technologies to understand the biology and genomic diversity of a few parasitic protists and bacteria with significant impact on human and animal health. Genome and transcriptome sequencing of these organisms is a critical first step towards our understanding of how these organisms grow and thrive in a susceptible host and in other environment. A better understanding of their biology could eventually lead to the development of new intervention strategies.

Within this program, a combination of high-throughput DNA and RNA sequencing-based methods, coupled with functional genomics and bioinformatics tools are being used in the following areas of research:
  1. Genomics of Apicomplexan parasites and Chromerids and host-parasite interactions. 
  2. Molecular and genomic characterization of enteric pathogens particularly during mass gatherings 
  3. Genome variation in Mycobacteria 
  4. Development of bioinformatic tools for genome-scale data visualization and mining

Selected Publications

  • Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant JM, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas T, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream M A, Shirley MW, Wan KL, Berriman M, Tomley FM & Pain, A. (2014). "Genomic analysis of the causative agents of coccidiosis in domestic chickens." Genome Res doi:10.1101/gr.168955.113
  • Guttery, DS, Poulin, B, Ramaprasad, A, Wall, RJ, Ferguson, DJ, Brady, D, Patzewitz, EM, Whipple, S, Straschil, U, Wright, MH, Mohamed, AM, Radhakrishnan, A, Arold, ST, Tate, EW, Holder, AA, Wickstead, B, Pain, A & Tewari, R. "Genome-wide Functional Analysis of Plasmodium Protein Phosphatases Reveals Key Regulators of Parasite Development and Differentiation." Cell Host Microbe 16, 128-140, doi:10.1016/j.chom.2014.05.020 (2014).
  • 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 genomic innovation underlying host-parasite interaction." Nucleic Acids Res 42, 7113-7131, doi:10.1093/nar/gku322
  • Abd El Ghany, M, Chander, J, Mutreja, A, Rashid, M, Hill-Cawthorne, GA, Ali, S, Naeem, R, Thomson, NR, Dougan, G & Pain, A. "The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India." PLoS Negl Trop Dis 8, e2981, doi:10.1371/journal.pntd.0002981 (2014).
  • Naeem, R, Hidayah, L, Preston, MD, Clark, TG & Pain, A. "SVAMP: sequence variation analysis, maps and phylogeny." Bioinformatics 30, 2227-2229, doi:10.1093/bioinformatics/btu176 (2014).
  • Woods, KL, Theiler, R, Muhlemann, M, Segiser, A, Huber, S, Ansari, HR, Pain, A & Dobbelaere, DA. "Recruitment of EB1, a master regulator of microtubule dynamics, to the surface of the Theileria annulata schizont." PLoS Pathog 9, e1003346, doi:10.1371/journal.ppat.1003346 (2013).
  • Reid, AJ, Vermont, SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Konen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees, AJ, Berriman M, Pain A* & Wastling JM*. (2012). "Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy." PLoS Pathog 8, e1002567, doi:10.1371/journal.ppat.1002567
  • Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A. "Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum." Genome Res (2008), doi: 10.1101/gr.6836108
  • Pain A, Böhme 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, Harper D, 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, Berriman M. (2008). "The genome sequence of simian and human malaria parasite Plasmodium knowlesi." Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306
  • Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R, Bouchier C, Cochet M, Coulson RM, Cronin A, de Villiers EP, Fraser A, Fosker N, Gardner M, Goble A, Griffiths-Jones S, Harris DE, Katzer F, Larke N, Lord A, Maser P, McKellar S, Mooney P, Morton F, Nene V, O'Neil S, Price C, Quail MA, Rabbinowitsch E, Rawlings ND, Rutter S, Saunders D, Seeger K, Shah T, Squares R, Squares S, Tivey A, Walker AR, Woodward J, Dobbelaere DA, Langsley G, Rajandream MA, McKeever D, Shiels B, Tait A, Barrell B, Hall N. (2005). "Genome of the host-cell transforming parasite Theileria annulata compared with T. parva". Science, 309(5731), 131-133.