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Dr. Muhammad Ali

November 15, 2018: 
March 31, 2019

Postdoctoral Fellow in Microbial Genomics



Alpha Genomics (Pvt) Limited is the pioneer research and development organization in private sector of Pakistan. Alpha Genomics has all the facilities for next generation sequencing (NGS) based research and hosts expert staff in bioinformatics and metagenomics. My Postdoctoral project is genomics and metagenomics of clinical and environmental samples to reveal the underlying mechanisms of pathogenesis, and to identify economically important flora for product development.


During PhD at COMSATS University Islamabad, I characterized Vibrio cholerae from Pakistan by whole genome sequencing in collaboration with Welcome Trust Sanger Institute (WTSI) and London School of Hygiene and Tropical Medicine (LSHTM), UK. My work on V. cholerae in Pakistan serves as a reference for further work on pathogen evolution and genome dynamics in future. I also worked on the mutagenesis of V. cholerae and evaluation of Galleria mellonella as an invertebrate infection model. Besides this, I was an active member of the research group which isolated and characterized diarrhoeagenic Escherichia coli and Campylobacter jejuni from diarrhoea patients. I also isolated and characterized heavy metals resistant bacteria from various environments for use in fluorescent whole cell based biosensor for detecting heavy metals. My MPhil research was to evaluate the bioassays of Bacillus thuriengensis as bio-insecticide against chickpea pod borer, Helicoverpa armigera. During my service at The University of Azad Jammu and Kashmir – Muzaffarabad, I studied the physiochemical and microbiological quality of springs and supplied water in Muzaffarabad under SRGP of Higher Education Commission, Pakistan. Now besides epidemiology of infectious pathogens, my focus is also to identify potential alternatives to combat multiple drug resistance pathogens, which are a major challenge worldwide.


⦁    Epidemiological investigation of common pathogens such as Vibrio cholerae, Diarrhoeagenic Escherichia coli, pathogens of urinary tract and their control by evaluating various alternate approaches.
⦁    Genomics of infectious pathogens.
⦁    Molecular mechanisms of drug resistance in community and hospital acquired infections.
⦁    Exploring and characterizing potential agents of medicinal importance from plants.
⦁    Nanomaterials and their role as cost effective and smart material in various fields such as agriculture, livestock, biodegradation and treating various human illnesses.
⦁    Microbial diversity and metagenomics of diverse environments and potential applications.
⦁    Microbial biotechnology.


⦁    Muhammad Ali Shah, Ankur Mutreja, Nicholas Thomson, Stephen Baker, Julian Parkhill, Gordon Dougan, Habib Bokhari, and Brendan W. Wren. "Genomic Epidemiology of Vibrio cholerae O1 Associated with Floods, Pakistan, 2010." Emerging infectious diseases 20, no. 1 (2014): 13. (IF: 7.42)

⦁    Robert Atterbury, Sudhakar Ganapati Bhandare, Joan Colom, Abiyad Baig, Paul Barrown,  Habib Bokhari, Muhammad Ali Shah, BL Sarkar,   Jingliang Su, Brendan W Wren. Reviving phage therapy for the treatment of cholera. (Accepted in Journal of Infectious Diseases) (IF: 5.183)

⦁    Bokhari, Habib, Muhammad Ali Shah, Saba Asad, Akhtar Sania, Muhammad Akram, and Brendan Wren. "Escherichia coli Pathotypes in Pakistan from Consecutive Floods in 2010 and 2011." The American journal of tropical medicine and hygiene (2013): 12-0365. (IF: 2.55)

⦁    Idrees, Muhammad, Muhammad Ali Shah, Shazia Michael, Raheel Qamar, and Habib Bokhari. "Antimicrobial resistant Escherichia coli strains isolated from food animals in Pakistan." Pakistan Journal of Zoology 43, no. 2 (2011): 303-310. (IF: 0.49)

⦁    Muhammad Iqbal, Naveed Iqbal Raja, Farhat Yasmeen, Mubashir Hussain, Muhammad Ejaz and Muhammad Ali Shah, “Impacts of Heat Stress on Wheat: A Critical Review.” Advances in Crop Science and Technology 5, (2017): 251.

⦁    Sumaira Aslam, Naveed Iqbal Raja, Mubashir Hussain, Muhammad Iqbal, Muhammad Ejaz, Danish Ashfaq, Hira Fatima, Muhammad Ali Shah, Abd-Ur-Rehman, Maria Ehsan, “Current Status of Withania somnifera (L.) Dunal: An Endangered Medicinal Plant from Himalaya.” American Journal of Plant Sciences 8, (2017): 1159-1169