Publications

Selected Publications


Tamir Tuller*, Asaf Carmi*, Kalin Vestsigain, Sivan Navon, Yuval Dorfan, John Zaborske, Tao Pan, Orna Dahan, Itay Furman, Yitzhak Pilpel. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell. 2010 Apr 16;141(2):344-54. (pdf).



Tamir Tuller, Yedael Y. Waldman, Martin Kupiec, Eytan Ruppin. Translation Efficiency Is Determined By Both Codon Bias and Folding Energy.Proc. Natl. Acad. Sci. USA. 2010 Feb 2 [Epub ahead of print]. (pdf).



Tamir Tuller*, Hadas Birin*, Uri Gophna, Martin Kupiec and Eytan Ruppin. Reconstructing Ancestral Gene content by Co-Evolution. Genome Research. 2009 Nov 30. [Epub ahead of print]. (pdf).



Yedael Y. Waldman*, Tamir Tuller*, Roded Sharan and Eytan Ruppin. TP53 cancerous mutations exhibit selection for translation efficiency. Cancer Research. 2009 Nov 15;69(22):8807-13. (pdf).



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. Genome Biol. 2009;10(5):R48. (pdf).



Efrat Oron, Tamir Tuller, Li Ling, Nina Rozovsky, Daniel Yekutieli, Daniel Segal, Benny Chor, Bruce Edgar, Sigal Rencus, Daniel Chamovitz. Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol. Syst. Biol. 3:108, 2007. (pdf).



Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Maximum likelihood of phylogenetic networks. Bioinformatics 22 (21): 2604-2611, 2006. (pdf) (supplementary meterial (pdf) ).



Benny Chor, Tamir Tuller. Finding a maximum likelihood tree is hard. J. ACM 53(5):722-744, 2006. (pdf).


All Publications

Journals


Tamir Tuller, Elchanan Mossel. Co-evolution is Incompatible with the Markov Assumption in Phylogenetics. to appear in TCBB.



Tamir Tuller*, Hadas Birin*, Martin Kupiec and Eytan Ruppin. Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. to appear in JCB 2010 (RECOMB-CG 2009 special issue).



Michael Gurevich, ,Tali Gritzman, Rotem Or-bach, Tamir Tuller,.Ana Feldman, Anat Achiron. Laquinimod suppress antigen presentation in relapsing-remitting multiple sclerosis: In-vitro high-throughput gene expression study. J Neuroimmunol. 2010 Apr 15;221(1-2):87-94.



Tamir Tuller*, Asaf Carmi*, Kalin Vestsigain, Sivan Navon, Yuval Dorfan, John Zaborske, Tao Pan, Orna Dahan, Itay Furman, Yitzhak Pilpel. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell. 2010 Apr 16;141(2):344-54.



Yedael Y. Waldman*, Tamir Tuller*, Tomer Shlomi, Roded Sharan, Eytan Ruppin. Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acid Res. 2010 Jan 21 [Epub ahead of print].



Tamir Tuller, Yedael Y. Waldman, Martin Kupiec, Eytan Ruppin. Translation Efficiency Is Determined By Both Codon Bias and Folding Energy.Proc. Natl. Acad. Sci. USA. 2010 Feb 2 [Epub ahead of print].



Tamir Tuller*, Yifat Felder*, Martin Kupiec. Discovering Local Patterns of Co - Evolution: Computational Aspects and Biological Examples.BMC Bioinformatics. 2010 Jan 22; 11(1). [Epub ahead of print].



Adi Mano, Tamir Tuller, Oded Beja, Ron Y. Pinter. Comparative Classification of Species and the Study of Pathway Evolution based on the Alignment of Metabolic Pathways. BMC Bioinformatics. 2010, 11(Suppl 1):S38 (APBC 2010 special issue).



Tamir Tuller*, Hadas Birin*, Uri Gophna, Martin Kupiec and Eytan Ruppin. Reconstructing Ancestral Gene content by Co-Evolution. Genome Research. 2009 Nov 30. [Epub ahead of print].



Yedael Y. Waldman*, Tamir Tuller*, Roded Sharan and Eytan Ruppin. TP53 cancerous mutations exhibit selection for translation efficiency. Cancer Research. 2009 Nov 15;69(22):8807-13.



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics. 2009 Aug 22;10:391.



Michael Gurevich*, Tamir Tuller*, Udi Rubinstein, Rotem Or-Bach and Anat Achiron. Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells. BMC Med. Genomics. 2009 Jul 22;2:46..



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. Genome Biol. 2009;10(5):R48.



Mathilda Mandel, Anat Achiron, Tamir Tuller, Tilda Barliya, Gideon Rechavi, Ninette Amariglio, Ron Loewenthal, Gad Lavie. Clone clusters in autoreactive T-cell lines from probable multiple sclerosis patients from disease characteristic signature. Immunology. 2009 Oct;128(2):287-300.



Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. J. Bioinform. Comput. Biol. 2009 Aug;7(4):625-44.



Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevitch, Eytan Ruppin and Martin Kupiec. Higher-order Genomic Organization of Cellular Functions in Yeast. J. Comput. Biol. 16(2):1-14, 2009 (RECOMB-SB-RG 2008 special issue).



Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE/ACM Trans. Comput. Biol. Bioinform. 2009 Jul-Sep;6(3):495-505.



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Evolutionary Rate and Gene Expression Across Different Brain Regions. Genome Biol. 9(9):R142, 2008.



Hadas Birin, Zohar Gal-or, Isaac Elias and Tamir Tuller. Inferring Horizontal Transfers in the Presence of Rearrangements by the Minimum Evolution Criterion. Bioinformatics 2008 24(6):826-32.



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae. PLoS Comput. Biol. 3(12):e248, 2007.



Tamir Tuller, Benny Chor, Nathan Nelson. Forbidden Penta-Peptides. Prot. Sci. 16(10):2251-2259, 2007.



Efrat Oron, Tamir Tuller, Li Ling, Nina Rozovsky, Daniel Yekutieli, Daniel Segal, Benny Chor, Bruce Edgar, Sigal Rencus, Daniel Chamovitz. Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol. Syst. Biol. 3:108, 2007.



Isaac Elias and Tamir Tuller. Reconstruction of Ancestral Genomic Sequences Using Likelihood. J. Comput. Biol. 14(2):216-37, 2007. (pdf).



Benny Chor and Tamir Tuller. Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. J. Comput. Biol. 14(6):617-38, 2007.



Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. Bioinformatics 23 (2):123-128, 2007. (pdf).



Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. Mol. Biol. Evol. 24 (1):324-37, 2007.



Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Maximum likelihood of phylogenetic networks. Bioinformatics 22 (21): 2604-2611, 2006. (pdf) (supplementary meterial (pdf) ).



Benny Chor, Tamir Tuller. Finding a maximum likelihood tree is hard. J. ACM 53(5):722-744, 2006. (pdf).



Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor. The Average Common Substring Approach to Phylogenomics. Journal of Computational Biology (JCB) 13(2):336-50, 2006. (pdf).



Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation. Bioinformatics 21(Suppl 1):i97-i106, 2005. (pdf).


Peer-Reviewed Conference Proceedings


Adi Mano, Tamir Tuller, Oded Beja, Ron Y. Pinter. Comparative Classification of Species and the Study of Pathway Evolution based on the Alignment of Metabolic Pathways. to appear in APBC 2010.



Tamir Tuller*, Hadas Birin*, Martin Kupiec and Eytan Ruppin. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological examples. to appear in RECOMB-CG 2009.



Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevitch, Eytan Ruppin and Martin Kupiec. Higher-order Genomic Organization of Cellular Functions in Yeast. The 4th Annual RECOMB Satellite on Systems Biology, MIT, MA, USA, Oct 29-Nov 2, 2008.



Yedael Waldman*, Tamir Tuller*, Tomer Shlomi, Shaul Karni, Roded Sharan and Eytan Ruppin. Gene Translation Efficiency in Healthy and Cancerous Human Tissues. The 5th Annual RECOMB Satellite on Regulatory Genomics, MIT, MA, USA, Oct 29-Nov 2, 2008.



Udi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, and Tamir Tuller. Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases. The 2008 IEEE International Conference on Bioinformatics and Biomedicine. Philadelphia, PA, USA, Nov. 5-7, 2008.



Yifat Felder and Tamir Tuller. Discovering Local Patterns of Co - Evolution. Comparative Genomics, International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008.



Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. The 8th workshop on Algorithms in Bioinformatics (WABI), Karlsruhe, Germany, September 15-19, 2008.



Hadas Birin, Zohar Gal-or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations and Horizontal Transfers by the Minimum Evolution Criterion. The 7th workshop on Algorithms in Bioinformatics (WABI), University of Pennsylvania , USA , September 7-9, 2007.



Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir 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),Georgia State University in Atlanta, USA, May 7-10, 2007.



Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. ECCB 2006, Eilat, Israel, January 21-24, 2007.



Tamir Tuller, Benny Chor. Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB 2006, Venice, Italy, 30-44, April 2-5, 2006. Abstract.



Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor. Time - Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. (WABI) 2005, Mallorca, Spain, Ooctober 3-6, 2005. Abstract.



Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation. ISMB 2005, Detroit Marriot Renaissance Center, Michigan, USA, June 25-29, 2005. Proceedings p. 97.Abstract.



David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor. Information Theoretic Approaches to Whole Genome Phylogenomics. RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005. Proceedings p. 283. Abstract.



Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees is Hard. RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005. Proceedings p. 296. Abstract.



Benny Chor, Tamir Tuller. Adding hidden nodes to gene network. The 4th workshop on Algorithms in Bioinformatics (WABI), 2004, Bergen, Norway, September 17-21, 2004. Proceedings p. 123. Abstract.


Theses


Tamir Tuller. Approximation of communication channel by finite-state model, and universal decoding. Master's thesis under the supervision of Prof. Jacob Ziv , Faculty of Electrical Engineering, Technion, Israel, 2002.



Tamir Tuller. Computational Aspects of Molecular Evolution. Ph.D thesis under the supervision of Prof. Benny Chor and Prof. Nathan Nelson, School of Computer Science, Tel-Aviv University, Israel, 2006.


Selected Posters


Tamir Tuller, Ohad Greenshpan, Eran Cohen, Benny Chor. Regulation and Genomic Arrangement of microRNA Genes. RECOMB 2006.



Tamir Tuller, Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. RECOMB 2007.



Yifat Felder, Tamir Tuller, Nana Ginzbourg, Udi Rubinstein, Michael Gurevich, Anat Achiron. A new approach for inferring regulatory networks from literature and gene expression measurements. RECOMB 2007.



Tamir Tuller, Martin Kupiec, Eytan Ruppin. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. RECOMB-CG 2008.