Publications

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

  1. G.M. Pinho, J.G.A. Martin, C. Farrell, A. Haghani, J.A. Zoller, J. Zhang, S. Snir, , M. Pellegrini, R.K. Wayne, D.T. Blumstein and S. Horvath, Hibernation slows epigenetic ageing in yellow-bellied marmots. Nat Ecol Evol 6, 418-426 (2022).
  2. S. Snir, O. Weissberg and R. Yuster. On the quartet distance given partial information. Journal of Graph Theory . 2021.
  3. V. Tsyvina, A. Zelikovsky, S. Snir and , P. Skums. Inference of mutability landscapes of tumors from single cell sequencing data. PLOS Computational Biology . 2020.
  4. C. Farrell, S. Snir* and M. Pellegrini*. The Epigenetic Pacemaker – modeling epigenetic states under an evolutionary framework. Bioinformatics . 2020. *Corresponding Authors; Equal Contribution.
  5. E. Avni and S. Snir. A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes. Scientific Reports . 2020.
  6. G. Sevillya, D. Doerr, Y. Lerner, J. Stoye, M. Steel* and S. Snir*. Horizontal Gene Transfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolution . 2019 *Authors contributed equally.
  7. T. Dencker; C.A. Leimeister; M. Gerth; C. Bleidorn; S. Snir; B. Morgenstern. Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction using Multiple Spaced-Word Matches and Quartet Trees. NAR Genomics and Bioinformatics . 2019, 2:1.
  8. S. Snir. Epigenetic PaceMaker: Closed From Algebraic Solutions. Accepted to BMC Genomics. 2019
  9. G. Sevillya; O. Adato; S. Snir. Detecting Horizontal Gene Transfer: A Probabilistic Approach. Accepted to BMC Genomics. 2019
  10. S. Snir, C. Farrell and M. Pellegrini. Human epigenetic ageing is logarithmic with time across the entire lifespan. Epigenetics . 2019.
  11. Gur Sevillya and Sagi Snir. Synteny Footprints Provide Clearer Phylogenetic Signal than Sequence Data for Prokayotic Classification. Molecular Phylogenetics and Evolution. 2019, volume 136, pp 128 — 137.
  12. S. Snir. Bounds on Identification of Genome Evolution Pacemakers. Accepted to Journal of Computational Biology.
  13. B. Yohay, S. Snir. Prokaryotic Evolutionary Mechanisms Accelerate Learning. Accepted to Discrete Applied Mathematics.
  14. B. Yohay, S. Snir. Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data. Accepted to Journal of Computational Biology.
  15. E. Avni, D. Montoya, D. Lopez, R. Modlin, M. Pellegrini*, S. Snir*. A Phylogenomic Study Quantifies Competing Mechanisms for Pseudogenization in Prokaryotes – the Mycobacterium Leprae Case. Accepted to PLOS ONE. *Joint last author.
  16. E. Avni, S. Snir. A new quartet-based statistical method for comparing sets of gene trees is developed using a generalized Hoeffding inequality. Accepted to Journal of Computational Biology.
  17. E. Avni*, Z. Yona*, R. Cohen, S. Snir. The performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input. Journal of Molecular Evolution. 2018, Volume 86, Issue 2, pp 150 — 165. *Authors contributed equally.
  18. S. Snir, M. Pellegrini. An Epigenetic PaceMaker is Detected via a Fast Conditional EM Algorithm.Epigenomics. 2018. VOLUME 10, ISSUE 6.
  19. E. Avni, S. Snir. Reconstruction of Real and Simulated Phylogenies Based on Quartet Plurality Inference. BMC Genomics. 2018. 19:4921
  20. D. Duong, L. Gai, S. Snir, E.Y. Kang, B. Han, J.H. Sul, E. Eskin. Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. Bioinformatics , Volume 33, Issue 14, 15 July 2017, Pages 67-74.
  21. E. Avni, S. Snir. Toxic genes present a unique phylogenetic signature. Molecular Phylogenetics and Evolution. Volume 116, November 2017, Pages 141-148.
  22. S. Snir, B.M. vonHoldt, M. Pellegrini. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLOS Computational Biology. 12(11): e1005183. 2016.
  23. W. Frenkel, Y. Kiat, I. Izhaki and S. Snir. Convex Recoloring as an Evolutionary Marker.Molecular Phylogenetics and Evolution (MPE). 107: 209-220, 2016.
  24. G. Sevillya, W. Frenkel, and S. Snir. Triplet MaxCut: A New Toolkit for Rooted Supertree.Methods in Ecology and Evolution. 7(11): 2041-210x, 2016.
  25. S. Snir. Ordered Orthology as a Tool in Prokaryotic Evolutionary Inference. Mobile Genetic Elements . 6(6): e1120576, 2015.
  26. O. Adato, N. Ninyo, U. Gophna, and S. Snir. Detecting Horizontal Gene Transfer Between Closely Related Taxa PLOS Computational Biology . 11 (10): e1004408, 2015.
  27. S. Talal, I. Tesler, J. Sivan, R. Ben-Shlomo, H. M. Tahir, L. Prendini, S. Snir, E. Gefen. Scorpion speciation in the Holy Land: Multilocus phylogeography corroborates diagnostic differences in morphology and burrowing behavior among Scorpio subspecies and justifies recognition as phylogenetic, ecological and biological species Molecular Phylogenetics and Evolution (MPE). 91: 226 – 237, 2015.
  28. E. Avni*, R. Cohen*, and S. Snir. Weighted Quartets Phylogenetics. Systematic Biology. 64 (2): 233-242, 2015. *Authors contributed equally.
  29. Z. Wang, J. Sul, S. Snir, J.A. Lozano, E. Eskin. Gene-Gene Interactions Detection Using a Two-Stage Model Journal of Computational Biology (JCB). 22(6): 563-576, 2015.
  30. S. Snir. On the Number of Genomic Pacemakers: A Geometric Approach. Algorithms for Molecular Biology. 9:26, 2014.
  31. N. Alon, S. Snir and R. Yuster. On the compatibility of quartet trees, SIAM J. Discrete Math (SIDMA) . 28(3), 2014. Extended version of ACM-SIAM Symposium on Discrete Algorithms (SODA) 2014.
  32. 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) 6 (6): 1268-1278, 2014.
  33. 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.15 (1): 252, 2014.
  34. 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.
  35. 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.
  36. 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.
  37. 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 inNature Review Genetics.
  38. S. Snir and R. Yuster. Reconstructing approximate phylogenetic trees from quartet samples. SIAM Journal on Computing (SICOMP). 41(6): 1466-1480 (2012)
  39. 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.
  40. S. Snir and S. Rao. Quartet MaxCut: A Fast Algorithm for Amalgamating Quartet Trees. Molecular Phylogenetics and Evolution (MPE), 2012.
  41. 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.
  42. 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.
  43. 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
  44. 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.
  45. S. Snir and L. Pachter. Tracing the Most Parsimonious Indel History. Journal of Computational Biology (JCB) ;18(8):967-86, 2011.
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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)
  51. 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
  52. 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
  53. 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
  54. S. Snir, “Lateral Transfers: a survey and new developments”. Israel Journal of Ecololgy and Evolution (IJEE). 52(3-4):443-459, 2007. pdf file
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. S. Skiena and S. Snir, Restricting SBH Ambiguity via Restriction Enzymes. Discrete Applied Math. 155(6-7): 857-867, April 2007. pdf file
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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

  1. S. Snir. Epigenetic PaceMaker: Closed From Algebraic Solutions. RECOMB – Comparative Genomics 2019 , October 2019, Montpellier, France.

  2. Sagi Snir. Greedy Partition Distance under Stochastic Models – Analytic Results . Accepted to ISBRA 2019.

  3. T. Dencker, C.A. Leimeister, M. Gerth, C. Bleidorn, S. Snir and B. Morgenstern. Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction using Multiple Spaced-Word Matches and Quartet Trees. Accepted to RECOMB Comparative Genomics 2018 , Oct 2018, Quebec.

  4. S. Snir. Bounds on Identification of Genome Evolution Pacemakers. ISBRA 2018 , June 2018, Beijing.

  5. S. Snir and B. Yohay. Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data. ISBRA 2018 , June 2018, Beijing.

  6. G. Sevillya, O. Adato and S. Snir. Detecting Horizontal Gene Transfer: A Probabilistic Approach. ISBRA 2018 , June 2018, Beijing.

  7. D. Duong, L. Gai, S. Snir, E.Y. Kang, B. Han, J.H. Sul, E. Eskin. Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. ISMB 2017 , July 2017,Prague.

  8. E. Avni and S. Snir, Reconstruction of Real and Simulated Phylogenies Based on Quartet Plurality Inference. ISBRA 2017. LNBI 10330, pages 47-48

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

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

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

  12. 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.

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

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

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

  23. 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

  24. 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

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

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

Theses

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

  2. 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

Software

  1. Quartet MaxCut – A fast algorithm for Amalgamating Quartet Trees.

Technical Reports

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

  1. Journals

 

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