Mohammad Asif Khan


Mohammad Asif Khan

Charles M. Wiener, M.D.
Dr. Mohammad Asif Khan
Lead, Bioinformatics

BSc (Singapore), MSc (Singapore), PhD (Singapore)
Email: asif@perdanauniversity.edu.my

Dr. Mohammad Asif Khan is currently appointed as the Director of the Perdana University Centre for Bioinformatics (PU-CBi), Assistant Professor to the faculty of the Perdana University Graduate School of Medicine (PUGSOM) and School of Postgraduate Studies (PU-SPS), Malaysia and Visiting Scientist to the Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine (JHUSOM), USA.

He obtained his Ph.D in Bioinformatics from the National University of Singapore (NUS) in 2010. After a short postdoctoral fellowship at NUS, he was appointed to the faculty of JHUSOM as a Research Associate in the Department of Pharmacology and Molecular Sciences. In 2011, he joined the faculty of PUGSOM as an Assistant Professor in Bioinformatics, with an adjunct Assistant Professor appointment at the same department in JHUSOM till 2014. He also held a Visiting Scientist position at the Immunology Frontier Research Center (iFReC), Osaka University, Japan, under their Young Researchers Program.

Dr. Khan’s broad research interests are in the area of biological data warehousing and applications of bioinformatics to the study of immune responses, vaccines, venom toxins, drug design, and disease biomarkers. Specifically, he is interested in understanding the human-pathogen interactome, defined as the pathogen and human genetic sets (DNA, RNA, Protein) that are directly or indirectly involved in the complex, dynamic interactions between the two, relevant for the survival of each other. He has authored/co-authored a total of 38 published articles (http://bit.ly/1xDXelB) in various international journals, conferences, and books, and has presented his work at numerous international conferences. His scientific contributions include development of several novel bioinformatics methodologies, tools, and specialized databases, and currently has three patents filed.

Dr. Khan’s teaching experiences have been in bioinformatics, imparting to undergraduate/graduate students at NUS (~1568 students; 2006-2010), and has assisted in the supervision of research projects of more than 50 students (45 bachelors, 6 masters and 3 PhDs). His publications include two bioinformatics pedagogy related journal articles and a book chapter. At PUGSOM, he teaches the bioinformatics components of the Genes to Society Curriculume. He led the development of the programmes and curricula for the Postgraduate Diploma and MSc in Bioinformatics to be taught at the Perdana University School of Postgraduate Studies, through the Centre for Bioinformatics. Furthermore, the School now also offers PhD in Health, with the option for specialisation in Bioinformatics.

Dr. Khan is currently the ExCo Vice President (Corporate) for the Asia-Pacific Bioinformatics Network (APBioNet) and a Honorary Director for APBIoNet Public Limited. He is also a member of the International Society for Computational Biology (ISCB). His services to the scientific community include as a reviewer for journals, conferences, and funding agencies, and is active in the organization of local and international bioinformatics conferences, meetings and workshops.

Journal Articles (Peer-Reviewed)

  1. Tan PT, Khan AM, Brusic V. Bioinformatics for venom and toxin sciences. Brief Bioinform.  2003; 4 (1): 53-62. [Impact Factor 2010 = 9.283; Citations = 28]
  2. Fry BG, Wüster W, Kini RM, Brusic V, Khan A, Venkataraman D, Rooney AP. Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol. 2003; 57 (1): 110-29. [Impact Factor 2010 = 2.311; Citations = 144; Award = Zuckerkandl prize]
  3. Brahmachary M, Krishnan SP, Koh JL, Khan AM, Seah SH, Tan TW, Brusic V, Bajic VB. ANTIMIC: a database of antimicrobial sequences. Nucleic Acids Res. 2004; 32 (Database issue): D586-9. [Impact Factor 2010 = 7.836; Citations = 138]
  4. Lenffer J, Lai P, El Mejaber W, Khan AM, Koh JL, Tan PT, Seah SH, Brusic V. CysView: protein classification based on cysteine pairing patterns. Nucleic Acids Res. 2004; 32 (Web Server issue): W350-5. [Impact Factor 2010 = 7.836; Citations = 21]
  5. Srinivasan KN, Zhang GL, Khan AM, August JT, Brusic V. Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. Bioinformatics. 2004; 20 (Suppl 1): i297-302. [Impact Factor 2010 = 4.877; Citations = 35]
  6. Siew JP, Khan AM, Tan PT, Koh JL, Seah SH, Koo CY, Chai SC, Armugam A, Brusic V, Jeyaseelan K. Systematic analysis of snake neurotoxins’ functional classification using a data warehousing approach. Bioinformatics. 2004; 20 (18): 3466-80. [Impact Factor 2010 = 4.877; Citations = 14]
  7. Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V. MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res. 2005; 33 (Web Server issue): W172-9. [Impact Factor 2010 = 7.836; Citations = 106]
  8. Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V. Neural models for predicting viral vaccine targets. J Bioinform Comput Biol. 2005; 3 (5): 1207-25. [Citations = 25]
  9. Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT, Brusic V. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics. 2006; 7 (Suppl 5): S4. [Impact Factor 2010 = 3.028; Citations = 22]
  10. Khan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento EJ, Marques ET, Brusic V, Tan TW, August JT. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol. 2006; 244(2), 141-7. [Impact Factor 2010 = 2.575; Citations = 32]
  11. Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, Tan TW, August JT. Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS ONE. 2007; 2(11), e1190. [Impact Factor 2010 = 4.411; Citations = 86]
  12. Sangket U, Phongdara A, Chotigeat W, Nathan D, Kim WY, Bhak J, Ngamphiw C, Tongsima S, Khan AM, Lin H, Tan TW. Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Bioinformatics. 2008; 24 (2): 299-301. [Impact Factor 2010 = 4.877; Citations = 5]
  13. Zhang GL, Khan AM*, Srinivasan KN, Heiny A, Lee K, Kwoh CK, August JT, Brusic V. Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics. 2008; 9 (Suppl 1): S19. [Impact Factor 2010 = 3.028; Citations = 16; *contributed equally as the first author]
  14. Khan AM, Miotto O, Nascimento EJ, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis. 2008; 2 (8), e272. [Impact Factor 2010 = 4.752; Citations = 26]
  15. Koo QY, Khan AM*, Jung KO, Ramdas S, Miotto O, Tan TW, Brusic V, Salmon J, August. Conservation and variability of West Nile virus proteins. PLoS ONE. 2009; 4(4): e5352. [Impact Factor 2010 = 4.411; Citations = 9; *contributed equally as the first author]
  16. Lim SJ, Khan AM, Silva MD, Lim KS, Hu Y, Tan CH, Tan TW. The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the National University of Singapore. BMC Bioinformatics. 2009; 10(Suppl 15): S12. [Impact Factor 2010 = 3.028; Citations = 5]
  17. Tan TW, Lim SJ, Khan AM, Ranganathan S. A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the “-omics” era. BMC Genomics. 2009; 10(Suppl 3): S36. [Impact Factor 2010 = 4.206; Citations = 11]
  18. Simon G, Hu Y, Khan AM, Zhou J, Salmon J, Chikhlikar PR, Jung KO, Marques ETA, August JT. Efficient activation of HLA DR4-restricted T-cell epitope responses by dendritic cell mediated delivery of plasmid DNA encoding LAMP/HIV-1 Gag immunogen and analysis of epitope peptide variability. PLoS ONE. 2010; 5(1): e8574. [Impact Factor 2010 = 4.411; Citations = 4]
  19. Gomes AV, Wee LJK, Khan AM, Gil LHV, Marques Jr ETA, Calzavara-Silva CE, Tan TW. Classification of dengue fever patients based on gene expression data using support vector machines. PLoS ONE. 2010; 5(6): e11267 [Impact Factor 2010 = 4.411; Citations = 6]
  20. Kothapalli R, Khan AM, Basappa, Gopalsamy A, Seng CY, Annamalai L. Identification and Characterisation of Inhibitors Targeting the Characteristic Residues of the Hemopexin Domain of MMP-13 using Cheminformatics-based Drug Design Approach. PLoS ONE. 2010; 5(8): e12494. [Impact Factor 2010 = 4.411; Citation = 2]
  21. Tay DMM, Govindarajan KR, Khan AM, Ong TYR, Samad HM, Soh WW, Tong M, Zhang F, Tan TW. T3SEdb: Data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics. 2010; 11(Suppl 7): S4. [Impact Factor 2010 = 3.028; Citations = 10]
  22. Tan TW, Tong JC, Khan AM, de Silva M, Lim KS, Ranganathan S. Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi). BMC Genomics. 2010; 11(Suppl 4): S27. [Impact Factor 2010 = 4.206; Citations = 8]
  23. Tan PTJ, Khan AM, August JT. Highly conserved influenza A sequences as T cell epitopes-based vaccine targets to address the viral variability. Human Vaccines. 2011; 7(4) [Impact Factor 2010 = 2.042; Citation = 8]
  24. Jung KO*, Khan AM*, Tan BY, Yongli H, Simon GG, Nascimento EJ, Lemonnier F, Brusic V, Miotto O, Tan TW, Marques ET, Dhalia R, Salmon J, August JT. West Nile Virus T-cell Ligand Sequences Shared with Other Flaviviruses: A Multitude of Variant Sequences as Potential Altered Peptide Ligands. J Virol. 2012 May 9 [Impact Factor 2010 = 5.189; Citation = 2; *Contributed equally]
  25. Rathakrishnan A, Wang SM, Hu Y, Khan AM, Ponnampalavanar S, Lum LCS, Sekaran SD. Cytokine Expression Profile of Dengue Patients at Different Phases of Illness. 2012; PLoS ONE 7(12): e52215 [Impact Factor 2010 = 4.092]
  26. Hu Y, Tan PTJ, Tan TW, August JT, Khan AM. Dissecting the dynamics of HIV-1 protein sequence diversity. 2013; PLoS ONE 8(4): e59994 [Impact Factor 2010 = 4.092]
  27. Khan AM, Tan TW, Schönbach C, Ranganathan S. APBioNet – transforming bioinformatics in the Asia-Pacific Region. PLoS Computational Biology. 2013 Oct 31; 9(10):e1003317. (IF 2013 : 4.468).
  28. Tan TW, Xie C, De Silva M, Lim KS, Patro CPK, Lim SJ, Govindarajan KR, Tong JC, Choo KH, Ranganathan S, Khan AM*. Simple Re-instantiation of Small Databases using Cloud Computing. BMC Genomics. 2013 Oct 16; 14(Suppl5):S13 (Impact Factor 2012 = 4.09; *Corresponding author)
  29. Nascimento E, Mailliard R, Khan AM, Sidney J, Sette A, Guzman N, Paulaitis M, Melo A, Cordeiro M, Gil L, Lemonnier F, Rinaldo C, August JT, Marques ETA. Identification of conserved and HLA promiscuous DENV-3 T-cell Epitopes. PLoS Neglected Tropical Disease. 2013 Oct 10; 7(10):e2497. (IF 2012: 4.569).
  30. Sumpio BJ, Chitragari G, Moriguchi T, Shalaby S, Pappas-Brown V, Khan AM, Sekaran SD, Sumpio BE, Grab DJ. African trypanosome induced blood-brain barrier dysfunction under shear stress may not require ERK activation. International Journal of Angiologyi. 2014. (In press; IF 2012:1.462).
  31. Yeo ASL, Azhar NA, Yeow W, Talbot Jr. CC, Khan AM, Easakimuthu S, Rathakrishnan A, Azizan A, Wang SM, Lee SK, Fong MY, Manikam R, Sekaran SD. Lack of clinical manifestations in asymptomatic dengue infection is attributed to broad down-regulation and selective up-regulation of host defence response genes. PLoS ONE. 2014. (Accepted; IF 2012:3.73)
  32. Patro CPK, Khan AM, Tan TW. STATdb: A specialised resource for the STATome. PLoS ONE. 2014. (Conditionally Accepted; IF 2012:3.73)

Conference Articles (peer-reviewed)

  1. Koh JLY, Krishnan SPT, Seah SH, Tan PT, Khan AM, Lee ML, Brusic V. BioWare: A framework for bioinformatics data retrieval, annotation and publishing. Proceedings of the 27th Annual International ACM SIGIR Conference on Research and Development in IR. Sheffield, UK, July 29, 2004. [Citations = 12]
  2. Koh JLY, Lee ML, Khan AM, Tan PTJ, Brusic V. Duplicate Detection in Biological Data using Association. Proceedings of the 2nd European Workshop on Data Mining and Text Mining for Bioinformatics. Pisa, Italy, September 24, 2004. [Citations = 19]
  3. Rajapakse M, Veeramani A, Gopalakrishnan K, Ananthanarayan S, Srinivasan KN, August JT, Khan AM, Brusic V. Temporal and antigenic analysis of dengue virus serotype 1 genome polyprotein sequences. Proceedings of the International Conference on Biomedical and Pharmaceutical Engineering, Singapore, December 11, 2006.

Others

  1. Tan TW, Khan AM, Lim SJ, Hu YL, De Silva M, Lim KS (2010). Metacuration Standards and Minimum Information about a Bioinformatics Investigation. Nature Precedings. http://dx.doi.org/10.1038/npre.2010.5078.1.
  2. Lim SJ, Khan AM, De Silva M, Lim KS, Hu Y, Tan CH, and Tan TW. Integration of e-learning tools into the Problem-based Learning Approach to enhance teaching and learning in undergraduate bioinformatics modules. 2010. E-learning Volume, Centre for Development of Teaching and Learning (CDTL), National University of Singapore.
  3. Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Raman HSA, Brusic V, Tan TW and August, JT. Analysis of Viral Diversity for Vaccine Target Discovery in Methods of Molecular Biology volume on Immunogenicity Prediction. Moise L, De Groot A and Vladimir Brusic, Eds. Humana Press. New York. 2014. [Book chapter accepted]

Project title: Introducing Bioinformatics at the secondary-school level in Malaysia: the pupils’ viewpoint. Research Team: Mohamed NE, Tan S, Veerakumarasivam A, and Khan MA.

Project title: Predicting Avian Influenza Virus Transmission to Humans. Research Team: Tan S, Mohamed NE, Raman HSA, Chan CX, August JT, and Khan MA.

Project title: Influenza A Virus Vaccine Coverage. Research Team: Tan S, Mohamed NE, Raman HS, August JT, and Khan MA

Project title: Dissecting the dynamics of Influenza A virus proteome diversity. Research Team: Raman HSA, Tan S, and Khan MA.

Project title: Gene expression profiling to determine the immune correlates conferring protection to individuals with asymptomatic dengue infection. Research Team: Yeo AS, Azhar NA, Yeow W, Talbot CC, Khan MA, Muthu SE, Rathakrishnan A, Azizan A, Wang SM, Lee SK, Fong MY, Manikam R, and Sekaran SD.

Project title: Molecular profiling analysis of endothelial cell barrier responses to African Trypanosomes and dengue virus infection. Research Team: Rathakrishnan A, Tang YQ, Azhar NA, Talbot C, Sumpio B, Sumpio BE, Khan MA, Sekaran SD, and Grab DJ.

Project title: Protecting the blood brain barrier from African Trypanosomes infection. Research Team: Azhar NA, Samsudin M, Talbot C, Sumpio B, Sumpio BE, Khan MA, Sekaran SD, and Grab DJ.

Project title: Assessing the feasibility of smart devices in a clinical setting. Research Team: Tan S, Shah NFN, August PN, Gravitt P, Dumler S, Sekaran SD, and Khan MA.

Project title: Molecular and metabolic distinctions between non alcoholic fatty liver disease and Type 2 diabetes mellitus. Research Team: Azhar NA, Tan S, Khan MA, Goh KL, and Hussain AM.