Raeece Naeem

Research Staff

Moved to KAUST Facilities


Research Interests

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).


  • 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

Research Interests Keywords