Convex Recoloring

  1. S. Moran, S. Snir and K. Sung "Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds". Submitted.
  2. B. Chor, M. R. Fellows, M. A. Ragan, F. A. Rosamond, S. Snir and I. Razgon. "Connected Coloring Completion for General Graphs: Algorithms and Complexity". COCOON, 2007.
  3. S. Moran and S. Snir, "Convex Recolorings of Phylogenetic Trees: Definitions, Hardness Results and Algorithms". accepted to Journal of Computer and System Sciences (JCSS). Extended abstract appeared in WADS 2005 . Conference version invited to a special issue of selected papers in Algorithmica.
  4. S. Moran and S. Snir, "Efficient Approximation of convex Recolorings". Journal of Computer and System Sciences (JCSS). Extended abstract appeared in APPROX 2005.

    5. Maximum Likelihood and Hadamard Conjugation

  5. B. Chor and S. Snir, Molecular Clock Fork Phylogenies: Closed Form Analytic Maximum Likelihood Solutions , Systematic Biology , Vol. 53, Issue 6, December 2004, pp. 963--967.
  6. B. Chor, M. Hendy and S. Snir, Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions . Molecular Biology and Evolution (MBE), Vol. 23, Issue 3 , March 2006, pp. 626-632
  7. B. Chor, A. Khetan and S. Snir, Maximum Likelihood on Molecular Clock Comb: Analytic Solutions , Journal of Computational Biology (JCB). Vol. 13, Issue 3 , April 2006, pp. 819--837
  8. B. Chor and S. Snir, Molecular Clock Forks: Symbolic Mathematical Analysis , Mathematical Biosciences.Volume 208, Issue 2, August 2007, Pages 347-358.
  9. 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).
  10. 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

    Lateral Gene Transfer

  11. S. Snir and E. Trifonov, "Towards Rigorous Handling of Horizontal Transfer Events: Enterobacteria". submitted.
  12. G. Jin L. Nakhleh, S. Snir and T. Tuller, "On Approximating the Parsimony Score of Phylogenetic Networks". Submitted.
  13. S. Snir, "Lateral Transfers: a survey and new developments". Israel Journal of Ecololgy and Evolution (IJEE). 52(3-4):443-459, 2007.
  14. 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), 2007.
  15. G. Jin L. Nakhleh, S. Snir and T. Tuller, Maximum Likelihood of Phylogenetic Networks , Bioinformatics, Vol 22, Number 21, November 2006, pages 2604 - 2611.
  16. G. Jin L. Nakhleh, S. Snir and T. Tuller, Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction , Bioinformatics 2007 23(2):e123-e128;
  17. 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) 2007 24(1):324-337;
  18. G. Jin L. Nakhleh, S. Snir and T. Tuller, "Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction", European Conference on Computational Biology (ECCB) 2006.
  19. S. Snir and T. Tuller, "The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks". Submitted. .

    Comparative Genomics

  20. V. Kirzhner, S. Snir and A. Korol. Analytical framework for analyzing genome heterogeneity on above-gene-level using fuzzy linguistic-like approach.
  21. S. Snir and L. Pachter, "Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes", Lecture Notes in Computer Science, Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), (2006) p 265--280.
  22. M. Halpern, Y. Senderovich and S. Snir. "Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass". Accepted to International Journal of Systematic and Evolutionary Microbiology (IJSEM).

    23. Supertree

  23. I. Gronau, S. Moran and S. Snir, "Fast and Reliable Reconstruction of Phylogenetic Trees with Very Short Branches.", ACM-SIAM Symposium on Discrete Algorithms (SODA) 2008.
  24. S. Snir and S. Rao, "Using Max Cut to Enhance Rooted Trees Consistency", Appearedin a special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. 3, Number 4, December 2006, pp. 323--333.
  25. S. Snir, T. Warnow and S. Rao, "Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm". Journal of Bioinformatics Biology (JCB) .
  26. S. Snir and S. Rao, "Quartets MaxCut: A Divide and Conquer Quartets Algorithm".

    27. Sequence Analysis

  27. E. Eskin, S. Snir,"Incorporating Homologues into Sequence Embeddings for Protein Analysis." Journal of Bioinformatics and Computational Biology (JBCB) .
  28. S. Skiena and S. Snir, "Restricting SBH Ambiguity via Restriction Enzymes", Discrete Applied Math. 155(6-7): 857-867 (2007).
  29. S. Snir, E. Yeger-Lotem, B. Chor and Z. Yakhini, "Using Restriction Enzymes to Improve Sequencing by Hybridization", abstract and ps

    Distributed Algorithms

  30. S. Moran and S. Snir, "Simple and Efficient Network Decomposition and Synchronization", Theoretical Computer Science, 243(1-2), pp. 217-241, August 2000. pdf file

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