Siavash Mirarab (Mir arabbaygi)

[Siavash Mirarab]

I am a second year PhD student working under the supervision of Prof. Tandy Warnow. My PhD research has been supported through NSERC PGS award and Howard Hughes Medical Institute international student fellowship.

I work in the area of computational biology, more specifically large scale phylogenetics. My research spans many topics, in particular metagenomic analysis using phylogenetic placement, large scale multiple sequence alignment, and gene tree species tree discordance.

Software:

FastSP: Fast and Memory efficient software for comparison of multiple sequence alignments (computes SP-FN and TC scores)
SEPP: Software for fast phylogenttics placement based on SATe decomposition
I also work on and contribute code to SATé

Papers: (see here for my citations)

  1. Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient , BMC bioinformatics, available online: 2013.
  2. Bayzid M. S., Mirarab, S., Warnow, T. Inferring optimal species trees under gene duplication and loss, Proceedings of Pacific Symposium on Biocomputing, available online: 2013.
  3. Nguyen, N., Mirarab, S., Warnow, T. MRL and SuperFine+MRL: new supertree methods, Algorithms for Molecular Biology: vol. 7, no. 1, 3+, doi:10.1186/1748-7188-7-3: 2012.
  4. S. Mirarab, N. Nguyen, T. Warnow, SEPP: SATe-Enabled Phylogenetic Placement. Proceedings of Pacific Symposium on Biocomputing, available on-line: 2012.
  5. Mirarab, S., Warnow, T. FastSP: Linear time calculation of alignment accuracy, Bioinformatics, doi:10.1093/bioinformatics/btr553: 2011
  6. Mirarab, S., Akhlaghi, S., and Tahvildari, L. Size-constrained Test Case Selection Using Multi-Criteria Optimization, IEEE Transactions on Software Engineering (TSE), doi:10.1109/TSE.2011.56: 2011.
  7. Do, H., Mirarab, S., Tahvildari, L., and Rothermel, G. The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments, IEEE Transaction on Software Engineering (TSE), doi:10.1109/TSE.2010.58: 2010.
  8. Do, H., Mirarab, S., Tahvildari, L., Rothermel, G. An Empirical Study of the Effect of Time Constraints on the Cost-beneffits of Regression Testing. ACM Int. Symp. on Foundations of Software Engineering (FSE), doi: 10.1145/1453101.1453113: 2008.
  9. Mirarab, S., Ganjali, A., Tahvildari, L., Shimin Li, Weining Liu, and Morrissey, M. A Requirement-based Software Testing Framework: An Industrial Practice. IEEE Int. Conf. Software Maintenance (ICSM): 2008.
  10. Mirarab, S., Tahvildari, L. An Empirical Study on Bayesian Network-Based Approach for Test Case Prioritization. Int. Conf. on Soft. Testing, Veriffication, and Validation (ICST): 2008.
  11. Amoui, M., Salehie, M., Mirarab, S., and Tahvildari, L. Adaptive Action Selection in Autonomic Software Using Reinforcement Learning. Int. Conf. on Autonomic and Autonomous Systems (ICAS): 2008.
  12. Mirarab, S., Hassouna, A., and Tahvildari, L. Using Bayesian Belief Networks to Predict Change Propagation in Software Systems. IEEE Int. Conf. on Program Comprehension (ICPC): 2007.
  13. Mirarab, S., Tahvildari, L. A Prioritization Approach for Software Test Cases Based on Bayesian Networks. Int. Conf. on Fundamental Approaches to Software Engineering (FASE), Springer Lecture Notes on Comput. Sci., 4422: 2007.
  14. Amoui, M., Mirarab, S., Ansari, S., Lucas, C. A Genetic Algorithm Approach to Design Evolution using Design Pattern Transformation, Int. Journal of Information Technology and Intelligent Computing. vol 1, no. 2: 2006.

And here is my (hopefully updated) CV: mirarab.pdf

Siavash Mir arabbaygi
Dept of Computer Science
University of Texas at Austin
1616 Guadalupe, Suite 2.408
Austin, TX  78701
smirarab at cs dot utexas dot edu