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Publications S. Snir

Book Chapters

1. J. Al-Aidroos and S. Snir, Analysis of Point Mutations in Vertebrate Genomes, in Algebraic Statistics for Computational Biology. Edited by L. Pachter and B. Sturmfels, Cambridge University Press. Pages 375-387, 2005. Link

Papers in Refereed Journals:

1. Z.M. Frenkel, Z.M. Frenkel, E.N. Trifonov and S.Snir . Structural relatedness via flow networks in protein sequence space. Journal of Theoretical Biology (JTB), 260(3): 438-444,2009. Link

2. S. Snir and T. Tuller. The NET-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and HiddenMarkovModels .Journal of Bioinformatics and Computational Biology (JBCB),6(3):495-505. 2009. Authors contributed equally. Link

3. G. Jin, L. Nakhleh, S. Snir, and T. Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 6(3): 495-505, 2009. All authors contributed equally. Link

4. M. Hendy and S. Snir. Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof using Path-Sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 5(3): 461-471, 2008. Link

5. S. Moran and S. Snir. Convex Recolorings of Phylogenetic Trees: Definitions, Hardness Results and Algorithms. Journal of Computer and System Sciences (JCSS), 74(5): 850-869, 2008.

6. S. Snir, T. Warnow and S. Rao. Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm. Journal of Computational Biology (JCB), 15(1): 91-103, 2008. Link

7. B. Chor and S. Snir. Molecular Clock Forks: Symbolic Mathematical Analysis. Mathematical Biosciences, 208(2): 347-58, 2007. Link

8. E. Eskin and S. Snir. Incorporating Homologues into Sequence Embeddings for Protein Analysis. Journal of Bioinformatics and Computational Biology (JBCB), 5(3): 717-738, 2007. Link

9. S. Moran and S. Snir. Efficient Approximation of convex Recolorings. Journal of Computer and System Sciences (JCSS), 73: 1078-1089, 2007. Link

10. M. Halpern, Y. Senderovich and S. Snir. Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass. International Journal of Systematic and Evolutionary Microbiology (IJSEM), 57: 1872-1875, 2007. Link

11. S. Skiena and S. Snir. Restricting SBH Ambiguity via Restriction Enzymes. Discrete Applied Mathematics (DAM), 155(6-7): 857-867, 2007. Link

12. G. Jin, L. Nakhleh, S. Snir, and T. Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. Bioinformatics, 23(2): e123-e128, 2007. All authors contributed equally. Link

13. G. Jin, L. Nakhleh, S. Snir, and T. Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. Molecular Biology and Evolution (MBE), 24(1): 324-337, 2007. All authors contributed equally. Link

14. S. Snir. Lateral Transfer: A Survey and New Developments. Israel Journal of Ecology and Evolution, 52(3-4): 443-459. Link

15. B. Chor, A. Khetan and S. Snir. Maximum Likelihood on Molecular Clock Comb: Analytic Solutions. Journal of Computational Biology (JCB), 13(3): 819-837, 2006.

16. G. Jin , L. Nakhleh, S. Snir, and T. Tuller. Maximum Likelihood of Phylogenetic Networks. Bioinformatics, 22(21): 2604-2611, 2006. All authors contributed equally. Link

17. S. Snir and S. Rao. Using Max Cut to Enhance Rooted Trees Consistency. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 3(4): 323-333, 2006.

18. B. Chor, M. Hendy and S. Snir. Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions. Molecular Biology and Evolution (MBE), 23(3): 626-632, 2006. Link

19. B. Chor and S. Snir. Molecular Clock Fork Phylogenies: Closed Form Analytic Maximum Likelihood Solutions. Systematic Biology , 53(6): 963-967, 2004. Link

20. S. Moran and S. Snir. Simple and Efficient Network Decomposition and Synchronization. Theoretical Computer Science (TCS) 243(1-2): 217-241, 2000.

 In Press

•21.  S. Snir and S. Rao. QuartetsMaxCut: A Divide and Conquer Quartets Algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).

•22.  S. Moran, S. Snir and K. Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. ACM Transactions on Algorithms.

23. O. Pearlson, L. Blaustein, S. Snir, D. Goldberg and G. Degani. Molecular Variation in Triturus vittatus vittatus (Urodela) from Breeding Sites Near the Southern Limit of its Distribution Inferred from Mitochondrial DNA Sequence of Cytochrome b Gene and Control Region. Currnet Herpatology.

 Papers in Refereed Conference Proceedings

1. S. Snir and R. Yuster, Reconstructing approximate phylogenetic trees from quartet samples. ACMSIAM Symposium on Discrete Algorithms (SODA), 2010.

2. S. Snir and T. Tuller, Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models.Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science (LNCS 5251): 354-368, 2008. Authors contributed equally.

3. Gronau, S. Moran and S. Snir, Fast and Reliable Reconstruction of Phylogenetic Trees with Very Short Branches. ACM-SIAM Symposium on Discrete Algorithms (SODA), 379-388, 2008.

4. B. Chor, M. R. Fellows, M. A. Ragan, F. A. Rosamond, I. Razgon and S. Snir. Connected Coloring Completion for General Graphs: Algorithms and Complexity. The 13th Annual International Computing and Combinatorics Conference (COCOON), Lecture Notes in Computer Science (LNCS 4598): 75-85, 2007.

5. G. Jin, L. Nakhleh, S. Snir and T. Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. International Symposium on Bioinformatics Research and Applications (ISBRA), 61-72, 2007. All authors contributed equally.

6. G. Jin, L. Nakhleh, S. Snir and T. Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. The 5th European Conference on Computational Biology (ECCB), 2006. All authors contributed equally.

7. S. Snir and L. Pachter. Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. Proceedings of the tenth annual International Conference on Computational Molecular Biology (RECOMB). Lecture Notes in Computer Science 3909: 265-280. 2006.

8. S. Moran and S. Snir. Convex Recolorings of Phylogenetic Trees: Definitions, Hardness Results and Algorithms. Workshop on Algorithms and Data Structures (WADS), Lecture Notes in Computer Science (LNCS 3608): 218-232, 2005. Invited to a special issue of selected papers in Algorithmica.

9. S. Moran and S. Snir. Efficient Approximation of convex Recolorings. The 8th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX), Lecture Notes in Computer Science (LNCS 3624): 192-208, 2005.

10. S. Moran, S. Rao and S. Snir. Using Semi-Definite Programming to Enhance Supertree Resolvability. Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI): 89-103, 2005. Invited to a special issue of selected papers in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).

11. E. Eskin and S. Snir. The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space. The IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB): 179-186. 2005.

12. B. Chor, A. Khetan and S. Snir. Maximum Likelihood on Four Taxa Phylogenetic Trees: Analytic Solutions. Proceedings of the Seventh annual International Conference on Computational Molecular Biology (RECOMB), pages 76-83, 2003.

13. S. Skiena and S. Snir. Restricting SBH Ambiguity via Restriction Enzymes. Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI). Lecture Notes in Computer Science (LNCS 2452): 404-417, 2002. 

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