UoH
Sagi Snir                      שגיא   שניר
Institute of Evolution

Publications

      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

      Journals

    2. S. Snir. On the Number of Genomic Pacemakers: A Geometric Approach. Algorithms for Molecular Biology.

    3. E. Avni*, R. Cohen*, and S. Snir. Weighted Quartets Phylogenetics. Systematic Biology. *Authors contributed equally.

    4. N. Alon, S. Snir and R. Yuster. On the compatibility of quartet trees, SIAM J. Discrete Math (SIDMA) . Extended version of ACM-SIAM Symposium on Discrete Algorithms (SODA) 2014.

    5. S. Snir, Y. I. Wolf, and E. V. Koonin. Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms. Genome Biology and Evolution. (GBE). May, 2014.

    6. Paz A, Frenkel S, Snir S, Kirzhner V, Korol AB. Implications of human genome structural heterogeneity: functionally related genes tend to reside in organizationally similar genomic regions. BMC Genomics. 2014 Mar 31;15(1):252.

    7. A. Shifman, N. Ninyo, U. Gophna and S. Snir. Phylo SI: A New Genome Wide Approach for Prokaryotic Phylogeny. Nucleic Acids Research (NAR). 42 (4): 2391-2404, 2014.

    8. Y. I. Wolf, S. Snir, and E. V. Koonin. Stability along with extreme variability in core genome evolution. Genome Biology and Evolution. (GBE). 5(7): 1393 - 1402, 2013.

    9. S. Roch and S. Snir, Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis. Journal of Computational Biology (JCB). 20(2): 93-112, 2013.

    10. S. Snir, Y. I. Wolf and E. V. Koonin. Universal Pacemaker of Genome Evolution. PLOS Computational Biology , 8(11): e1002785, 2012. Also, read the Research Highlight article in Nature Review Genetics.

    11. S. Snir and R. Yuster. Reconstructing approximate phylogenetic trees from quartet samples. SIAM Journal on Computing (SICOMP). 41(6): 1466-1480 (2012)

    12. I. Gronau, S. Moran, S. Snir. Fast and Reliable Reconstruction of Phylogenetic Trees with Indistinguishable Edges. Random Structures and Algorithms. 40(3): 350-384, 2012.

    13. S. Snir and S. Rao. Quartet MaxCut: A Fast Algorithm for Amalgamating Quartet Trees. Molecular Phylogenetics and Evolution, 2012.

    14. Hadid Y, Nemeth A, Snir S, Pavlicek T, Csorba G, Kazmer M, Major A, Mezhzherin S, Rusin M, Coskun Y, Nevo E Is evolution of blind mole rats determined by climate oscillations? PLoS One 2012.

    15. S. Snir and R. Yuster. A Linear Time Approximation Scheme for Maximum Quartet Consistency on Sparse Sampled Inputs. SIAM J. Discrete Math. 25(4): 1722-1736, 2011.

    16. K.S. Makarova, Y.I. Wolf, S. Snir and E.V. Koonin. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 2011

    17. S. Moran, S. Snir and K. Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. ACM Transactions on Algorithms (TALG).7(4): 42, 2011.

    18. S. Snir and L. Pachter. Tracing the Most Parsimonious Indel History. Journal of Computational Biology (JCB) ;18(8):967-86, 2011.

    19. S. Snir and E.N. Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. Journal of Computational Biology (JCB), Volume 17(11): 1417-1430, 2010. pdf file

    20. Z. Frenkel, Z.M. Frenkel, E.N. Trifonov, and S. Snir. Structural Relatedness via Flow Networks in Protein Sequence Space . Journal of Theoretical Biology (JTB), Volume 260(3):438-44 (2009). pdf file

    21. S. Snir and S. Rao. Quartets MaxCut: A Divide and Conquer Quartets Algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 7(4): 704-718 (2010). pdf file

    22. 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), Volume 6(3): 495-505 (2009). All authors contributed equally. pdf file

    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. Volume 29(1): 11-22, (2010)

    24. S. Snir and T. Tuller, The NET-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. Journal of Bioinformatics and Computational Biology (JBCB), 2009 Aug;7(4):625-44. Authors contributed equally. pdf file

    25. 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). pdf file

    26. 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). Conference version invited to a special issue of selected papers in Algorithmica. pdf file

    27. S. Snir, "Lateral Transfers: a survey and new developments". Israel Journal of Ecololgy and Evolution (IJEE). 52(3-4):443-459, 2007. pdf file

    28. 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). pdf file

    29. 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. pdf file

    30. 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. pdf file

    31. 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; pdf file

    32. B. Chor and S. Snir, Analytic solutions of maximum likelihood on forks of four taxa , Mathematical Biosciences.Volume 208, Issue 2, August 2007, Pages 347-358. pdf file

    33. S. Skiena and S. Snir, Restricting SBH Ambiguity via Restriction Enzymes, Discrete Applied Math. 155(6-7): 857-867, April 2007. pdf file

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

    35. 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; All authors contributed equally. pdf file

    36. 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. pdf file

    37. G. Jin L. Nakhleh, S. Snir and T. Tuller, Maximum Likelihood of Phylogenetic Networks , Bioinformatics, Vol 22, Number 21, November 2006, pages 2604 - 2611. All authors contributed equally. pdf file

    38. 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 pdf file

    39. 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 pdf file

    40. 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. pdf file

    41. 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

    42. S. Snir, Pacemaker Partition Identification . WABI 2014: 281-295.

    43. Z. Wang, J. Sul, S. Snir, J. Lozano, E. Eskin, Gene-Gene Interactions Detection Using A Two-stage Model. RECOMB 2014: 340-355.

    44. N. Alon, S. Snir and R. Yuster, On the compatibility of quartet trees, ACM-SIAM Symposium on Discrete Algorithms (SODA) 2014: 535-545.

    45. S. Roch and S. Snir, "Recovering a tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis". RECOMB 2012, LNBI 7262, pp. 224--238, 2012.

    46. S. Snir and R. Yuster, "Reconstructing approximate phylogenetic trees from quartet samples", APPROX 2011, Lecture Notes in Computer Science 6845 Springer 2011: 339--350.

    47. S. Snir and R. Yuster, "Reconstructing approximate phylogenetic trees from quartet samples", ACM-SIAM Symposium on Discrete Algorithms (SODA) 2010. pdf file

    48. 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), 2008: 354--368. pdf file

    49. 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. pdf file

    50. 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. pdf file

    51. 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. pdf file

    52. 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. pdf file

    53. G. Jin L. Nakhleh, S. Snir and T. Tuller, "Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction", European Conference on Computational Biology (ECCB) 2006. pdf file

    54. 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. pdf file

    55. S. Moran and S. Snir, Efficient Approximation of convex Recolorings , APPROX 2005: 192--208. pdf file

    56. 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. pdf file

    57. 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

    58. B. Chor, A. Khetan and S. Snir, "Maximum Likelihood on Four Taxa Phylogenetic Trees: Analytic Solutions".RECOMB 2003: 76--83. pdf file

    59. S. Skiena and S. Snir, "Restricting SBH Ambiguity via Restriction Enzymes", (WABI 02), (LNCS 2452),pages 404-417. pdf file

      Theses

    60. S. Snir, "Simple and Efficient Network Decomposition and Synchronization",M.Sc. Thesis, Department of Computer Science, Technion, Haifa, Israel, August, 2004. Advisor: Shlomo Moran.

    61. 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

    62. S. Snir, E. Yeger-Lotem, B. Chor and Z. Yakhini, "Using Restriction Enzymes to Improve Sequencing by Hybridization", abstract and ps
     
Sagi SnirDepartment of Evolutionary & Environmental BiologyUniversity of Haifa