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Tamir Tuller's lab

Research Interests

Computational Gene Translation - We are interested in developing computational models to study and simulate the process of gene translation, considering the tRNA pools, various characteristics of coding sequences, properties of the ribosome, properties of the un-translated regions and other cellular features. In addition, our models are based on the physical and statistical nature of this process.
Evolutionary Systems Biology - We study questions that are related to the co-evolution of determinants of the architecture of genomes, the function of genes, the co-evolution and the co-organization of gene families, the co-evolution of tRNA pools and coding sequences, and the evolution of sequence determinants of gene translation.
Computational Study of Molecular Evolution - We design algorithms for inferring phylogenetic trees, phylogenetic networks, ancestral genomic sequences, and for studying co-evolution. I then apply these algorithms to answer questions in evolutionary systems biology.
Others - Gene expression signatures in autoimmune diseases and Cancer evolution.

Selected Publications


Shlomi Reuveni*, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller*. Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol. 2011 Sep;7(9):e1002127.



Tamir Tuller, Shimshi Atar, Eytan Ruppin, Michael Gurevich, and Anat Achiron. Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions. Hum Mol Genet. 2011 Sep 15;20(18):3606-19..



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. .



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;107(8):3645-50 .



Tamir Tuller*, Hadas Birin*, Uri Gophna, Martin Kupiec and Eytan Ruppin. Reconstructing Ancestral Gene content by Co-Evolution. Genome Research. 2009; 20(1):122-32. .



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. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. Genome Biol. 2009;10(5):R48. .



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. .



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



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


You can find a full list of my publication here.

Recent Publications (2011 - 2012)



M. Margaliot and T. Tuller. Stability Analysis of the Ribosome Flow Model. Accepted to TCCB 2012.



H. Zur and T. Tuller. RFMapp: Ribosome Flow Model Application. Bioinformatics. 2012 Apr 11.



S. Mahlab, T. Tuller*, M. Linial*. Conservation of the relative tRNA compositions in healthy and cancerous tissues. RNA. 2012 Apr;18(4)640-52



H. Zur and T. Tuller. Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO-Rep. 2012 Mr 1; 13(3):272-7.



G. Lenz, A. Doron-Faigenboim, E. Z. Ron, T. Tuller, and U. Gophna. Sequence features of E. coli mRNAs affect their degradation. PLoS-one. 2011;6(12):e28544.



T. Tuller*, I. Veksler*, N. Gazit, M. Kupiec, E. Ruppin, M. Ziv . Composite Effects of the Coding Sequences Determinants on the Speed and Density of Ribosomes. Genome Biol. 2011 Nov 3; 12(11):R110.



A. Dana and T. Tuller. Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate -- an Analytical Approach. J. Comput. Biol. (special issue of RECOMB-RG 2011). 2012 Feb; 19(2):200-31



H. Birin and T. Tuller. Efficient Algorithms for Reconstructing Genomic Sequences by Co-Evolution. BMC Bioinformatics (special issue of RECOMB-CG 2011). 2001 Oct 5; 12 Suppl 9:12.



Y. Y. Waldman, T. Tuller*, A. Keinan*, and E. Ruppin*. Selection for translation efficiency in human SNPs. Genome Biol. Evol. 2011;3:749-61.



T. Tuller, S. Atar, E. Ruppin, M. Gurevich, A. Achiron. Global Map of Physical Interactions among Differentially Expressed Genes in Multiple Sclerosis Relapses and Remissions. Hum. Mol. Gen. 2011 Sep 15;20(18):3606-19.



S. Reuveni*, I. Meilijson, M. Kupiec, E. Ruppin and T. Tuller*. Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model.PLoS Comput. Biol. Sep 2011;7(9):e1002127.



X. Zhang*, M. Kupiec, U. Gophna and T. Tuller*. Analysis of Co-evolving Gene Families Using Evolutionarily Reciprocal Orthologous Modules. Genome Biol. Evol. 2011;3:413-23.



T. Tuller. Codon bias, tRNA pools, and horizontal gene transfer. Mobile Genetic Elements 2011; 1(1):75 - 77.



K. Yizhak, T. Tuller, B. Papp, E. Ruppin. Metabolic modeling of endosymbiont genome reduction on a temporal scale. Nature Mol. Sys. Biol. 2011 Mar 29;7:479.



T. Tuller, Y. Gir, Y. Sella, A. Kreimer, S. Freilich, M. Kupiec, U. Gophna, E. Ruppin. Associations Between Translation Efficiency and Horizontal Gene Transfer Within Microbial Communities. Nucleic Acids Res. 2011 Feb 22 [Epub ahead of print].



Shlomi Reuveni*, Isaac Meilijson, Martin Kupiec, Eytan Ruppin and Tamir Tuller* . Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. Accepted to RECOMB 2011, Vancouver,BC, March 28-31, 2011.



T. Tuller and H. Zur. Computational modeling of gene translation and its potential applications in individualized medicine. Book chapter in "Patient-Specific Modeling in Tomorrow's Medicine". To appear.


You can find a full list of my publication here.