Journals

  1. S. Snir, T. Warnow and S. Rao, "Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm". Journal of Computational Biology (JCB)
  2. S. Moran and S. Snir, Convex Recolorings of Phylogenetic Trees: Definitions, Hardness Results and Algorithms. accepted to Journal of Computer and System Sciences (JCSS). Conference version invited to a special issue of selected papers in Algorithmica.
  3. S. Snir, "Lateral Transfers: a survey and new developments". Israel Journal of Ecololgy and Evolution (IJEE). 52(3-4):443-459, 2007.
  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. S. Moran and S. Snir, Efficient Approximation of convex Recolorings. Journal of Computer and System Sciences (JCSS). Volume 73, Issue 7, November 2007, Pages 1078-1089.
  6. E. Eskin, S. Snir, Incorporating Homologues into Sequence Embeddings for Protein Analysis. Journal of Bioinformatics and Computational Biology (JBCB) , Vol. 5, No. 3 (2007) 717-738.
  7. M. Halpern, Y. Senderovich and S. Snir. Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass. Int J Syst Evol Microbiol, 57 (2007), 1872-1875;
  8. B. Chor and S. Snir, Molecular Clock Forks: Symbolic Mathematical Analysis , Mathematical Biosciences.Volume 208, Issue 2, August 2007, Pages 347-358.
  9. S. Skiena and S. Snir, "Restricting SBH Ambiguity via Restriction Enzymes", Discrete Applied Math. 155(6-7): 857-867, April 2007.
  10. G. Jin L. Nakhleh, S. Snir and T. Tuller, Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction , Bioinformatics 2007 23(2):e123-e128;
  11. 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;
  12. S. Snir and S. Rao, "Using Max Cut to Enhance Rooted Trees Consistency", A special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. 3, Number 4, December 2006, pp. 323--333.
  13. G. Jin L. Nakhleh, S. Snir and T. Tuller, Maximum Likelihood of Phylogenetic Networks , Bioinformatics, Vol 22, Number 21, November 2006, pages 2604 - 2611.
  14. 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
  15. 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
  16. 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.
  17. 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

    Conference Proceedings

  18. 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.
  19. 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". COCOON, 2007: 75--85.
  20. 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: 61--72.
  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. G. Jin L. Nakhleh, S. Snir and T. Tuller, "Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction", European Conference on Computational Biology (ECCB) 2006.
  23. S. Moran and S. Snir, "Convex Recolorings of Phylogenetic Trees: Definitions, Hardness Results and Algorithms", WADS 2005:218--232 . Invited to a special issue of selected papers in Algorithmica.
  24. S. Moran and S. Snir, Efficient Approximation of convex Recolorings , APPROX 2005: 192--208.
  25. S. Moran, S. Rao and S. Snir, Using Semi-Definite Programming to Enhance Supertree Resolvability , WABI 2005: 89--103. Invited to a special issue of selected papers at ACM/IEEE TCBB.
  26. E. Eskin, S. Snir,"The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space.", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology CIBCB 2005:179--186
  27. B. Chor, A. Khetan and S. Snir, "Maximum Likelihood on Four Taxa Phylogenetic Trees: Analytic Solutions".RECOMB 2003: 76--83. pdf file
  28. S. Skiena and S. Snir, "Restricting SBH Ambiguity via Restriction Enzymes", (WABI 02), ( LNCS 2452),pages 404-417.

    Book Chapters

  29. 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

    Submitted

  30. S. Snir and S. Rao, "Quartets MaxCut: A Divide and Conquer Quartets Algorithm".
  31. S. Snir and L. Pachter, "Evolution by Micro Insertion and Deletion."
  32. S. Moran, S. Snir and K. Sung "Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds"
  33. S. Snir and T. Tuller, "The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks"
  34. G. Jin L. Nakhleh, S. Snir and T. Tuller, "On Approximating the Parsimony Score of Phylogenetic Networks".
  35. S. Snir and E. Trifonov, "Towards Rigorous Handling of Horizontal Transfer Events: Enterobacteria".
  36. V. Kirzhner, S. Snir and A. Korol. "Analytical framework for analyzing genome heterogeneity on above-gene-level using fuzzy linguistic-like approach".

    Theses

  37. S. Snir, "Simple and Efficient Network Decomposition and Synchronization",M.Sc. Thesis, Department of Computer Science, Technion, Haifa, Israel, August, 2004. Advisor: Shlomo Moran.
  38. S. Snir, "Computational Issues in Phylogenetic Reconstruction: Analytic Maximum Likelihood Solutions, and Convex Recoloring",Ph.D. Thesis, Department of Computer Science, Technion, Haifa, Israel, August, 2004. Advisor: Benny Chor. pdf file

    Technical Reports

  39. S. Snir, E. Yeger-Lotem, B. Chor and Z. Yakhini, "Using Restriction Enzymes to Improve Sequencing by Hybridization", abstract and ps

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