Arnab Pain

  Professor, Biocience ​

  Office Location: Ibn Al Haytham (Building 2) · Level 4 · Room 4236
  Faculty lab website:

Research Keywords
Genome and transcriptome analysis; Microbial genomics; Apicomplexan parasites; Evolution of obligate intracellular parasitism, Mycobacteria; Enteric pathogens; Host-pathogen interactions; Bioinformatic tools development for pathogen discovery .   

Research Interests

The primary focus of the Pathogen Genomics Laboratory (PGL) is to use high-throughput sequencing and other functional genomic technologies to understand the biology and genomic diversity of apicomplexan protists and a few selected bacterial pathogens with significant impact on human and animal health. Genome and transcriptome analysis of these organisms is a critical first step towards our understanding of how these organisms grow and thrive in a susceptible host and cause disease. 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 their free-living relatives.

2.  Characterization of enteric pathogens during mass gatherings.

3. Genome biology and transcriptome variation in Mycobacteria.

4. Development of bioinformatic tools for genome-scale data visualization and pathogen discovery.    

Main Techniques
High-throughput sequencing-based functional genomics methods to study the genome and metagenomes, transcriptome and the epigenome, Basic cell culturing and microbiology techniques, Genome assembly and variation, Pathogen discovery tools using NGS datasets.    

Members of the Lab

Dr Hifzur Rahman Ansari: Post-doctoral fellow focusing on bioinformatic analysis of apicomplexan and chromerid genomes. His research interests include immuno-informatics and comparative genomics and biological databases. Dr Ansari obtained his PhD degree from the Jawaharlal Nehru University, New Delhi (India).

Dr Amit Kumar Subudhi: Post-doctoral fellow focusing on bioinformatic analysis of Plasmodium genomes and transcriptomes. His research interests include studying analysis of transcriptome datasets and systems biology of apicomplexan parasites. Dr Subudhi obtained his PhD degree from Birla Institute of Technology and Science (BITS-Pilani), Rajasthan, (India).

Dr Fathia Ben Rached: Post-doctoral fellow focusing on cell biology and regulation of gene expression in apicomplexan parasites and other related organisms. Her research interests include studying cell biology and molecular biology of obligate intracellular parasites. Dr Ben Rached obtained her PhD degree from Institut Cochin, Université Paris Descartes (France).

Raeece Naeem: Research (Software) engineer focusing on development of bioinformatic tools for genome-scale data visualization and mining. His research interests include bioinformatic tools development and implementation, sequence analysis, high performance computing.

Yasmeen Hashish: Bioinformatician focusing on transcriptome analysis and other bioinformatic analysis software pipeline development.

Zineb Rchiad: PhD student focusing on host-parasite interaction in Theileria-transformed bovine lymphocytes with focus on transcriptomics and epigenomics.

Abhinay Ramprasad: PhD student focusing on phenotype-genotype correlations and phylogenomics in rodent malaria parasites P. vinckei.

Mona Alsomali: PhD student focusing on molecular characterisation of enteric pathogens during the annual mass gathering event, Hajj.

Sharif Hala: PhD student. Precise PhD project is yet to be decided. Now working on getting experienced with various NGS protocols commonly followed in our laboratory.

Qingtian Guan: MS thesis student focusing on studying Mycobacterial genomics.    

Selected Publications

Assefa, S.A., 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.* (2015). Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi.  Proceedings of the National Academy of Sciences of the United States of America Oct 5. pii: 201509534. [Epub ahead of print])

Woo, Y.H., Ansari, H., Otto, T.D., Linger, C.M.K., Olisko, M.K., Michálek, J., Saxena, A., Shanmugam, D., Tayyrov, A., Veluchamy, A., Ali, S., Bernal, A., Del Campo, J., Cihlář, J., Flegontov, P., Gornik, S.G., Hajdušková, E., Horák, A., Janouškovec, 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., Tomčala, 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., Lukeš, J., Oborník, M., Pain, A. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites eLife, art. no. E06974, pp. 1-41.  DOI: 10.7554/eLife.06974. 

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 Research doi:10.1101/gr.168955.113 

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 Research 42, 7113-7131, doi:10.1093/nar/gku322 

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.​