Dr. Muhammad Ishaq
Associate Professor (Tenured)
- +92 91 9221323
- +92 332 9075981
- +92 91 9221262
- drmishaq@aup.edu.pk
- www.aup.edu.pk
- HEC Approved Supervisor
Education
2016
Postdoctoral Fellow — TWAS-UPM Fellowship
Universiti Putra Malaysia (UPM), Selangor, Malaysia
Dept. of Computer Science, Faculty of Computer Science & Information Technology.
Supervisor: Assoc. Prof. Dr. Lilly Suriani Affendy
Research: Next-Generation Sequence Alignment of Enormous Biological Sequencing Data in Hadoop
TWAS-UPM International FellowshipSupervisor: Assoc. Prof. Dr. Lilly Suriani Affendy
Research: Next-Generation Sequence Alignment of Enormous Biological Sequencing Data in Hadoop
2014
Postdoctoral Fellow — Biomedical Engineering
Catholic University of Daegu, Gyungsan, South Korea
Dept. of Biomedical Engineering, College of Medical Science.
Supervisor: Dr. Yeon Soo Lee (Assistant Professor)
Research: Anti-Malaria Bioinformatics — Malaria Cell Detection (93% accuracy) aligned with 8 UN Millennium Development Goals (MDGs)
International Research CollaborationSupervisor: Dr. Yeon Soo Lee (Assistant Professor)
Research: Anti-Malaria Bioinformatics — Malaria Cell Detection (93% accuracy) aligned with 8 UN Millennium Development Goals (MDGs)
2012
Doctor of Philosophy — Computer Science
Harbin Engineering University, Harbin, China
Specialization: Computer Applied Technology · Bioinformatics
Supervisor: Prof. Yin GuiSheng (Dean, CS College)
Thesis unanimously passed; declared "master of the field of Bioinformatics" by the defence committee.
HEC Pakistan & CSC China Full ScholarshipSupervisor: Prof. Yin GuiSheng (Dean, CS College)
Thesis unanimously passed; declared "master of the field of Bioinformatics" by the defence committee.
2005
MSc, Information Technology
Kohat University of Science & Technology, Pakistan
Area of Specialization
Bioinformatics
Sequence analysis, molecular docking, NGS alignment, anti-Malaria & anti-cancer genomics
Neuro-Symbolic AI & AGI
Integrating neural networks with ontological reasoning toward explainable general intelligence
Knowledge Graphs & Semantic Web
Ontology engineering, RDF/OWL, biomedical KGs, causal inference frameworks
LLMs & Computational Linguistics
Fine-tuning large language models over biomedical ontologies for domain reasoning
Molecular Dynamic Simulation
Therapeutic target characterization, epigenetic regulation, drug repurposing via simulation
AI in Agriculture & Biotechnology
Precision spraying, agri-informatics semantics, gut microbiome analysis, crop genomics
Data Science
Big data pipelines (Hadoop), ML workflows, Picrust2, scientific computing
Health & Biomedical Informatics
Disease gene characterization, intellectual disability, diabetes, zebrafish gut microbiome
Professional Responsibilities
Associate Professor (Tenured)
HEC Approved PhD Supervisor
NCEAC Focal Person
DLSEI Focal Person
BS Bioinformatics Coordinator
BS Artificial Intelligence CoordinatorDr. Ishaq has been a transformative force at the University of Agriculture, Peshawar — single-handedly pioneering Pakistan's first MS in Data Science, BS in Artificial Intelligence, BS in Bioinformatics, and PhD in Computer Science at the institution. He has supervised 7 PhD and 15 MSc theses, producing researchers who are now active across academia and industry.
Research Projects
1
Architecting Explainable AGI: A Neuro-Symbolic Framework Derived from Specialized AI Programming Agents
2
OntoGPT: Fine-tuning LLMs over Biomedical Ontologies for Causal Inference
3
AGI-KG: A Knowledge Graph Framework to Track LLM "Understanding" vs. Memorization GitHub ↗
4
Characterization of Potential Therapeutic Targets for Intellectual Disability-Related Genes Using Molecular Docking and Dynamic Simulation
5
Computational Investigation of the Epigenetic Regulation of HKT Genes in Complex Wheat Varieties
6
Evaluating the Effect of Co-Exposure of Microplastics and Pesticides on Zebrafish Gut Microbiome Using Picrust2
7
Discriminative Deep Intelligent Precision Sprayer / Laser Destroyer for Weeds and Crops
8
Computational Investigation of Resveratrol's Therapeutic Potential in Type 2 Diabetes
9
Comprehensive Improvements in Agri-Informatics Semantics
Awards
Full PhD Scholarship — HEC Pakistan & CSC China (2008–2012)
Competitive dual-government scholarship for doctoral studies at Harbin Engineering University, one of China's premier research institutions (ranked 201–250 in Asia).
TWAS-UPM Postdoctoral Fellowship — Universiti Putra Malaysia (2016)
Awarded by TWAS (The World Academy of Sciences) in partnership with UPM for research on Next-Generation Sequence Alignment of biological sequencing data in Hadoop, supervised by Assoc. Prof. Dr. Lilly Suriani Affendy.
Postdoctoral Research Invitation — Catholic University of Daegu, South Korea (2014)
Personally invited by Prof. Dr. Yeon Soo Lee (Dept. of Biomedical Engineering) for collaborative Anti-Malaria bioinformatics research achieving 93% detection accuracy — surpassing all existing Malaria prediction algorithms, in support of 8 UN Millennium Development Goals.
Plenary / Keynote Speaker — International Conferences
Delivered plenary speeches at the 2017 EMN Meeting on Biomedical Engineering (The Hong Kong Polytechnic University) and IEEE ICCSNT International Conference, Harbin Normal University (December 2011). Chaired sessions at IEEE ICCSIT 2011 and IEEE ICCSNT 2011.
Anthropic Claude — Top 1000 Scientists in Agri-Environment Domain (Global)
Recognised by Anthropic Claude among the top 1000 scientists worldwide in the Agriculture & Environment domain — a distinction reflecting the international impact of Dr. Ishaq's research contributions at the intersection of AI, agri-informatics, and environmental bioinformatics.
Invited Scholar — Reasoning Web Summer School (RW 2023), OsloMet, Norway
Accepted and invited to the prestigious Reasoning Web Summer School 2023 (21–24 September 2023), co-organised by OsloMet – Oslo Metropolitan University, University of Oslo, and SINTEF AS under Declarative AI 2023. Registration fee waived in full by the organising committee, with a travel & accommodation contribution awarded. Invited by Prof. Ahmet Soylu, Dept. of Computer Science, OsloMet.
Peer Reviewer — Leading International Journals
Oxford Journal of Bioinformatics · Elsevier Journal of Computational Biology and Chemistry · ASME ICCTD · Springer Journal of Ambient Intelligence and Humanized Computing · IEEE Access
Catch me at
Mailing Address
Contact & Profiles
University of Agriculture, Peshawar 25130
Khyber Pakhtunkhwa, Pakistan