Qualitative modeling and analysis of the indoleamine 2, 3-dioxygenase regulatory network in homeostasis and disease. - Kashif Asghar; Jamil Ahmad; Javaria Ashraf; Amjad Ali 001; Hussnain Ahmed Janjua; Sheeba Murad (FSKD, 2014)

On the modelling and analysis of the regulatory network of dengue virus pathogenesis and clearance. - Babar Aslam; Jamil Ahmad; Amjad Ali 001; Rehan Zafar Paracha; Samar Hayat Khan Tareen; Umar Khan Niazi; Tariq Saeed (Comput. Biol. Chem., 2014)

Insilico study of anti-carcinogenic lysyl oxidase-like 2 inhibitors. - Syed Aun Muhammad; Amjad Ali 001; Tariq Ismail; Rehan Zafar Paracha; Umair Ilyas; Jamil Ahmad (Comput. Biol. Chem., 2014)

Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr106. - Rehan Zafar Paracha; Amjad Ali 001; Jamil Ahmad; Riaz Hussain; Umar Khan Niazi; Syed Aun Muhammad (Comput. Biol. Chem., 2014)

Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase. - Amnah Siddiqa; Jamil Ahmad; Amjad Ali 001; Rehan Zafar Paracha; Zurah Bibi; Babar Aslam (Comput. Biol. Chem., 2016)

On the modeling and analysis of the biological regulatory network of NF- ({ kappa } )B activation in HIV-1 infection. - Zurah Bibi; Jamil Ahmad; Amjad Ali 001; Amnah Siddiqa; Shaheen Shahzad; Samar H. K. Tareen; Hussnain Ahmed Janjua; Shah Khusro (Complex Adapt. Syst. Model., 2016)

VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. - Muhammad Rizwan; Anam Naz; Jamil Ahmad; Kanwal Naz; Ayesha Obaid; Tamsila Parveen; Muhammad Ahsan; Amjad Ali 001 (BMC Bioinform., 2017)

Formal Modeling of the Key Determinants of Hepatitis C Virus (HCV) Induced Adaptive Immune Response Network: An Integrative Approach to Map the Cellular and Cytokine-Mediated Host Immune Regulations. - Ayesha Obaid; Anam Naz; Shifa Tariq Ashraf; Faryal Mehwish Awan; Aqsa Ikram; Muhammad Tariq Saeed; Abida Raza; Jamil Ahmad; Amjad Ali 001 (ICCSA (4), 2018)

On the Use of Betweenness Centrality for Selection of Plausible Trajectories in Qualitative Biological Regulatory Networks. - Muhammad Tariq Saeed; Jamil Ahmad; Amjad Ali 001 (IWBBIO (1), 2018)

Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. - Muhammad Tariq Saeed; Jamil Ahmad; Jan Baumbach; Josch Pauling; Aamir Shafi; Rehan Zafar Paracha; Asad Hayat; Amjad Ali 001 (BMC Syst. Biol., 2018)

Analyzing the Behavior of Neuronal Pathways in Alzheimer's Disease Using Petri Net Modeling Approach. - Javaria Ashraf; Jamil Ahmad; Amjad Ali 001; Zaheer-ul-Haq (Frontiers Neuroinformatics, 2018)

Computational modeling and analysis of the impacts of sleep deprivation on glucose stimulated insulin secretion. - Hufsah Ashraf; Jamil Ahmad; Azka Hassan; Amjad Ali 001 (Biosyst., 2019)

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. - Kanwal Naz; Anam Naz; Shifa Tariq Ashraf; Muhammad Rizwan; Jamil Ahmad; Jan Baumbach; Amjad Ali 001 (BMC Bioinform., 2019)

Structural and functional annotation of PR/SET Domain (PRDM) protein family: In-silico study elaborating role of PRDM12 mutation in congenital insensitivity to pain. - Sarmad Mehmood; Rubina Dad; Arsalan Ahmad; Muhammad Ikram Ullah; Peter John; Amjad Ali 001; Christian A. Hubner; Aisha Mohyuddin; Muhammad Jawad Hassan (Comput. Biol. Chem., 2020)

Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach. - Asim Mehmood; Samar Naseer; Amjad Ali 001; Hina Fatimah; Shazia Rehman; Aysha Karim Kiani (Comput. Biol. Chem., 2020)

Practically Implementation of Information Loss: Sensitivity, Risk by Different Feature Selection Techniques. - Amjad Ali 001; Faiz Jillani; Rabbiah Zaheer; Ahmad Karim; Yasser Obaid Alharbi; Mohammad Salih Alsaffar; Khalid Alhamazani (IEEE Access, 2022)

Accessible interactive learning of mathematical expressions for school students with visual disabilities. - Amjad Ali 001; Shah Khusro; Tahani Jaser Alahmadi (PeerJ Comput. Sci., 2024)

SA-MEAS: Sympy-based automated mathematical equations analysis and solver. - Amjad Ali 001; Shah Khusro (SoftwareX, 2024)

AIME-solve: Accessible interactive mathematical expressions solver for optimized learning and visual empowerment. - Amjad Ali 001; Shah Khusro; Fakhre Alam; Inayat Khan; Shabbab Ali Algamdi (SoftwareX, 2025)