Siavash Mirarab

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I am a fourth year PhD student working under the supervision of Prof. Tandy Warnow and Prof. Keshav Pingali. 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 estimation of species trees from gene trees (phylogenomics), large scale multiple sequence alignment, and metagenomic analysis using phylogenetic placement.

Here is my (hopefully up-to-date) CV.

Software

See my gitub page to see all my publicly available software programs.

News

Publications (see citations at google scholar)

  1. Nam Nguyen, Siavash Mirarab, Keerthana Kumar, and Tandy Warnow. “Ultra-large alignments using ensembles of Hidden Markov Models”. Research in Computational Molecular Biology (2015): accepted.

  2. Mirarab, Siavash, Md. Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow. “Statistical binning enables an accurate coalescent-based estimation of the avian tree.” Science 346, no. 6215 (2014). doi:10.1126/science.1250463

  3. Jarvis, Erich D, Siavash Mirarab (co-first author), Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, et al. “Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds.” Science 346 , no. 6215 (2014): 1320–1331. doi:10.1126/science.1253451

  4. Wickett, Norman J., Siavash Mirarab (co-first author), Nam Nguyen, Tandy Warnow, Eric Carpenter, Naim Matasci, Saravanaraj Ayyampalayam, Michael Barker, J. Gordon Burleigh, Matthew A. Gitzendanner, Brad R. Ruhfel, Eric Wafula, Joshua P. Der, Sean W. Graham, Sarah Mathews, Michael Melkonian, Douglas E. Soltish, Pamela S. Soltish, Nicholas W. Miles, Carl J. Rothfels, Lisa Pokorny, A. Jonathan Shaw, Lisa DeGironimo, Dennis W. Stevenson, Barbara Surek, Juan Carlos Villarreal, B ́eatrice Rourev, Herv ́e Philippe, Claude W. dePamphilis, Tao Chen, Michael K. Deyholos, Regina S. Baucom, Toni M. Kutchan, Megan M. Augustin, Jun Wang, Yong Zhang, Zhijian Tian, Zhixiang Yan, Xiaolei Wu, Xiao Sun, Gane Ka-Shu Wong, and James Leebens-Mack. A phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences (PNAS), 111, no. 45 (2014): E4859–4868. doi:10.1073/pnas.1323926111.

  5. Mirarab, Siavash, Shamsuzzoha Bayzid, and Tandy Warnow. “Evaluating Summary Methods for Multi-Locus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.” Systematic Biology (2014): doi: 10.1093/sysbio/syu063.

  6. Mirarab, Siavash, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Theo Zimmermann, M Shel Swenson, and Tandy Warnow. “ASTRAL: Genome-Scale Coalescent-Based Species Tree.” Bioinformatics 30, no. 17 (2014): i541–i548. doi:10.1093/bioinformatics/btu462.

  7. Mirarab, Siavash, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment.” Journal of Computational Biology (2014): in press.

  8. Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment.” Edited by Roded Sharan. Research in Computational Molecular Biology (2014): 177–191. doi:10.1007/978-3-319-05269-4_15.

  9. Nguyen, Nam , Siavash Mirarab, Bo Liu, Mihai Pop, and Tandy Warnow. “TIPP: Taxonomic identification and phylogenetic profiling”. Bioinformatics (2014). doi:10.1093/bioinformatics/btu721.

  10. Zimmerman, Théo, Siavash Mirarab, and Tandy Warnow. “BBCA: improving the scalability of *BEAST using random binning.” BMC Genomics 15, no. 6 (2014): S11. doi:10.1186/1471-2164-15-S6-S11

  11. Stoltzfus, Arlin, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, ... Siavash Mirarab, ... et al. “Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient.” BMC Bioinformatics 14 (2013): 158. doi:10.1186/1471-2105-14-158.

  12. Bayzid, M S, Siavash Mirarab, and Tandy Warnow. “Inferring Optimal Species Trees under Gene Duplication and Loss.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2013): 250–61. PMID: 23424130.

  13. Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “SEPP: SATé-Enabled Phylogenetic Placement.” Pacific Symposium On Biocomputing (2012): 247–58. PMID: 22174280.

  14. Nguyen, Nam, Siavash Mirarab, and Tandy Warnow. “MRL and SuperFine+ MRL: New Supertree Methods.” Algorithms for Molecular Biology 7, no. 1 (2012): 3. doi:10.1186/1748-7188-7-3.

  15. Mirarab, Siavash, Soroush Akhlaghi, and Ladan Tahvildari. “Size-Constrained Regression Test Case Selection Using Multicriteria Optimization.” Software Engineering, IEEE Transactions on 38, no. 4 (2012): 936–956.

  16. Mirarab, Siavash, and Tandy Warnow. “FastSP: Linear Time Calculation of Alignment Accuracy.” Bioinformatics (Oxford, England) 27 (2011): 3250–8. doi:10.1093/bioinformatics/btr553.

  17. Do, Hyunsook, Siavash Mirarab, Ladan Tahvildari, and Gregg Rothermel. “The Effects of Time Constraints on Test Case Prioritization: A Series of Controlled Experiments.” Software Engineering, IEEE Transactions on 36, no. 5 (2010): 593–617.

  18. Mirarab, Siavash, and Ladan Tahvildari. “An Empirical Study on Bayesian Network-Based Approach for Test Case Prioritization.” In Software Testing, Verification, and Validation, 2008 1st International Conference on, 278–287. IEEE, 2008.

  19. Do, Hyunsook, Siavash Mirarab, Ladan Tahvildari, and Gregg Rothermel. “An Empirical Study of the Effect of Time Constraints on the Cost-Benefits of Regression Testing.” In Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of Software Engineering, 71–82. ACM, 2008.

  20. Amoui, Mehdi, Mazeiar Salehie, Siav ash Mirarab, and Ladan Tahvildari. “Adaptive Action Selection in Autonomic Software Using Reinforcement Learning.” In Autonomic and Autonomous Systems, 2008. ICAS 2008. Fourth International Conference on, 175–181. IEEE, 2008.

  21. Mirarab, Siavash, Afshar Ganjali, Ladan Tahvildari, Shimin Li, Weining Liu, and Mike Morrissey. “A Requirement-Based Software Testing Framework: An Industrial Practice.” In Software Maintenance, 2008. ICSM 2008. IEEE International Conference on, 452–455. IEEE, 2008.

  22. Mirarab, Siavash, Alaa Hassouna, and Ladan Tahvildari. “Using Bayesian Belief Networks to Predict Change Propagation in Software Systems.” In Program Comprehension, 2007. ICPC’07. 15th IEEE International Conference on, 177–188. IEEE, 2007.

  23. Mirarab, Siavash, and Ladan Tahvildari. “A Prioritization Approach for Software Test Cases Based on Bayesian Networks.” In Fundamental Approaches to Software Engineering, 276–290. Springer Berlin Heidelberg, 2007.

  24. Amoui, Mehdi, Siavash Mirarab, Sepand Ansari, and Caro Lucas. “A Genetic Algorithm Approach to Design Evolution Using Design Pattern Transformation.” International Journal of Information Technology and Intelligent Computing 1, no. 2 (2006): 235–244.

Contact

Siavash Mir arabbaygi
Dept of Computer Science
University of Texas at Austin
2317 Speedway, Stop D9500
Austin, TX 78701
smirarab at cs dot utexas dot edu