Research Areas

  • Microbial Genomics & Bioinformatics
  • Systems & Network Biology
  • Whole Genome Sequencing, Assembly and Annoation
  • Genomic Epidemiology and Antimicrobial Resistance
  • Pangenome-Reverse Vaccinology (Pan-RV)

Microbial Genomics & Bioinformatics

We are microbial- genomics and bioinformatics research (MGB) group interested in genomic epidemiology and comparative genomics to study the evolution and transmission of bacterial pathogens. We are particularly interested in the regional crisis of growing antimicrobial resistance and dissemination of multidrug resistant pathogens, also like to develop of tools, databases for pathogen genome analysis, prospective surveillance and tracking of emerging pathogens in the environment and clinical settings using whole genome sequencing and bioinformatics analysis. We are using comparative pangenome analysis and phylogenetics approaches to study the genome evolution, transmission, and resistance patterns in bacterial pathogens such as staphylococcus, pseudomonas, Klebsiella and Acinetobacter etc. We have developed high-throughput screening Tools/Software capable to analyses of microbial pangenome (big data) and therapeutic (vaccine/drugs) candidates’ identification, these include:

1. VacSol : 2. PanRV : 3.Vacsol-ML(ESKAPE) :4. AbAMPdb: 5. rtAMPs: 

In the Structural Bioinformatics domain, we are employing the Homology structural modeling, Ab-initio modeling, Protein-protein interaction studies, Protein-Ligand interaction studies, Protein-nucleotide studies, Pharmacophore modeling, structural visualization of protein by using different tools

Systems & Network Biology

We are also interested in system-level analysis and tools for studying the complex biological systems and processes such as diseases and pathways, Together with collaborators we are constructing and analyses the Biological Regulatory Networks (BRNs) and Models through formal modeling approaches. Through these model simulation we try to understand the behavior of an entire biological system (holistic) and relationships between its components (individual entities) and identification markers (states/paths/trajectories) involved in genomic variation and their association with processes/ diseases, identification of therapeutic targets in these pathways. 

Research Grants: (PI & Co-PI/Partner)

02/23 – 2025
Study on Accurate Early Warning Methods for Dangerous Strains of Global Emerging Infectious Diseases. ANSO Collaborative Grant (China, Pakistan, France & Brazil) worth ±1.3 Million RMB
01/22 – 2024
An artificial intelligence framework for data-driven analysis of microbial pangenomes. PI- HEC NRPU.
00/21 – 2024
Prediction, Designing and Experimental Validation of Potential Vaccine Candidates for Respiratory Syncytial Virus. Punjab Government, Co- PI.
10/19 – 2021
Assessment of indigenous Lactobacillus spp. for cholesterol reduction; a step towards probiotic designer foods” Co-PI HEC NRPU
06/18 – 06/21
Genome-wide meta-analysis of cDNA datasets and molecular validation of genetic variants in type II diabetes mellitus. Co- PI HEC- NRPU 2017.
09/19 – 12/22
Partner from Pakistan: TWIW: Two Weeks in the World- Capturing a snapshot of the world’s human clinical bacterial pathogens A research project exploring antimicrobial resistance in bacteria, from diagnostic samples collected all over the world. An initiative of the Technical University of Denmark (DTU).
04/17 – 12/19
Analyzing the Tumor Educated Platelets as Potential Biomarker in Molecular Diagnosis of Liver Cancer: A Minimally Invasive Approach alternative to Tissue Biopsy. Co-PI HEC NRPU 08/16 – 08/19
Pangenome analysis of multidrug-resistant Staphylococcus aureus strains to get insights into the mechanism of pathogenicity and to identify new therapeutic interventions to replace the current antimicrobial drugs. PI –HEC-NRPU.
08/15 – 08/19
Analysis of gene variants and investigation of novel prognostic host factor targets to predict treatment response to peg- IFN/RBV therapy in HCV infected Pakistani patients and, qualitative and quantitative modelling of pathways associated with HCV infection and the host immune response. PI – HEC- NRPU.
08/15 – 02/19
Formal Analysis of the Impact of Feeding on Hepatocyte Circadian Oscillators. Co-PI – HEC-NRPU 2015.

2022 – (waiting)
Reverse Linkage Programmes: Diagnostics and vaccine designing” COMSTECH- IsDB cooperation. “Accepted and awaited” 2022

Integrative Biology Laboratory, Atta-ur-Rahman School of Applied Biosciences (ASAB) 
1st floor, D Block, National University of Sciences and Technology (NUST), H-12 Islamabad.
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