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UCSD

  1. Sayyari, Erfan, James B Whitfield, and Siavash Mirarab. “Fragmentary gene sequences negatively impact gene tree and species tree reconstruction”. Molecular Biology and Evolution (early access) (2017) msx261. doi:10.1093/molbev/msx261
  2. Mai, Uyen, and Siavash Mirarab. “TreeShrink: Efficient Detection of Outlier Tree Leaves.” In RECOMB-CG 2017, Proceedings, 116–40. 2017. doi:10.1007/978-3-319-67979-2_7.
  3. Zhang, Chao, Erfan Sayyari, and Siavash Mirarab. “ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches.” In RECOMB-CG 2017, Proceedings, 53–75. 2017. doi:10.1007/978-3-319-67979-2_4.
  4. Mai, Uyen, Erfan Sayyari, and Siavash Mirarab. “Minimum Variance Rooting of Phylogenetic Trees and Implications for Species Tree Reconstruction.” PLOS ONE 12, no. 8 (2017): e0182238. doi:10.1371/journal.pone.0182238.
    • Best paper award at GLBIO 2017.
  5. Mirarab, Siavash. “Phylogenomics: Constrained Gene Tree Inference”. Nature Ecology & Evolution 1 (2017): 56. doi:10.1038/s41559-016-0056.
  6. Shekhar, Shubhanshu, Sebastien Roch, and Siavash Mirarab. “Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?” IEEE/ACM Transactions on Computational Biology and Bioinformatics (2017). early access. 10.1109/TCBB.2017.2757930 arxiv
    • An earlier version was presented at RECOMB-2017.
  7. Sayyari, Erfan and Siavash Mirarab. “Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction”. BMC Genomics 17, no. 10 (2016): 101–113. doi:10.1186/s12864-016-3098-z
  8. Sayyari, Erfan and Siavash Mirarab. “Fast coalescent-based computation of local branch support from quartet frequencies”. Molecular Biology and Evolution 33, no. 7 (2016): 1654-1668. doi:10.1093/molbev/msw079

PhD work

  1. Nguyen, Nam, Michael Nute, Siavash Mirarab and Tandy Warnow. “HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs”. BMC Genomics 17, no. 10 (2016): 89-100. doi:10.1186/s12864-016-3097-0.
  2. Tarver, James E, Mario Dos Reis, Siavash Mirarab, Raymond J Moran, Sean Parker, Joseph E O’Reilly, Benjamin L King, Mary J O’Connell, Robert J Asher, Tandy Warnow, Kevin J Peterson, Philip C J Donoghue, and Davide Pisani. “The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.” Genome Biology and Evolution (2016): evv261. doi:10.1093/gbe/evv261.

  3. Mirarab, Siavash, Md. Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow. 2015. “Response to Comment on ‘Statistical Binning Enables an Accurate Coalescent-Based Estimation of the Avian Tree.’” Science 350, no. 6257 (2015): 171. doi:10.1126/science.aaa7719.

  4. Cracraft, Joel, Peter Houde, Simon Y W Ho, David P Mindell, Jon Fjeldså, Bent Lindow, Scott V Edwards, Carsten Rahbek, Siavash Mirarab, Tandy Warnow, M Thomas P Gilbert, Guojie Zhang, Edward L Braun, Erich D Jarvis. “Response to Comment on ‘Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds.’” Science 349, no. 6255 (2015): 1460. doi:10.1126/science.aab1578.

  5. Davidson, Ruth, Pranjal Vachaspati, Siavash Mirarab, and Tandy Warnow. “Phylogenomic Species Tree Estimation in the Presence of Incomplete Lineage Sorting and Horizontal Gene Transfer.” BMC Genomics 16, Suppl 10 (2015): S1. doi:10.1186/1471-2164-16-S10-S1.

  6. Chou, Jed, Ashu Gupta, Shashank Yaduvanshi, Ruth Davidson, Mike Nute, Siavash Mirarab, and Tandy Warnow. “A Comparative Study of SVDquartets and Other Coalescent-Based Species Tree Estimation Methods.” BMC Genomics 16, Suppl 10 (2015): S2. doi:10.1186/1471-2164-16-S10-S2.

  7. Mirarab, Siavash, Tandy Warnow. “ASTRAL-II: Coalescent-Based Species Tree Estimation with Many Hundreds of Taxa and Thousands of Genes.”. Bioinformatics 31, no. 12 (2015): i44–i52. doi:10.1093/bioinformatics/btv234

  8. Shamsuzzoha Md Bayzid, Siavash Mirarab, Bastien Boussau, and Tandy Warnow. “Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses.” PLoS ONE 10, no. 6 (2015): e0129183. doi:10.1371/journal.pone.0129183.

  9. Nam Nguyen, Siavash Mirarab, Keerthana Kumar, and Tandy Warnow. “Ultra-Large Alignments Using Phylogeny-Aware Profiles.”. Genome Biology 16, no. 1 (2015): 124. doi:10.1186/s13059-015-0688-z.
    • presented at RECOMB - 2015, Warsaw, Poland. Also appears as a one page abstract in the conference proceedings.
  10. Mirarab, Siavash, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.” Journal of Computational Biology 22, no. 05 (2015): 377–386. doi:10.1089/cmb.2014.0156
    • an earlier version appeared at RECOMB 2014 proceedings (see below)
  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.
    • presented at ECCB - 2014, Strasbourg, France
  16. Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment.” Proceedings of RECOMB (2014): 177–191. doi:10.1007/978-3-319-05269-4_15.

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

  18. 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

  19. 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.

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

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

  22. 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.

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

MS work

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.