Qualifications:

• PhD, 2018-2023, Wageningen University, The Netherlands
• MS, 2007-2009, Pakistan Institute of Engineering and Applied Science (PIEAS)
• BSc (Hons) in Computer Science, 2002-2006, University of the Punjab, Lahore

Honors and awards

• 2018: PhD fellowship from Wageningen University, The Netherlands
• 2015-2016: Member Technical committee of International Nathiagali Summer College (INSC) for the 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:

I am a multidisciplinary science lover and eager to learn newer skills all the time. Now a days, I mostly work in developing and applying bioinformatics tools to explore quantitative genetics problem of linking genotypes and phenotypes (e.g., Genomic Predictions and Genome-wide Association Analysis) using both statistical learning and using machine learning / deep learning approaches. For this, I am interested in improving methodologies by incorporating prior biological knowledge. Moreover, I am eager to develop innovative solutions for smart-breeding and on-field high-throughput phenotyping by integrating genomics and phenomics. For this, I am always looking for talented and multi-disciplinary students eager to learn at the cross-sections of biology, agriculture, computing and engineering.

Highlighted Publications:

• Muhammad, Farooq, D. J. van Dijk Aalt, Nijveen Harm, and Mansoor Shahid. "Genomic prediction in plants: opportunities for ensemble machine learning based approaches." F1000Research 11 (2023).
• Muhammad Farooq, Aalt DJ Van Dijk, Harm Nijveen, Mark GM Aarts, Willem Kruijer, Thu-Phuong Nguyen, Shahid Mansoor, and Dick de Ridder. "Prior biological knowledge improves genomic prediction of growth-related traits in Arabidopsis thaliana." Frontiers in genetics 11 (2021): 609117.
• Athar Hussain, Muhammad Farooq, Rubab Zahra Naqvi, Muhammad Qasim Aslam, Hamid Anees Siddiqui, Imran Amin, Chengcheng Liu et al. "Whole-genome resequencing deciphers new insight into genetic diversity and signatures of resistance in cultivated cotton Gossypium hirsutum." Molecular Biotechnology 65, no. 1 (2023): 34-51. 
• Muhammad Farooq, Rubab Zahra Naqvi, Imran Amin, Atiq Ur Rehman, Muhammad Asif, and Shahid Mansoor. "Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads." Gene 852 (2023): 147065.
• Muhammad Anas, Muhammad Farooq, Muhammad Asif, Waqas Rafique Ali, and Shahid Mansoor. "A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan." Animals 13, no. 15 (2023): 2543.
• 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)
• Muhammad Farooq, Shahid Mansoor, Hui Guo, Imran Amin, Peng W. Chee, M. Kamran Azim and Andrew H. Paterson, "Identification and characterization of microRNA transcriptome in Asiatic cotton Gossypium arboreum using High Throughput Sequencing", Frontiers in Plant science, doi: 10.3389/fpls.2017.00969 (accepted: May 23, 2017)
• 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. 

Grants: