1. Abd El Ghany, M.*, Alsomali, M., El Masry, M., Padron Regalado, E., Naeem, R., Tukestani, A.H., Asiri, A., Hill-Cawthorne, G.A., Pain, A.*, Memish, Z.A.* Characterization of enteric infections circulating during Hajj seasons 2011–2013. Emerging Infectious Diseases (2017, in press).
  2. Abkallo, H. M., Martinelli, A., Inoue, M., Ramaprasad, A., Xangsayarath, P., Gitaka, J., Tang, J., Yahata, K., Zoungrana, A., Mitaka, H., Acharjee, A., Datta, P. P., Hunt, P., Carter, R., Kaneko, O., Mustonen, V., Illingworth, C. J. R., Pain, A. & Culleton, R. Rapid identification of genes controlling virulence and immunity in malaria parasites PLoS Pathog 13, e1006447 doi:10.1371/journal.ppat.1006447(2017).
  3. Dippenaar, A., Parsons, S. D. C., Miller, M. A., Hlokwe, T., van Pittius, N. C. G., Adroub, S. A., Abdallah, A. M., Pain, A., Warren, R. M., Michel, A. L. & van Helden, P. D. Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem Infect Genet Evol 51, 235-238 doi:10.1016/j.meegid.2017.04.012(2017).
  4. Moussa, E., Huang, H., Ahras, M., Lall, A., Thezenas, M. L., Fischer, R., Kessler, B. M., Pain, A., Billker, O. & Casals-Pascual, C. Proteomic profiling of the brain of mice with experimental cerebral malaria J Proteomics doi:10.1016/j.jprot.2017.06.002(2017).
  5. Crawford, J. E., Alves, J. M., Palmer, W. J., Day, J. P., Sylla, M., Ramasamy, R., Surendran, S. N., Black, W. C. t., Pain, A. & Jiggins, F. M. Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector BMC Biol 15, 16 doi:10.1186/s12915-017-0351-0(2017).
  6. Lu, F., Culleton, R., Zhang, M., Ramaprasad, A., von Seidlein, L., Zhou, H., Zhu, G., Tang, J., Liu, Y., Wang, W., Cao, Y., Xu, S., Gu, Y., Li, J., Zhang, C., Gao, Q., Menard, D., Pain, A., Yang, H., Zhang, Q. & Cao, J. Emergence of Indigenous Artemisinin-Resistant Plasmodium falciparum in Africa N Engl J Med doi:10.1056/NEJMc1612765(2017).
  7. Dheda, K., Limberis, J. D., Pietersen, E., Phelan, J., Esmail, A., Lesosky, M., Fennelly, K. P., Te Riele, J., Mastrapa, B., Streicher, E. M., Dolby, T., Abdallah, A. M., Ben-Rached, F., Simpson, J., Smith, L., Gumbo, T., van Helden, P., Sirgel, F. A., McNerney, R., Theron, G., Pain, A., Clark, T. G. & Warren, R. M. Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study Lancet Respir Med doi:10.1016/S2213-2600(16)30433-7(2017).

  8. 2016

  9. Mourier, T. Transposable elements and circular DNAs Mob Genet Elements 6, e1240748 doi:10.1080/2159256X.2016.1240748(2016).
  10. Refregier, G., Abadia, E., Matsumoto, T., Ano, H., Takashima, T., Tsuyuguchi, I., Aktas, E., Comert, F., Gomgnimbou, M. K., Panaiotov, S., Phelan, J., Coll, F., McNerney, R., Pain, A., Clark, T. G. & Sola, C. Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor Infect Genet Evol 45, 461-473 doi:10.1016/j.meegid.2016.10.009(2016).
  11. Wong, Y. C., Abd El Ghany, M., Naeem, R., Lee, K. W., Tan, Y. C., Pain, A. & Nathan, S. Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS Front Microbiol 7, 1288 doi:10.3389/fmicb.2016.01288(2016).
  12. Abd El Ghany, M., Shi, X., Li, Y., Ansari, H. R., Hill-Cawthorne, G. A., Ho, Y. S., Naeem, R., Pickard, D., Klena, J. D., Xu, X., Pain, A. & Hu, Q. Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China J Clin Microbiol 54, 2014-2022 doi:10.1128/JCM.00052-16(2016).
  13. Ansari, H. R., Templeton, T. J., Subudhi, A. K., Ramaprasad, A., Tang, J., Lu, F., Naeem, R., Hashish, Y., Oguike, M. C., Benavente, E. D., Clark, T. G., Sutherland, C. J., Barnwell, J. W., Culleton, R., Cao, J. & Pain, A. Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species Int J Parasitol doi:10.1016/j.ijpara.2016.05.009(2016).
  14. Antony, B., Soffan, A., Jakse, J., Abdelazim, M. M., Aldosari, S. A., Aldawood, A. S. & Pain, A. Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by anti:ARTN 69iptome analysis Bmc Genomics 17
  15. Lakshman, D. K., Roberts, D. P., Garrett, W. M., Natarajan, S. S., Darwish, O., Alkharouf, N., Pain, A., Khan, F., Jambhulkar, P. P. & Mitra, A. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence J Agric Food Chem 64, 3101-3110 doi:10.1021/acs.jafc.5b05735(2016).
  16. Moon, R. W., Sharaf, H., Hastings, C. H., Ho, Y. S., Nair, M. B., Rchiad, Z., Knuepfer, E., Ramaprasad, A., Mohring, F., Amir, A., Yusuf, N. A., Hall, J., Almond, N., Lau, Y. L., Pain, A., Blackman, M. J. & Holder, A. A. Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi Proc Natl Acad Sci U S A 113, 7231-7236 doi:10.1073/pnas.1522469113(2016).
  17. Phelan, J., Coll, F., McNerney, R., Ascher, D. B., Pires, D. E., Furnham, N., Coeck, N., Hill-Cawthorne, G. A., Nair, M. B., Mallard, K., Ramsay, A., Campino, S., Hibberd, M. L., Pain, A., Rigouts, L. & Clark, T. G. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance BMC Med 14, 31 doi:10.1186/s12916-016-0575-9(2016).
  18. Phelan, J. E., Coll, F., Bergval, I., Anthony, R. M., Warren, R., Sampson, S. L., Gey van Pittius, N. C., Glynn, J. R., Crampin, A. C., Alves, A., Bessa, T. B., Campino, S., Dheda, K., Grandjean, L., Hasan, R., Hasan, Z., Miranda, A., Moore, D., Panaiotov, S., Perdigao, J., Portugal, I., Sheen, P., de Oliveira Sousa, E., Streicher, E. M., van Helden, P. D., Viveiros, M., Hibberd, M. L., Pain, A., McNerney, R. & Clark, T. G. Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages BMC Genomics 17, 151 doi:10.1186/s12864-016-2467-y(2016).
  19. Rao, P. N., Santos, J. M., Pain, A., Templeton, T. J. & Mair, G. R. Translational repression of the cpw-wpc gene family in the malaria parasite Plasmodium Parasitol Int 65, 463-471 doi:10.1016/j.parint.2016.06.007(2016).
  20. Templeton, T. J. & Pain, A. Diversity of extracellular proteins during the transition from the 'proto-apicomplexan' alveolates to the apicomplexan obligate parasites Parasitology 143, 1-17 doi:10.1017/S0031182015001213(2016).
  21. Waller, R. F., Gornik, S. G., Koreny, L. & Pain, A. Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid Commun Integr Biol 9, e1116653 doi:10.1080/19420889.2015.1116653(2016).

  22. 2015

  23. Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A. R., Carninci, P., Hayashizaki, Y., Daub, C. O., consortium, F., Okada-Hatakeyama, M. & Mar, J. C. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage PLoS One 10, e0144176 doi:10.1371/journal.pone.0144176(2015).
  24. Hurst, L. D., Ghanbarian, A. T., Forrest, A. R., consortium, F. & Huminiecki, L. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome PLoS Biol 13, e1002315 doi:10.1371/journal.pbio.1002315(2015).
  25. Roques, M., Wall, R.J., Douglass, A.P., Ramaprasad, A., Ferguson, D.J.P., Kaindama, M.L., Brusini, L., Joshi, N., Rchiad, Z., Brady, D., Guttery, D.S., Wheatley, S.P., Yamano, H., Holder, A.A., Pain, A., Wickstead, B., Tewari, R. Plasmodium P-type cyclin CYC3 modulates endomitotic growth during oocyst development in mosquitoes. PLoS Pathogens 11(11):e1005273. doi:10.1371/journal.ppat.1005273 (2015).
  26. Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. Black, P.A., de Vos, M., Louw, G.E., van der Merwe, R.G., Dippenaar, A., Streicher, E.M., Abdallah, A.M.A, Sampson, S.L., Victor, T.C., Dolby, T., Simpson, J.A., van Helden, P.D., Warren, R.M.*, Pain, A.* BMC Genomics 16:857. doi:10.1186/s12864-015-2067-2 (2015).
  27. Phelan, J., Maitra, A., McNerney, R., Nair, M., Gupta, A., Coll, F., Pain, A., Bhakta, S., Clark, T.G. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. International Journal of Mycobacteriology. doi:10.1016/j.ijmyco.2015.05.001 (2015).
  28. Dippenaar, A., Parsons, S.D.C., Sampson, S.L., van der Merwe, R.G., Drew, J.A., Abdallah, A.M.A., Siame, K.K., Gey van Pittius, N.C., van Helden, P.D., Pain, A.*, Warren, R.M*. Whole genome sequence analysis of Mycobacterium suricattae. Tuberculosis doi:10.1016/ (2015).
  29. Benavente, E.D., Coll, F., Furnham, N., McNerney, R., Glynn, J.R., Campino, S., Pain, A., Mohareb, F.R., Clark, T.G. PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics 16:155. doi: 10.1186/s12859-015-0603-3 (2015).
  30. Dalla Costa, E.R., Vasconcelos, S.E., Esteves, L.S., Gomes, H.M., Gomes, L.L., Almeida da Silva, P., Perdigão, J., Portugal, I., Viveiros, M., McNerney, R., Pain, A., Clark, T.G., Rastogi, N., Unis, G., Rossetti, M.L., Suffys, P.N. Multidrug resistant Mycobacterium tuberculosis of the Latin American Mediteranean lineage wrongly identified as Mycobacterium pinnipedii (ST863) causing active tuberculosis in south Brazil. J Clin Microbiol. doi: 10.1128/JCM.02012-15 (2015).
  31. Abdallah, M.A., Hill-Cawthorne, G., Otto, T. , Coll, F., Guerra-Assunção, J.A., Gao, G., Naeem, R., Ansari, H.R. , Malas, T. , Adroub, S., Verboom, T., Ummels, R., Zhang, H., Panigrahi, A., Mcnerney, R., Brosch, R., Clark, T., Behr, M., Bitter, W., Pain, A. Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports 5:15443. doi: 10.1038/srep15443 (2015).
  32. Assefa, SA., Lim, C., Preston, M.D., Duffy, C.W., Nair, M.B., Adroub, S.A., Kadir, K.A., Goldberg, J.M., Neafsey, D.E., Divis, PCS, Clark, T.G., Duraisingh, M.T., Conway, D.J.*, Pain, A.*, Singh, B.* Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. PNAS 112(42):13027-32. doi: 10.1073/pnas.1509534112 (2015).
  33. Abdel-Haleem, A.M., Rchiad, Z., Khan, B.K., Abdallah, A.M., Naeem, R., Sheerin, S.N., Solovyev, V., Ahmed, A., Pain, A. Genome Sequence of a MDR Strain of Stenotrophomonas maltophilia with Carbapenem Resistance Isolated from King Abdullah Medical City, Makkah, Saudi Arabia. Genome Announcement 3(5). pii: e01166-15. doi: 10.1128/genomeA.01166-15 (2015).
  34. Antony, B., Soffan, A., Jakse, J., Alfaifi, S., Sutanto, K. D., Aldosari, S. A., Aldawood, A. S. & Pain, A. Genes involved in sex pheromone biosynthesis of Ephestia cautella, an important food storage pest, are determined by transcriptome sequencing. BMC Genomics 16, doi:10.1186/S12864-015-1710-2 (2015).
  35. Vega, F. E., Brown, S. M., Chen, H., Shen, E., Nair, M. B., Ceja-Navarro, J. A., Brodie, E. L., Infante, F., Dowd, P. F. & Pain, A. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. Scientific Reports 5, doi:10.1038/Srep12525 (2015).
  36. Woo, Y. H., Ansari, H., Otto, T. D., Klinger, C. M., Kolisko, M., Michalek, J., Saxena, A., Shanmugam, D., Tayyrov, A., Veluchamy, A., Ali, S., Bernal, A., del Campo, J., Cihlar, J., Flegontov, P., Gornik, S. G., Hajduskova, E., Horak, A., Janouskovec, J., Katris, N. J., Mast, F. D., Miranda-Saavedra, D., Mourier, T., Naeem, R., Nair, M., Panigrahi, A. K., Rawlings, N. D., Padron-Regalado, E., Ramaprasad, A., Samad, N., Tomcala, A., Wilkes, J., Neafsey, D. E., Doerig, C., Bowler, C., Keeling, P. J., Roos, D. S., Dacks, J. B., Templeton, T. J., Waller, R. F., Lukes, J., Obornik, M. & Pain, A. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife 4, doi:10.7554/eLife.06974 (2015).
  37. Coll, F., McNerney, R., Preston, M. D., Guerra-Assuncao, J. A., Warry, A., Hill-Cawthorne, G., Mallard, K., Nair, M., Miranda, A., Alves, A., Perdigao, J., Viveiros, M., Portugal, I., Hasan, Z., Hasan, R., Glynn, J. R., Martin, N., Pain, A.* & Clark, T. G.* Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 7, 51, doi:10.1186/s13073-015-0164-0 (2015).
  38. Benavente, E. D., Coll, F., Furnham, N., McNerney, R., Glynn, J. R., Campino, S., Pain, A., Mohareb, F. R. & Clark, T. G. PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics 16, 155, doi:10.1186/s12859-015-0603-3 (2015).
  39. Ates, L. S., Ummels, R., Commandeur, S., van der Weerd, R., Sparrius, M., Weerdenburg, E., Alber, M., Kalscheuer, R., Piersma, S. R., Abdallah, A. M., Abd El Ghany, M., Abdel-Haleem, A. M., Pain, A., Jimenez, C. R., Bitter, W. & Houben, E. N. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLoS Genet 11, e1005190, doi:10.1371/journal.pgen.1005190 (2015).
  40. Gornik, S. G., Febrimarsa, Cassin, A. M., MacRae, J. I., Ramaprasad, A., Rchiad, Z., McConville, M. J., Bacic, A., McFadden, G. I., Pain, A. & Waller, R. F. Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate. Proc Natl Acad Sci U S A 112, 5767-5772, doi:10.1073/pnas.1423400112 (2015).
  41. Kanji, A., Hasan, Z., Ali, A., McNerney, R., Mallard, K., Coll, F., Hill-Cawthorne, G., Pain, A., Nair, M., Clark, T. G., Zaver, A., Jafri, S. & Hasan, R. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. International Journal of Mycobacteriology , doi:10.1016/j.ijmyco.2014.10.051 (2015).
  42. Perdigão, J., Silva, H., Machado, D., Macedo, R., Maltez, F., Silva, C., Jordao, L., Couto, I., Mallard, K., Coll, F., Hill-Cawthorne, G. A., McNerney, R., Pain, A., Clark, T. G., Viveiros, M. & Portugal, I. Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology. International Journal of Mycobacteriology , doi:10.1016/j.ijmyco.2015.01.001 (2015).
  43. Hasan, Z., Ali, A., McNerney, R., Mallard, K., Hill-Cawthorne, G., Coll, F., Nair, M., Pain, A., Clark, T. G. & Hasan, R. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan. International Journal of Mycobacteriology , doi:10.1016/j.ijmyco.2014.10.050 (2015).
  44. Ramaprasad, A., Mourier, T., Naeem, R., Malas, T. B., Moussa, E., Panigrahi, A., Vermont, S. J., Otto, T. D., Wastling, J. & Pain, A. Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features. PLoS One 10, e0124473, doi:10.1371/journal.pone.0124473 (2015).
  45. Juneja, P., Ariani, C. V., Ho, Y. S., Akorli, J., Palmer, W. J., Pain, A. & Jiggins, F. M. Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response. PLoS Pathog 11, e1004765, doi:10.1371/journal.ppat.1004765 (2015).
  46. Ali, A., Hasan, Z., McNerney, R., Mallard, K., Hill-Cawthorne, G., Coll, F., Nair, M., Pain, A., Clark, T. G. & Hasan, R. Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan. PLoS One 10, e0117771, doi:10.1371/journal.pone.0117771 (2015).
  47. Weerdenburg, E. M., Abdallah, A. M., Rangkuti, F., Abd El Ghany, M., Otto, T. D., Adroub, S. A., Molenaar, D., Ummels, R., Ter Veen, K., van Stempvoort, G., van der Sar, A. M., Ali, S., Langridge, G. C., Thomson, N. R., Pain, A.* & Bitter, W.* Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infect Immun , doi:10.1128/IAI.03050-14 (2015).
  48. Bergval, I., Coll, F., Schuitema, A., de Ronde, H., Mallard, K., Pain, A., McNerney, R., Clark, T. G. & Anthony, R. M. A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture. FEMS Microbiol Lett 362, 1-7, doi:10.1093/femsle/fnu037 (2015).
  49. Flegontov, P., Michalek, J., Janouskovec, J., Lai, H., Jirku, M., Hajduskova, E., Tomcala, A., Otto, T. D., Keeling, P. J., Pain, A., Obornik, M. & Lukes, J. Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol Biol Evol , doi:10.1093/molbev/msv021 (2015).

  50. 2014

  51. Perdigao, J., Silva, H., Machado, D., Macedo, R., Maltez, F., Silva, C., Jordao, L., Couto, I., Mallard, K., Coll, F., Hill-Cawthorne, G. A., McNerney, R., Pain, A., Clark, T. G., Viveiros, M. & Portugal, I. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics 15, 991, doi:10.1186/1471-2164-15-991 (2014).
  52. Guerreiro, A., Deligianni, E., Santos, J. M., Silva, P. A., Louis, C., Pain, A., Janse, C. J., Franke-Fayard, B., Carret, C. K., Siden-Kiamos, I. & Mair, G. R. Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte. Genome Biol 15, 493, doi:10.1186/s13059-014-0493-0 (2014).
  53. Otto, T. D., Bohme, U., Jackson, A. P., Hunt, M., Franke-Fayard, B., Hoeijmakers, W. A., Religa, A. A., Robertson, L., Sanders, M., Ogun, S. A., Cunningham, D., Erhart, A., Billker, O., Khan, S. M., Stunnenberg, H. G., Langhorne, J., Holder, A. A., Waters, A. P., Newbold, C. I., Pain, A., Berriman, M. & Janse, C. J. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol 12, 86, doi:10.1186/PREACCEPT-1233682211145405 (2014).
  54. Ummels, R., Abdallah, A. M., Kuiper, V., Aajoud, A., Sparrius, M., Naeem, R., Spaink, H. P., van Soolingen, D., Pain, A. & Bitter, W. Identification of a novel conjugative plasmid in mycobacteria that requires both type IV and type VII secretion. MBio 5, e01744-01714, doi:10.1128/mBio.01744-14 (2014).
  55. Coll, F., McNerney, R., Guerra-Assuncao, J. A., Glynn, J. R., Perdigao, J., Viveiros, M., Portugal, I., Pain, A., Martin, N. & Clark, T. G. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun 5, 4812, doi:10.1038/ncomms5812 (2014).
  56. Otto, T. D., Rayner, J. C., Bohme, U., Pain, A., Spottiswoode, N., Sanders, M., Quail, M., Ollomo, B., Renaud, F., Thomas, A. W., Prugnolle, F., Conway, D. J., Newbold, C. & Berriman, M. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun 5, 4754, doi:10.1038/ncomms5754 (2014).
  57. Abd El Ghany, M., Chander, J., Mutreja, A., Rashid, M., Hill-Cawthorne, G. A., Ali, S., Naeem, R., Thomson, N. R., 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).
  58. Baranasic, D., Zucko, J., Nair, M., Pain, A., Long, P. F., Hranueli, D., Cullum, J. & Starcevic, A. Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements. Genome Announc 2, doi:10.1128/genomeA.00517-14 (2014).
  59. Reid, A. J., Blake, D. P., Ansari, H. R., Billington, K., Browne, H. P., Bryant, J. M., Dunn, M., Hung, S. S., Kawahara, F., Miranda-Saavedra, D., Malas, T., Mourier, T., Naghra, H., Nair, M., Otto, T. D., Rawlings, N. D., Rivailler, P., Sanchez-Flores, A., Sanders, M., Subramaniam, C., Tay, Y. L., Woo, Y., Wu, X., Barrell, B., Dear, P. H., Doerig, C., Gruber, A., Ivens, A. C., Parkinson, J., Rajandream, M. A., Shirley, M. W., Wan, K. L., Berriman, M., Tomley, F. M. & Pain, A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res , doi:10.1101/gr.168955.113 (2014).
  60. Guttery, D. S., Poulin, B., Ramaprasad, A., Wall, R. J., Ferguson, D. J., Brady, D., Patzewitz, E. M., Whipple, S., Straschil, U., Wright, M. H., Mohamed, A. M., Radhakrishnan, A., Arold, S. T., Tate, E. W., Holder, A. A., 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).
  61. Hill-Cawthorne, G. A., Hudson, L. O., El Ghany, M. F., Piepenburg, O., Nair, M., Dodgson, A., Forrest, M. S., Clark, T. G. & Pain, A. Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus. PLoS One 9, e101419, doi:10.1371/journal.pone.0101419 (2014).
  62. Preston, M. D., Campino, S., Assefa, S. A., Echeverry, D. F., Ocholla, H., Amambua-Ngwa, A., Stewart, L. B., Conway, D. J., Borrmann, S., Michon, P., Zongo, I., Ouedraogo, J. B., Djimde, A. A., Doumbo, O. K., Nosten, F., Pain, A., Bousema, T., Drakeley, C. J., Fairhurst, R. M., Sutherland, C. J., Roper, C. & Clark, T. G. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nat Commun 5, 4052, doi:10.1038/ncomms5052 (2014).
  63. Jackson, A. P., Otto, T. D., Darby, A., Ramaprasad, A., Xia, D., Echaide, I. E., Farber, M., Gahlot, S., Gamble, J., Gupta, D., Gupta, Y., Jackson, L., Malandrin, L., Malas, T. B., Moussa, E., Nair, M., Reid, A. J., Sanders, M., Sharma, J., Tracey, A., Quail, M. A., Weir, W., Wastling, J. M., Hall, N., Willadsen, P., Lingelbach, K., Shiels, B., Tait, A., Berriman, M., Allred, D. R. & Pain, A. 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 (2014).
  64. Naeem, R., Hidayah, L., Preston, M. D., Clark, T. G. & Pain, A. SVAMP: sequence variation analysis, maps and phylogeny. Bioinformatics 30, 2227-2229, doi:10.1093/bioinformatics/btu176 (2014).
  65. Forrest, A. R (FANTOM5 Consortium - 259 authors). A promoter-level mammalian expression atlas. Nature 507, 462-470, doi:10.1038/nature13182 (2014).
  66. Coll, F., Preston, M., Guerra-Assuncao, J. A., Hill-Cawthorn, G., Harris, D., Perdigao, J., Viveiros, M., Portugal, I., Drobniewski, F., Gagneux, S., Glynn, J. R., Pain, A., Parkhill, J., McNerney, R., Martin, N. & Clark, T. G. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb) 94, 346-354, doi:10.1016/ (2014).
  67. Cotton, J. A., Lilley, C. J., Jones, L. M., Kikuchi, T., Reid, A. J., Thorpe, P., Tsai, I. J., Beasley, H., Blok, V., Cock, P. J., Eves-van den Akker, S., Holroyd, N., Hunt, M., Mantelin, S., Naghra, H., Pain, A., Palomares-Rius, J. E., Zarowiecki, M., Berriman, M., Jones, J. T. & Urwin, P. E. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol 15, R43, doi:10.1186/gb-2014-15-3-r43 (2014).
  68. Juneja, P., Osei-Poku, J., Ho, Y. S., Ariani, C. V., Palmer, W. J., Pain, A. & Jiggins, F. M. Assembly of the genome of the disease vector Aedes aegypti onto a genetic linkage map allows mapping of genes affecting disease transmission. PLoS Negl Trop Dis 8, e2652, doi:10.1371/journal.pntd.0002652 (2014).

  69. 2013

  70. Janouskovec, J., Sobotka, R., Lai, D. H., Flegontov, P., Konik, P., Komenda, J., Ali, S., Prasil, O., Pain, A., Obornik, M., Lukes, J. & Keeling, P. J. Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia. Mol Biol Evol 30, 2447-2462, doi:10.1093/molbev/mst144 (2013).
  71. Woods, K. L., Theiler, R., Muhlemann, M., Segiser, A., Huber, S., Ansari, H. R., Pain, A. & Dobbelaere, D. A. 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).
  72. Sepulveda, N., Campino, S. G., Assefa, S. A., Sutherland, C. J., Pain, A. & Clark, T. G. A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC Genomics 14, 128, doi:10.1186/1471-2164-14-128 (2013).
  73. Tichy, J., Gardian, Z., Bina, D., Konik, P., Litvin, R., Herbstova, M., Pain, A. & Vacha, F. Light harvesting complexes of Chromera velia, photosynthetic relative of apicomplexan parasites. Biochim Biophys Acta 1827, 723-729, doi:10.1016/j.bbabio.2013.02.002 (2013).
  74. Stabler, R. A., Negus, D., Pain, A. & Taylor, P. W. Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-gamma-d-Glutamic Acid Anthrax Capsule. Genome Announc 1, doi:10.1128/genomeA.00057-12 (2013).
  75. Moon, R. W., Hall, J., Rangkuti, F., Ho, Y. S., Almond, N., Mitchell, G. H., Pain, A., Holder, A. A. & Blackman, M. J. Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes. Proc Natl Acad Sci U S A 110, 531-536, doi:10.1073/pnas.1216457110 (2013).
  76. Oakes, R. D., Kurian, D., Bromley, E., Ward, C., Lal, K., Blake, D. P., Reid, A. J., Pain, A., Sinden, R. E., Wastling, J. M. & Tomley, F. M. The rhoptry proteome of Eimeria tenella sporozoites. Int J Parasitol 43, 181-188, doi:10.1016/j.ijpara.2012.10.024 (2013).
  77. Naeem, R., Rashid, M. & Pain, A. READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. Bioinformatics 29, 391-392, doi:10.1093/bioinformatics/bts684 (2013).

  78. 2012

  79. Ho, Y. S., Adroub, S. A., Aleisa, F., Mahmood, H., Othoum, G., Rashid, F., Zaher, M., Ali, S., Bitter, W., Pain, A. & Abdallah, A. M. Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621. J Bacteriol 194, 6337-6338, doi:10.1128/JB.01461-12 (2012).
  80. Ho, Y. S., Adroub, S. A., Abadi, M., Al Alwan, B., Alkhateeb, R., Gao, G., Ragab, A., Ali, S., van Soolingen, D., Bitter, W., Pain, A. & Abdallah, A. M. Complete genome sequence of Mycobacterium vaccae type strain ATCC 25954. J Bacteriol 194, 6339-6340, doi:10.1128/JB.01462-12 (2012).
  81. Hayashida, K., Hara, Y., Abe, T., Yamasaki, C., Toyoda, A., Kosuge, T., Suzuki, Y., Sato, Y., Kawashima, S., Katayama, T., Wakaguri, H., Inoue, N., Homma, K., Tada-Umezaki, M., Yagi, Y., Fujii, Y., Habara, T., Kanehisa, M., Watanabe, H., Ito, K., Gojobori, T., Sugawara, H., Imanishi, T., Weir, W., Gardner, M., Pain, A., Shiels, B., Hattori, M., Nene, V. & Sugimoto, C. Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. MBio 3, e00204-00212, doi:10.1128/mBio.00204-12 (2012).
  82. Abdallah, A. M., Rashid, M., Adroub, S. A., Elabdalaoui, H., Ali, S., van Soolingen, D., Bitter, W. & Pain, A. Complete genome sequence of Mycobacterium xenopi type strain RIVM700367. J Bacteriol 194, 3282-3283, doi:10.1128/JB.00482-12 (2012).
  83. Abdallah, A. M., Rashid, M., Adroub, S. A., Arnoux, M., Ali, S., van Soolingen, D., Bitter, W. & Pain, A. Complete genome sequence of Mycobacterium phlei type strain RIVM601174. J Bacteriol 194, 3284-3285, doi:10.1128/JB.00485-12 (2012).
  84. Burki, F., Flegontov, P., Obornik, M., Cihlar, J., Pain, A., Lukes, J. & Keeling, P. J. Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol Evol 4, 626-635, doi:10.1093/gbe/evs049 (2012).
  85. Lawton, J., Brugat, T., Yan, Y. X., Reid, A. J., Bohme, U., Otto, T. D., Pain, A., Jackson, A., Berriman, M., Cunningham, D., Preiser, P. & Langhorne, J. Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics 13, 125, doi:10.1186/1471-2164-13-125 (2012).
  86. Reid, A. J., Vermont, S. J., Cotton, J. A., Harris, D., Hill-Cawthorne, G. A., Konen-Waisman, S., Latham, S. M., Mourier, T., Norton, R., Quail, M. A., Sanders, M., Shanmugam, D., Sohal, A., Wasmuth, J. D., Brunk, B., Grigg, M. E., Howard, J. C., Parkinson, J., Roos, D. S., Trees, A. J., Berriman, M., Pain, A. & Wastling, J. M. 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 (2012).
  87. Ramaprasad, A., Pain, A. & Ravasi, T. Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics 99, 69-75, doi:10.1016/j.ygeno.2011.11.006 (2012).

  88. 2011

  89. Pfander, C., Anar, B., Schwach, F., Otto, T. D., Brochet, M., Volkmann, K., Quail, M. A., Pain, A., Rosen, B., Skarnes, W., Rayner, J. C. & Billker, O. A scalable pipeline for highly effective genetic modification of a malaria parasite. Nat Methods 8, 1078-1082, doi:10.1038/nmeth.1742 (2011).
  90. Gomes-Santos, C. S., Braks, J., Prudencio, M., Carret, C., Gomes, A. R., Pain, A., Feltwell, T., Khan, S., Waters, A., Janse, C., Mair, G. R. & Mota, M. M. Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio. PLoS Pathog 7, e1002046, doi:10.1371/journal.ppat.1002046 (2011).
  91. Ogun, S. A., Tewari, R., Otto, T. D., Howell, S. A., Knuepfer, E., Cunningham, D. A., Xu, Z., Pain, A. & Holder, A. A. Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathog 7, e1001288, doi:10.1371/journal.ppat.1001288 (2011).

  92. 2010

  93. Tewari, R., Straschil, U., Bateman, A., Bohme, U., Cherevach, I., Gong, P., Pain, A. & Billker, O. The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. Cell Host Microbe 8, 377-387, doi:10.1016/j.chom.2010.09.006 (2010).
  94. Hunt, P., Martinelli, A., Modrzynska, K., Borges, S., Creasey, A., Rodrigues, L., Beraldi, D., Loewe, L., Fawcett, R., Kumar, S., Thomson, M., Trivedi, U., Otto, T. D., Pain, A., Blaxter, M. & Cravo, P. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11, 499, doi:10.1186/1471-2164-11-499 (2010).
  95. Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, A., Otto, T. D., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, E. T. & Jeffares, D. C. Long- and short-term selective forces on malaria parasite genomes. PLoS Genet 6, e1001099, doi:10.1371/journal.pgen.1001099 (2010).
  96. Pain, A. & Hertz-Fowler, C. Plant killers on the spot. Nat Rev Microbiol 8, 615, doi:10.1038/nrmicro2433 (2010).
  97. Sutherland, C. J., Tanomsing, N., Nolder, D., Oguike, M., Jennison, C., Pukrittayakamee, S., Dolecek, C., Hien, T. T., do Rosario, V. E., Arez, A. P., Pinto, J., Michon, P., Escalante, A. A., Nosten, F., Burke, M., Lee, R., Blaze, M., Otto, T. D., Barnwell, J. W., Pain, A., Williams, J., White, N. J., Day, N. P., Snounou, G., Lockhart, P. J., Chiodini, P. L., Imwong, M. & Polley, S. D. Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. J Infect Dis 201, 1544-1550, doi:10.1086/652240 (2010).
  98. Otto, T. D., Wilinski, D., Assefa, S., Keane, T. M., Sarry, L. R., Bohme, U., Lemieux, J., Barrell, B., Pain, A., Berriman, M., Newbold, C. & Llinas, M. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 76, 12-24, doi:10.1111/j.1365-2958.2009.07026.x (2010).