I am focusing on development of bioinformatic tools for genome-scale data visualization and mining. My research interests include bioinformatic tools development and implementation, sequence analysis, high performance computing.
Selected Publications
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).
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).
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 Dis8, doi:10.1371/journal.pntd.0002981 (2014).
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, doi:10.1128/mBio.01744-14 (2014).
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, doi:10.1371/journal.pone.0124473 (2015).
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).
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 (2015, in press).
Education
1998-2002 Bachelor of Engineering in Information technology - Bharathidasan University, India
Professional Profile
2009-2011 Senior Software developer, Pathogen Genomics group - Wellcome Trust Sanger Institute, Cambridge, United Kingdom
2007-2009 Senior Java developer - DeskJump Ltd, London, United Kingdom
2004-2007 Systems engineer - Tata Consultancy Services, Tunbridge wells, United Kingdom
2003-2004 Systems engineer - Tata Consultancy Services, Chennai, India
