PSOMF: An algorithm for pattern discovery using PSO
with Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, Javad Mohammadzadeh, Abbas Nowzari-Dalini, Bahram Goliaei Proceedings of the Third IAPR International Conferences on Pattern Recognition in Bioinformatics, Melbourne
Australia, 61-72, (2008).
HubAlign: A software for the alignment of protein-protein interaction networks that is based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information.
NETAL: a software for the global alignment of protein-protein interaction networks. It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment. The running time of NETAL is much less than other available methods.
ConvexAlign: The program ConvexAlign finds a global alignment between multiple input PPI networks by convex optimization of a scoring function composed of sequence similarity, topological score, and interaction conservation score.
Research at university of Chicago's hospital (2015-2016) Project: Using different pre-designed tools such as WGCNA and Affymetrix Expression Console for analysis of RNA expression data of colon cancer patients
with Prof. Nikolai Khodarev , and Dr. Natalia Maltsev
Research at Computational Institute at university of Chicago (2012-2014) Project: Applying a Gaussian model for reconstructing tissue specific network, Using R packages for analysis of gene expression data of Asthma patients
with Prof. Steve White, and Dr. Natalia Maltsev
Research at Institute of Biochemistry and Biophysics (IBB), University of Tehran (2010-2011)
Project: Developing a computational method for alignment of protein-protein Interaction networks
with Prof. Bahram Goliaei
Reviewer for IEEE/ACM Transactions on Computational Biology and Bioinformatics
Reviewer for BMC Bioinformatics
Reviewer for RECOMB conference 2016
Reviewer for Engineering in Medicine and Biology Conference
I like running. Sometimes, I run half marathon ;)
I enjoy backpacking and mountain climbing. I've done off-trail backpacking in Alaska and stood on top of Damavand, the tallest mountain of Iran (about 18,400 ft).