Monday, August 03, 2020

Muhammad Farooq,

Senior Scientist

Work Phone: +92-41-9201316-20 Ext 232
Fax Phone: +92-41-6201472
Cell/Direct Phone: +92-344-5399512
Muhammad Farooq




  • MS, 2007-2009, Pakistan Institute of Engineering and Applied Science (PIEAS)
  • BSc (Hons) in Computer Science,  2002-2006, University of the Punjab, Lahore

Honours and awards


  • 2016: Member Technical committee of International Nathiagali Summer College (INSC) for Computational Biology activity.
  • 2015: USDA Norman E. Borlaug Fellowship on Bioinformatics at High Performance Computing Laboratory, Mississippi State University, MS, United States
  • 2007: Government of Pakistan PAEC Fellowship for MS Studies
  • 2006: First Position in University of The Punjab Lahore in BSCS (honors)



Research Interests:

My research interests lie in the inter-disciplinary area of computational biology / bioinformatics.

I am not only interested in the development of bioinformatics tools but their applications in the analysis of various biological datasets esp. sequence data analysis by Next Generation Sequencing (NGS) platforms.

Currently I am working on computational genomics for study of Geminivirus diversity in their different hosts and cotton transcriptomics and mirNomics. I am working on multiple genome assembly and resequencing projects incl. Bemisia tabaci and cattle for variant analysis and annotations.

Moreover, the work on comparative genomics for different bacteriophages e.g. Salmonella enterica typhi is also ongoing. I am interested to develop different pipelines and bioinformatics tools from -omic data.



  • Corrinne E Grover, Mark A Arick II, Justin Conover, Adam Thrash, Guanjing Hu, William S. Sanders, Hsu Chuan-Yu, Rubab Naqvi, Muhammad Farooq, Xiaochong Li, Lei Gong, Joann Mudge, Thiru Ramaraj, Joshua A Udall, Daniel G Peterson, Jonathan F Wendel, "Comparative genomics of an unusual biogeographic disjunction in the cotton tribe (Gossypieae) yields insights into genome downsizing", Genome Biology and Evolution(2017) [IF=3.979]
  • Muhammad Farooq, Shahid Mansoor, Hui Guo, Imran Amin, Peng W. Chee, M. Kamran Azim and Andrew H. Paterson, "Identification and characterization of microRNA trancriptome in Asiatic cotton Gossypium arboreum using High Throughput Sequencing", Frontiers in Plant science, doi: 10.3389/fpls.2017.00969 (accepted: May 23, 2017) [IF= 4.298]
  • Zaidi, S. S., Sara Shakir, Muhammad Farooq, Imran Amin, and Shahid Mansoor. "First Report of a Novel Strain of Tomato yellow leaf curl virus Causing Yellow Leaf Curl Disease on Cluster Bean in Pa0kistan." Plant Disease (2017). [IF= 3.02]
  • Syed Shan-e-Ali Zaidi, Sara Shakir, Hassan Jameel Malik, Muhammad Farooq, Imran Amin and Shahid Mansoor. "First report of Tomato leaf curl New Delhi virus on Calotropis procera,a weed as potential reservoir begomovirus host in Pakistan." Plant Disease ja (2017).[IF= 3.02] 
  • Muhammad Zubair, Syed Shan-e-Ali Zaidi, Sara Shakir, Muhammad Farooq, Imran Amin, Jodi Scheffler, Brian Scheffler, and Shahid Mansoor, "Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton", Scientific reports, 7(1), 680.[IF= 4.259] 
  • Syed Shan-e-Ali Zaidi, Sara Shakir, Imran Amin, Muhammad Farooq, and Shahid Mansoor. "First report of Alternanthera yellow vein virus from Eclipta prostrata (L.) in Pakistan." Plant Disease ja (2016).[IF= 3.02] 
  • Syed Shan- e- Ali Zaidi, Darren P. Martin, Imran Amin, Muhammad Farooq, and Shahid Mansoor. "Tomato leaf curl New Delhi virus; a widespread bipartite begomovirus in the territory of monopartite begomoviruses." Molecular Plant Pathology (2016).[IF= 4.724] 
  • Muhammad Farooq, Aasma Aslam, Babar Hussain, Ghazanfar Hussain, and Masroor Ikram. "A comparison of image processing techniques for optical interference fringe analysis." Photonic Sensors 5, no. 4 (2015): 304-311. 

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