Ehsan Ullah

PhD Alumni
Department of Computer Science
Tufts University
Medford, MA

Email: ehsan dot ullah at alumni dot tufts dot edu

I did my Ph.D. at Tufts with Prof. Soha Hassoun and Prof. Kyongbum Lee. I was working at University of Engineering and Technology Lahore before coming to Boston. Currently I am a post doctoral researcher at Qatar Computing Research Institute.

My thesis focuses on three cellular pathway identification problems within metabolic networks. The novelty of this thesis is in utilizing graph-based methods to enumerate elementary flux modes and to efficiently explore the pathway design space. Overall, the thesis advances the state-of-the-art techniques for metabolic pathway analysis.

Currently I am working on genome-wide association study for type 2 diabetes focusing Arab population.

• E. Ullah, S. Aeron, S. Hassoun, “gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal”, IEEE/ACM Transactions on Computational Biology and Bioinformatics 99, 2015.
• E. Ullah, M. Walker, K. Lee, S. Hassoun, “PreProPath Algorithm: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks”, IEEE/ACM Transactions on Computational Biology and Bioinformatics 99, 2015.
• E. Ullah, M. Shahzad, R. Rawi, M. Dehbi, K. Suhre, M. Selim, D. Mook and H. Bensmail. “Integrative 1H-NMR-based Metabolomic Profiling to Identify Type-2 Diabetes Biomarkers: An Application to a Population of Qatar”, METABOLOMICS 5:1, 2015.
• GV. Sridharan, E. Ullah, S. Hassoun, K. Lee. “Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity”, BMC Systems Biology vol 9:5, 2015.
• E. Ullah, C. Hopkins, S. Aeron, S. Hassoun, “Decomposing biochemical networks into elementary flux modes using graph traversal”, International Conference on Bioinformatics, Computational Biology and Biomedical Informatics 2013, pp. 211-218.
• M. Yousofshahi, E. Ullah, R. Stern, S. Hassoun, “MC3: a steady-state model and constraint consistency checker for biochemical networks”, BMC Systems Biology vol 7:129, 2013.
• E. Ullah, K. Lee, S. Hassoun, “A Weighted Graph Algorithm for Identifying Dominant-Edge Metabolic Pathways”, International Conference on Computer-Aided Design (ICCAD), pp. 144-150, November, 2009.
• E. Ullah, K. Lee, S. Hassoun, “An Algorithm for Identifying Dominant-Edge Metabolic Pathways”, Proceedings of International Workshop of Logic Synthesis 2009.
• E. Ullah, Z.A. Khan, S. Awan, Abdurehman, “Platform Independent Implementation of Java Telephony API (JTAPI) for data calls”, ICOSST 2007 17-18 December 2007. IEEE Catalog Number : 13451 Paper ID: 07-118.

• Enabling Selection in Directed Evolution of Enzymes Via Cellular Engineering @ AIChE 2015.
• GPU Programming for Bioinformatics Applications @ ACM BCB 2013.
• Computing Elementary Flux Modes Using a Graph-Based Approach @ AIChE 2013.
• Using Hierarchical Modularity to Identify Substrate Cycles in Metabolic Networks @ AIChE 2013.
• MC3: A Tool for Model and Constraint Consistency Checking of Stoichiometric Biochemical Network Models @ AIChE 2012.
• Predictably Profitable Paths in Metabolic Networks @ IWBDA 2010.
• Dominant-Edge Pathway: A Weighted Graph Algorithm for Identifying Dominant Metabolic Pathways @ IWBDA 2009.

• Department of Computer Science, Tufts