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Dr.Jamil
Ahmad |
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Date
and place of birth :
1973 in Saidu Sharif, Pakistan |
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My
current research focuses on the hybrid modeling and analysis of biological
regulatory networks (BRN) and neuron action potential. The parameters in our
models are the activation and inhibition time delays. For the analysis of
hybrid models, I use the model checking tool HyTech and PHAVer to synthesize
parametric constraints characterizing cyclic or non-cyclic behaviors. For the
stability analysis of the cyclic behavior, I use polyhedral libraries,
PolyLib and Barvinok, to compute the volume and diameter of the invariance
kernel (cyclic regions in the state space) of BRN. The featuring measures
volume and diameters are expressed in terms of delay parameters, and which
predict the stability and emptiness of the invariance kernel. I also work on
the modeling and reachability analysis of neuron action potential, synaptic
plasticity and Hebbian learning. |
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Post-Doc (Bioinformatics, 2010), University of Konstanz
Germany |
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1.
Ahmad J,Niazi U, Mansoor S, Siddique U, Bibby J (2012) Formal Modeling and Analysis of the MAL-Associated Biological Regulatory Network; Insight into Cerabral Malaria. PLoS ONE 7(3): e33532 doi;10.1371/journal.pone0033532 2. 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 3. 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 4. 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 5.
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 6.
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 7.
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 8. Jamil Ahmad and Olivier Roux, Invariance Kernel of Biological Regulatory Networks, IJDBM, 2010,
Vol. 4, No. 5 pp. 553-570 9.
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 10. 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 11. 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 12. 10.
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 13. 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 14. Jamil Ahmad, Temporal Modeling and
Verification of Biological Regulatory Networks (BRN), MOVEP 2006, France |
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PhD Thesis
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International Conference on Computer Networks and Information Technology,
July 11 - 13 2011, Bara Gali Campus, KPK, Pakistan • Symposium on
Emerging Massively Parallel Computer Architecture and Applications in
scientific
Simulations, 06 April 2011, RCMS NUST
Islamabad
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Seminar on “Bioinformatics and the Pakistani Industries”, November 2010, IIU
Islamabad •
International Symposium on Frontiers fo Computational Sciences 7-8 June 2010,
Islamabad Pakistan •
Toward Systems Biology, 8-10 October 2007,Université Joseph Fourier -
Grenoble - France Genopole®, Tower Évry2, 10th floor, 523
Terrasses de l'Agora, 91000 Évry, France (near Paris). • International
Workshop on Bioinformatics Research and Applications (IWBRA 2006, IWBRA 2007) |
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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: graph and for defining logical parameters |
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Assistant
Professor of Computer Science (7th Feb 2010 to date) Lecturer
in Computer Science (1999 to 2004), NUST at College of Aeronautical
Engineering Risalpur campus Professional Activities • Member,
Program Committee, International Conference on Computer Networks and Information Technology, July 11 - 13 2011 •
Member, Board of Studies of Computer Science, University of Peshawar •
Member, Pakistan France Alumni Network (PFAN), Embassy of France in Islamabad. |
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Model
Checking, Computational Biology, Artificial Intelligence, Software Engineering,
Computer languages (Java, C, C++, Assembly), Digital logic, Compiler
Construction and Computer Graphics |
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HyTech:
The HYbrid TECHnology Tool SpaceEx:
Reachability and safety verification of continuous and hybrid systems |
