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Dr. Jamil Ahmad
Assistant Professor
Department of Computational Sciences

RCMS
National University of Sciences and Technology (NUST)
Research Center of Modeling and Simulation(RCMS), Academic-I Building, NUST Campus, H-12, Islamabad, Pakistan
Tel : +92-51-9085-5726​
Email : jamil.ahmad(at)rcms.nust.edu.pk

Specialization
Model Checking & Bioinformatics

Education
PhD (Ecole Centrale de Nantes,  France, 2009)

Jamil Ahmad received his PhD in Applied Computer Science from Ecole Centrale de Nantes (ECN), France.  He has been working as assistant professor at RCMS NUST since February 2010. His research interests include model checking, hybrid systems and modeling and verification of complex biological regulatory networks.​

​Bioinformatics:

Biological regulatory networks, Neural networks,Model checking

Software Engineering:

Use of formal methods in the design of complex software systems
Modeling and Verification of embedded, reactive, real-time computer system

  • Amnah Siddiqa, Elisa Cirillo, Samar H.K. Tareen, Amjad Ali, Martina Kutmon, Lars Eijssen, Jamil Ahmad, Chris T. Evelo, Susan L. Coort “Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways”, Genomics, 2017
  • Zurah Bibi, Jamil Ahmad, Amnah Siddiqa, Rehan Zafar Paracha, Tariq Saeed, Amjad Ali, Hussnain Ahmed Janjua, Shakir Ullah, Emna Ben Abdallah, Olivier Roux, “Formal modeling of mTOR associated biological regulatory network reveals novel therapeutic strategy for the treatment of cancer”,  Frontiers in Physiology, Vol. 4, 2017
  • Muhammad Rizwan,  Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen,  Muhammad Ahsan and  Amjad Al, “  VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology”, BMC Bioinformatics, 18:106, 2017
  • Samra Khalid, Rumeza Hanif, Samar H.K. Tareen, Amnah Siddiqa, Zurah Bibi, Jamil Ahmad , “Formal modeling and analysis of ER- α associated Biological Regulatory Network in breast cancer’’,  Peerj,  Vol. 4, October 20, 2016
  • Afreenish Hassan, Anam Naz, Ayesha Obaid, Rehan Zafar Paracha, Kanwal Naz, Faryal Mehwish Awan, Syed Aun Muhmmad, Hussnain Ahmed Janjua, Jamil Ahmad, Amjad Ali, ‘’ Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets’’, BMC Genomics, Vol 17, September 15, 2016
  • Muhammad Tariq Saeed , Jamil Ahmad, Shahzina Kanwal , Andreana N. Holowatyj , Iftikhar A. Sheikh , Rehan Zafar Paracha , Aamir Shafi , Amnah Siddiqa , Zurah Bibi , Mukaram Khan1 and Amjad Ali, ‘’Formal modeling and analysis of the hexosamine biosynthetic pathway: Role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression’’, ,  Peerj,  Vol. 4, Sptember 27, 2016
  • Zia-ur-Rehman Farooqi, Samar H.K. Tareen, Jamil Ahmad and Najam-us-Sahar S. Zaidi, ‘’ Logical Analysis of Regulation of Interleukin-12 Expression Pathway Regulation During HCV Infection’’, Protein & Peptide Letters, vol 23, 2016
  • Syed Fazal Jalil, Maria Arshad, Attya Bhatti, Jamil Ahmad, Fazal Akbar, Peter John (2015). “Rheumatoid Arthritis: What have we learned about the causes? ”, PJPS, Vol. 29,  March 2016
  • Amnah Siddiqa, Jamil Ahmad, Amjad Ali, Rehan Zafar Paracha, Zurah Bibi, Babar Aslam, “Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase”, Computational Biology and Chemistry, Volume 61, April 2016, Pages 210-220, ISSN 1476-9271, http://dx.doi.org/10.1016/j.compbiolchem.2016.01.009.
  • Zurah Bibi, Jamil Ahmad*, Amjad Ali, Amnah Siddiqa, Shaheen Shahzad, Samar HK Tareen, Hussnain Ahmed Janjua and Shah Khusro (2015)"On the modeling and analysis of the biological regulatory network of NF- κ B activation in HIV-1 infection", Complex Adaptive Systems Modeling 2016, Vol 4(1), doi:10.1186/s40294-015-0013-4 
  • Misbah Razzaq, Jamil Ahmad*  (2015) Petri Net and Probabilistic Model Checking Based Approach for the Modelling, Simulation and Verification of Internet Worm Propagation. PLoS ONE 10(12): e0145690. doi: 10.1371/journal.pone.0145690
  • Awan FM, Naz A, Obaid A, Ali A, Ahmad J, et al. (2015) Identification of Circulating Biomarker Candidates for Hepatocellular Carcinoma (HCC): An Integrated Prioritization Approach. PLoS ONE 10(9): e0138913. doi: 10.1371/journal.pone.0138913
  • Tareen SHK, Jamil Ahmad  and Roux O (2015) Parametric linear hybrid automata for complex environmental systems modeling. Front. Environ. Sci. 3:47. doi: 10.3389/fenvs.2015.00047
  • Umar Khan, Jamil Ahmad, Tariq Saeed, Sikandar Hayat Mirza, “Real time    Modeling of Interlocking Control System of Rawalpindi Cantt Train Yard”, IEEE FIT 2015
  • Babar Aslam , Jamil Ahmad*, Amjad Ali , Rehan Zafar Paracha , Samar H K Tareen, Shah Khusro, Taseer Ahmad, Syed Aun Muhammad, Umar Niazi, Vasco Azevedo*, “Structural modeling and analysis of denguemediated inhibition of interferon signaling pathway” Genet. Mol. Res. 14 (2),2015, pp. 4215 - 4237
  • Tareen SHK, Jamil Ahmad* (2015) “Modelling and Analysis of the Feeding Regimen Induced Entrainment of Hepatocyte Circadian Oscillators Using Petri Nets”. PLoS ONE 10(3): e0117519. doi:10.1371/journal.pone.0117519
  • Ayesha Obaid, Jamil Ahmad, Anam Naz, Faryal Mehwish Awan, Rehan Zafar Paracha, Samar Hayat Tareen, Sadia Anjum, Abida Raza, Jan Baumbach, Amjad Ali, “Modeling and analysis of innate immune responses induced by the host cells against hepatitis C virus infection” , Integr. Biol., 2015, DOI: 10.1039/C4IB00285G
  • Anam Naz, Faryal Mehwish Awan, Ayesha Obaid, Syed Aun Muhammad, Rehan Zafar Paracha, Jamil Ahmad, Amjad Ali, " Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse vaccinology based approach, int. journal Infection, Genetics and Evolution ", Volume 32, June 2015, Pages 280-291, ISSN 1567-1348, http://dx.doi.org/10.1016/j.meegid.2015.03.027.
  • Farzana Bibi and Jamil Ahmad, “Hybrid modeling of p53 and Akt associated gene regulatory network”,  Emerging Technologies (ICET 2014), IEEE, pp. 48 – 53, DOI: 10.1109/ICET.2014.7021015
  • Babar Aslam, Jamil Ahmad, Amjad Ali, Rehan Zafar Paracha, Samar Hayat Khan Tareen, Umar Niazi, Tariq Saeed, On the Modelling and Analysis of the Regulatory Network ofDengue Virus Pathogenesis and Clearance, Computational Biology and Chemistry (2014), http://dx.doi.org/10.1016/j.compbiolchem.2014.10.003
  • Rehan Zafer, Jamil Ahmad , Amjad Ali, Hussain R, Niazi U, et al. (2014) Formal Modelling of Toll like Receptor 4 and JAK/STAT Signalling Pathways: Insight into the Roles of SOCS-1, Interferon-β and Proinflammatory Cytokines in Sepsis. PLoS ONE 9(9): e108466. doi:10.1371/journal.pone.0108466
  • Kashif Asgher, Jamil Ahmad, Javaria Ashraf, Amjad Ali, Hussnain Ahmed Janjua, S.Murad “Qualitative Modeling and Analysis of the Indoleamine 2,3-dioxygenase Regulatory Network in Homeostasis and Disease”, IEEE ICNC-FSKD 2014,  Xiamen, China
  • Rehan Zafar, Amjad Ali, Jamil Ahmad,  Riaz Hussain Shaikh, Umar Niazi, Syed Aun Muhammad  “Structural evaluation of BTK and PKC<delta> mediated phosphorylation of MAL at positions Tyr86 and Tyr106”, accepted, Computational Biology and Chemistry, ISSN: 1476-9271, 2014
  • Syed Aun Muhammad, Amjad Ali, Tariq Ismail, Rehan Zafar, Umair Ilyas, Jamil Ahmad, "In-silico study of anti-carcinogenic Lysyl Oxidase-Like2 inhibitors",  2014, http://dx.doi.org/10.1016/j.compbiolchem.2014.03.002
  • Tariq Saeed, Jamil Ahmad, A Parallel  Approach for Accelerated Parameter Identification of Gene Regulatory Networks, International Work-Conference on Bioinformatics and Biomedical Engineering-IWBBIO 2014 . 7-9 April, 2014. Granada (SPAIN)
  • Muhammad Abdul Basit-Ur-Rahim, Fahim Arif, Jamil Ahmad, Formal Verification of Sequence Diagram using DiVinE, IEEE ICCSA 2014, Tunisia
  • Abdul Basit,Arif Fahim, Jamil ahmad, verification of UML using DiVinE tool, IEEE Conference on Computer Science and Information Technology (CSIT), 2013,  Jordan
  • Azmat Ali, Jamil Ahmad, Identification of crosstalk in Insulin pathway using Pathway Logic, 2013 IEEE 9th International conference on Emerging Technologies (ICET), Pakistan 
  • Sohail, Ammar, Afzal, Muhammad Tanvir, Ahmad, Jamil, Discovery of medical experts, 2013 IEEE 9th International conference on Emerging Technologies (ICET), Pakistan
  • ArsalanGohar, Jamil Ahmad, Ayesha Gohar, “NERVE CONDUCTION USING KOCH MODEL”, 2nd International Symposium on Frontiers of Computational Sciences (ISFCS2012), Islamabad,
  • Ayesha Gohar, Arsalan Gohar, Jamil Ahmad, HYBRID MODELING AND BIOLOGICAL NEURAL NETWORK ANALYSIS USING NON-DETERMINISTIC DELAYS 2nd International Symposium on Frontiers of Computational Sciences (ISFCS2012), Islamabad, Pakistan
  • Syed Sajjad Sattar, Saqib Khan, Jamil Ahmad, Baber Imran,
    ANALYSIS OF POWER PRODUCTION FROM SOLID WASTE USING INCINERATION TECHNOLOGY IN PAKISTAN 2nd International Symposium on Frontiers of Computational Sciences (ISFCS2012), Islamabad, Pakistan
  • Jamil Ahmad, Ayesha Gohar, Saqib Khan, Arsalan Gohar, Syed Sajjad Sattar, 
    LINEAR HYBRID MODELING OF SYNAPTIC PLASTICITY 2nd International Symposium on Frontiers of Computational Sciences (ISFCS2012), Islamabad, Pakistan
  • Humaira Gul, Jamil Ahmad,Fareed Gul and Mian Ilyas, "Modeling and Formal Verification of Inverted Pendulum Based Two-Wheeled Transportation Vehicle", International conference: The Society of Instrument and Control Engineers (SICE), Japan, 2012.
  • Ahmad J,Niazi U, Mansoor S, Siddique U, Bibby J (2012) Formal Modeling Analysis of the MAL-Associated Biological Regulatory Network;Insight into Cerabral Malaria. PLoS ONE 7(3): e33532 doi;10.1371/journal.pone0033532
  • Mahum Riaz, Sayeda Sadaf, Beena Gul,  Jamil Ahmad “Boolean Modeling of the Half Centre Rhythm Generator Including Fast Persistent Inward Currents”, Accepted in iCBBE , 2012
  • Shah Khusro, Jamil Ahmad, and Azhar Rauf,  “User Modeling: From Early Shell Systems to the Desktop and Smartphones”, PUTAJ Sciences, ISSN 2219-2468, vol. 18-2011, p. 293-30, 2011
  • Usman Rauf, Umair Siddique Jamil Ahmad and  Umar Niazi, “Formal Modeling and Analysis of Biological Regulatory Networks Using Spin”, 2011 IEEE BioInformatics and BioMedicine, Atlanta, Georgia, ISBN 978-0-7695-4574-5, 304-308, 2011
  • Zurah, Jamil Ahmad and Umar Niazi ,"Dynamic Modeling of the Regulatory Network of NF-kB Activation in HIV-1 ”, International Conference on Computer Networks and Information Technology 2011 (ICCNIT).  pages 47-51. 2011
  • Jamil Ahmad , Javeria Ashraf and Umar Niazi,“Qualitative Modeling & Analysis of Regulatory Network of Indoleamine 2, 3-dioxygenase on Tumour Immunce Escape”, International Conference on Computer Networks and Information Technology 2011 (ICCNIT).  pages 41-45. 2011
  • Jamil Ahmad , Uzma and Umar Niazi. “ Discrete Modelling of P53 feedback loop”, IEEE GrC 2011, ISBN 978-1-4577-0370-6, p. 37-41, 2011
  • Jamil Ahmad and Olivier Roux, Invariance Kernel of Biological Regulatory Networks,   IJDBM, 2010, Vol. 4, No. 5 pp. 553-570
  • Jamil Ahmad, Jeremie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, and Christine Sinoque. Temporal constraints of a gene regulatory network: refining a qualitative Simulation. BioSystem, 2009, 98 (2009) 149-159, Dec 2009
  • J. Ahmad, O. Roux, G. Bernot, J.-P. Comet and A. Richard. Analysing formal models of genetic regulatory networks with delays: Applications to lambda phage and T-cell activation systems. Int. J. Bioinformatics Research and Applications, 4(3):240-262, 2008
  • J. Ahmad, G. Bernot, J.-P. Comet, D. Lime and O. Roux. Hybrid modelling and dynamical analysis of gene regulatory networks with delays. ComPlexUs, 3(4):231-251, 2007
  • Jamil Ahmad and Olivier Roux, Invariance Kernel of Biological Regulatory Networks, BIBM '08: Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine,135-140, IEEE Computer Society
  • Jamil Ahmad, Adrien Richard, Gilles Bernot, Jean-Paul Comet, and Olivier Roux. Delays in Biological Regulatory Networks (BRN). In International Workshop on Bioinformatics Research and Applications, (IWBRA'06), volume 3992 of Lecture Notes in Computer Science, pages 887-894 , Reading, UK, May 2006
  • Jamil Ahmad, Temporal Modeling and Verification of Biological Regulatory Networks (BRN), MOVEP 2006, France
  • ​PG Courses

  •  Model Checking
  •  Petri Nets, Graph Theory
  •  Computational System Biology
  •  Artificial Intelligence
  • UG Courses

  •  Digital Logic and Design
  •  Software Engineering
  •  Computer Graphics
  •  Compiler Construction
  • During my PhD, I worked on the development of the software GenoTech. The manual modeling of a Biological Regulatory Network (BRN) is a tedious job that takes hours even for a small biological regulatory network and which may result in an incorrect model.  GenoTech tool implements the kinetic logic formalism of R. Thomas to facilitate the qualitative modeling of genes/biological regulatory networks (GRN/BRN).  GenoTech has been developed in JAVA language with the following features:
     
  •  Graphical User Interface for the fast creation of Biological Regulatory Networks as a directed graph and for defining logical parameters
  •  Transforming a BRN into its discrete model
  •  Searching of the discrete graph for various behaviors (stable states and cycles)
  •  Transforming a BRN to hybrid model in HyTech format
  •  Saving the discrete model in dot format