Syed Ali, PhD

Associate Professor

Former affiliation
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Research activity per year

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Personal profile

Personal profile

Dr. Syed Ali obtained his Ph.D. in 1999, from Roswell Park Cancer Institute, and State University of New York, NY, USA. From 1999 to 2003, he was a post-doctoral fellow at Harvard Medical School and Dana-Farber Cancer Institute, in Boston, MA, USA.
Dr. Ali’s earlier work was on cellular transformation by oncogenic viruses. More recently his work has been focused on four viruses: Human Immunodeficiency, Human Papilloma, Hepatitis C and Hepatitis B viruses (HIV, HPV, and HCV, respectively). His research group investigates the immune evolution of HIV and HPV in Pakistan, Afghanistan, Nepal, and Kenya. Dr. Ali’s team studies the host and virus factors that drive the evolution of viral epitopes. In addition, they are investigating novel drugs and their mechanism of action against oncogenic viruses, using simian virus 40, HIV, and HCV as models.
Before joining Nazarbayev University in 2015, Dr. Ali was at The Aga Khan University, working in Pakistan, Kenya, and Afghanistan. He has supervised Ph.D. and Master’s students for their dissertation research in Virology, Oncology, Bioinformatics, and Drug Design. Dr. Ali has designed undergraduate and graduate-level courses in critical thinking, virology, oncology, and film criticism. He is an expert in e-learning and has offered several online courses, including a massive open online course (MOOC) in Drug Discovery.

Research interests

Drug screening against oncogenic viruses:

Dr. Ali’s group has developed cell culture models and has patented enzyme assays to test putative antiviral drugs and vaccines on SARS-CoV-2, HCV, JCV, and BKV. Additionally, his group constructs computer simulation models of viral protein targets with the drugs, testing the most potent in wet-lab experiments.

Viral evolution:

In the past, Dr. Ali’s group has explored the origins and patterns of transmission of HIV in several high risk groups. In Kazakhstan and Pakistan, they have studied the communities of injection drug users, men who have sex with men, migrants and refugees. Using bioinformatics tools, Dr. Ali’s group has developed phylogeny for the HIV epidemics in high risk groups in Kazakhstan, Pakistan, Kenya, Nepal, and Afghanistan.


  1. Viral co-infections in high-risk communities of Pakistan. Shah AA, Abidi SH, Kalish ML, Vermund SH, Ali S. Lancet HIV. 2015 Apr;2(4):e124-5. doi: 10.1016/S2352-3018(15)00039-9. 2015. PMID:26424672
  2. Prevalence of Transmitted Drug Resistance Mutations in HIV-1-Infected Drug-Naive Patients from Urban and Suburban Regions of Kenya. Onsongo S, Abidi SH, Khamadi S, Shah R, Kageha S, Ojwang P, Ali S, Okinda N. AIDS Res Hum Retroviruses. 2015. PMID: 26401720
  3. How Pakistan’s media spreads the message about reproductive and sexual health. Abidi SH, Raees M, Ali S. BMJ. 2015 Mar 16;350:h1309. doi: 10.1136/bmj.h1309. PMID:25779596
  4. Abidi SH, Shahid A, Lakhani LS, Shah R, Okinda N, et al. HIV-1 progression links with viral genetic variability and subtype, and patient’s HLA type: analysis of a Nairobi-Kenyan cohort. Med Microbiol Immunol. 2014 Feb;203(1):57-63. PubMed PMID: 24142198.
  5. Abidi SH, Kalish ML, Abbas F, Rowland-Jones S, Ali S. HIV-1 subtype A gag variability and epitope evolution. PLoS One. 2014;9(6):e93415. PubMed PMID: 24892852; PubMed Central PMCID: PMC4043486.
  6. Abidi SH, Shahid A, Lakhani LS, Khanani MR, Ojwang P, et al. Population-specific evolution of HIV Gag epitopes in genetically diverged patients. Infect Genet Evol. 2013 Jun;16:78-86. PubMed PMID: 23403357.
  7. Raees MA, Abidi SH, Ali W, Khanani MR, Ali S. HIV among women and children in Pakistan. Trends Microbiol. 2013 May;21(5):213-4. PubMed PMID: 23648136.
  8. Siddiqui S, Khan I, Zarina S, Ali S. Use of the SYBR Green dye for measuring helicase activity. Enzyme Microb Technol. 2013 Mar 5;52(3):196-8. PubMed PMID: 23410932.
  9. Abidi SH, Ali F, Shah F, Abbas F, Ali S. Burden of communicable disease among the native and repatriating Afghans. PLoS Pathog. 2012;8(10):e1002926. PubMed PMID: 23133369; PubMed Central PMCID: PMC3486882.
  10. Khan IA, Siddiqui S, Rehmani S, Kazmi SU, Ali SH. Fluoroquinolones inhibit HCV by targeting its helicase. Antivir Ther. 2012;17(3):467-76. PubMed PMID: 22293206.
  11. Shahid A, Dixit SM, Gurbacharya VL, Karmacharya D, Ali S. HIV-1 circulating recombinant form in Nepal. J Virol. 2011 Aug;85(16):8458. PubMed PMID: 21680516; PubMed Central PMCID: PMC3147966.
  12. Ansari AS, Khanani MR, Abidi SH, Shah F, Shahid A, et al. Patterns of HIV infection among native and refugee Afghans. AIDS. 2011 Jul 17;25(11):1427-30. PubMed PMID: 21516026.
  13. Kassi M, Afghan AK, Khanani MR, Khan IA, Ali SH. Safe blood transfusion practices in blood banks of Karachi, Pakistan. Transfus Med. 2011 Feb;21(1):57-62. PubMed PMID: 21029219.
  14. Khanani MR, Somani M, Rehmani SS, Veras NM, Salemi M, et al. The spread of HIV in Pakistan: bridging of the epidemic between populations. PLoS One. 2011;6(7):e22449. PubMed PMID: 21799857; PubMed Central PMCID: PMC3143131.
  15. Khanani MR, Somani M, Khan S, Naseeb S, Ali SH. Prevalence of single, double, and triple infections of HIV, HCV and HBV among the MSM community in Pakistan. J Infect. 2010 Dec;61(6):507-9. PubMed PMID: 20932999.
  16. Khanani MR, Ansari AS, Khan S, Somani M, Kazmi SU, et al. Concentrated epidemics of HIV, HCV, and HBV among Afghan refugees. J Infect. 2010 Nov;61(5):434-7. PubMed PMID: 20831883.
  17. Raza SA, Franceschi S, Pallardy S, Malik FR, Avan BI, et al. Human papillomavirus infection in women with and without cervical cancer in Karachi, Pakistan. Br J Cancer. 2010 May 25;102(11):1657-60. PubMed PMID: 20407442; PubMed Central PMCID: PMC2883157.
  18. Rai MA, Nerurkar VR, Khoja S, Khan S, Yanagihara R, et al. Evidence for a “Founder Effect” among HIV-infected injection drug users (IDUs) in Pakistan. BMC Infect Dis. 2010 Jan 12;10:7. PubMed PMID: 20064274; PubMed Central PMCID: PMC2820481.
  19. Rai MA, Rajabali A, Khan MN, Khan MA, Ali SH. Educating the power: HIV/AIDS and parliamentarians of Pakistan. Health Res Policy Syst. 2009 Sep 16;7:20. PubMed PMID: 19758449; PubMed Central PMCID: PMC2753331.
  20. Rajabali A, Moin O, Ansari AS, Khanani MR, Ali SH. Communicable disease among displaced Afghans: refuge without shelter. Nat Rev Microbiol. 2009 Aug;7(8):609-14.
  21. PubMed PMID: 19609262.
  22. Khan S, Rai MA, Khan A, Farooqui A, Kazmi SU, et al. Prevalence of HCV and HIV infections in 2005-Earthquake-affected areas of Pakistan. BMC Infect Dis. 2008 Oct 27;8:147. PubMed PMID: 18954443; PubMed Central PMCID: PMC2583978.
  23. Khoja S, Ojwang P, Khan S, Okinda N, Harania R, et al. Genetic analysis of HIV-1 subtypes in Nairobi, Kenya. PLoS One. 2008 Sep 11;3(9):e3191. PubMed PMID: 18784834; PubMed Central PMCID: PMC2527130.
  24. Rajabali A, Khan S, Warraich HJ, Khanani MR, Ali SH. HIV and homosexuality in Pakistan. Lancet Infect Dis. 2008 Aug;8(8):511-5. PubMed PMID: 18652997.
  25. Rai MA, Khanani MR, Warraich HJ, Hayat A, Ali SH. Crimean-Congo hemorrhagic fever in Pakistan. J Med Virol. 2008 Jun;80(6):1004-6. PubMed PMID: 18428123.
  26. Khan S, Jaffer NN, Khan MN, Rai MA, Shafiq M, et al. Human papillomavirus subtype 16 is common in Pakistani women with cervical carcinoma. Int J Infect Dis. 2007 Jul;11(4):313-7. PubMed PMID: 17291804.
  27. Rai MA, Warraich HJ, Ali SH, Nerurkar VR. HIV/AIDS in Pakistan: the battle begins. Retrovirology. 2007 Mar 21;4:22. PubMed PMID: 17376244; PubMed Central PMCID: PMC1847529.
  28. Ali SH, Chandraker A, DeCaprio JA. Inhibition of Simian virus 40 large T antigen helicase activity by fluoroquinolones. Antivir Ther. 2007;12(1):1-6. PubMed PMID: 17503741.
  29. Rai MA, Ali SH. Cervical cancer vaccine: the Indian sub-continental context. Vaccine. 2006 Nov 30;24(49-50):7024. PubMed PMID: 16904797.
  30. Khan S, Rai MA, Khanani MR, Khan MN, Ali SH. HIV-1 subtype A infection in a community of intravenous drug users in Pakistan. BMC Infect Dis. 2006 Nov 14;6:164.
  31. PubMed PMID: 17105667; PubMed Central PMCID: PMC1654165.
  32. Shafiq M, Ali SH. Sexually transmitted infections in Pakistan. Lancet Infect Dis. 2006 Jun;6(6):321-2. PubMed PMID: 16728317.
  33. Rai MA, Khan MN, Khan S, Khanani R, Ali SH. Pakistan/India open borders to HIV?. AIDS. 2006 Feb 28;20(4):634-5. PubMed PMID: 16470135.
  34. Kasper JS, Kuwabara H, Arai T, Ali SH, DeCaprio JA. Simian virus 40 large T antigen’s association with the CUL7 SCF complex contributes to cellular transformation. J Virol. 2005 Sep;79(18):11685-92. PubMed PMID: 16140746; PubMed Central PMCID: PMC1212609.
  35. Ali SH, O’Donnell AL, Mohamed S, Mousa S, Dandona P. Overexpression of estrogen receptor-alpha in the endometrial carcinoma cell line Ishikawa: inhibition of growth and angiogenic factors. Gynecol Oncol. 2004 Dec;95(3):637-45. PubMed PMID: 15581976.
  36. Ali SH, Kasper JS, Arai T, DeCaprio JA. Cul7/p185/p193 binding to simian virus 40 large T antigen has a role in cellular transformation. J Virol. 2004 Mar;78(6):2749-57. PubMed PMID: 14990695; PubMed Central PMCID: PMC353757.

Education/Academic qualification

Virology, PhD

External positions


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