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Selected Publications


Alon Raveh, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller. A model for competition for ribosomes in the cell. J. R. Soc. Interface. 2016 Mar;13(116). .



Tuval Ben-Yehezkel*, Shimshi Atar*, Hadas Zur, Alon Diament, Eli Goz, Tzipy Marx, Rafael Cohen, Alex Dana, Anna Feldman, Ehud Shapiro, Tamir Tuller. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants. RNA Biol. 2015 Sep 2;12(9):972-84. .



Tamir Tuller, Hadas Zur. Multiple roles of the coding sequence 5' end in gene expression regulation. Nucleic Acids Res. 2015 Jan;43(1):13-28. .



Alon Diament, Ron Y. Pinter, Tamir Tuller. Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function. Nature Communications. 16 Dec 2014. .



Hadas Zur, Tamir Tuller. Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code without Prior Knowledge. Bioinformatics. 2014 Nov 29. pii: btu797. .



Alexandra Dana, Tamir Tuller. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res. 2014 Jul 23. .



Hadas Zur, Tamir Tuller. New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol. 9(7), 2013.
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Hadas Zur, Tamir Tuller. Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO Rep. 13(3), 2012. .



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. .



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 (2012 - 2016)



Y. Zarai, M. Margaliot, T. Tuller. On the Ribosomal Density that Maximizes Protein Translation Rate. To appear in PLoS-1. 2016.



R. Sabi, R. Volvovich, T. Tuller. stAIcalc: tRNA Adaptation Index Calculator based on Species-Specific weights. To appear in Bioinformatics. 2016.



H. Zur, T. Tuller. Biophysical Modeling and Understanding of the Dynamics of mRNA Translation and its Evolution. To appear in Nucleic Acids Res. 2016.



E. Goz, T. Tuller. Evidence of a direct evolutionary selection for strong folding and mutational robustness within HIV coding regions. To appear in Journal of Computational Biology. 2016.



A. Diament, T. Tuller. Estimation of ribosome profiling performance and reproducibility at various levels of resolution. Biology Direct.2016, 11:24.



A. Raveh, M. Margaliot, Eduardo D. Sontag, and T. Tuller. A Model for Competition for Ribosomes in the Cell. To appear in Journal of the Royal Society Interface. 2016.



Z. Zafrir, H. Zur, T. Tuller. Selection for Reduced Intronic Translation Costs in Fungi. To appear in DNA Research. 2016.



H. Zur*, R. Aviner* and T. Tuller. Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. To appear in Scientific reports. 2016.



R. Sabi, and T. Tuller. A comparative genomics study on the effect of individual amino acids on ribosome stalling. BMC genomics 2015 (special issue of RECOMB-CG 2015)



E. Goz, T. Tuller. Widespread Signatures of Local mRNA Folding Structure Selection in Four Dengue Serotypes. BMC genomics 2015 (special issue of RECOMB-CG 2015)



E. D. Sontag, M. Margaliot and T. Tuller. Contraction After Small Transients. To appear in Automatica 2015.



T. Ben-Yehezkel*, S. Atar*, H. Zur, A. Diament, E. Goz, T. Marx, R. Cohen A. Dana, A. Feldman, E. Shapiro, T. Tuller. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants. RNA Biol. 2015.



Z. Zafrir and T. Tuller. Nucleotide Sequences Composition Adjacent to Intronic Splice Sites Improves Splicing Efficiency via its Effect on pre-mRNA Local Folding in Fungi. RNA. 2015.



A. Diament and T. Tuller. Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PLoS Compt. Biol. 2015.



A. Raveh, Y. Zarai, M. Margaliot, and T. Tuller. Ribosome Flow Model on a Ring. IEEE/ACM Trans Comput Biol Bioinform. 2015.



G. Poker, M. Margaliot, T. Tuller. Sensitivity of mRNA Translation. Scientific reports. 2015.



T. Tuller, H. Zur. Multiple Roles of the Coding Sequence 5' End in Gene Expression Regulation. Nucleic Acids Res. 2014.



H. Zur and T. Tuller. Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code without Prior Knowledge. Bioinformatics. 2014.



A. Dana and T. Tuller. The Mean of the typical decoding rates: a new translation efficiency index based on ribosome analysis data. G3: GENES, GENOMES, GENETICS. 2014.



A. Diament, R. Pinter, and T. Tuller. Three Dimensional Genomic Organization of Eukaryotic Genes Is Strongly Correlated With Their Codon Usage, Expression And Function. Nature communications. 2014.



G. Poker, Y. Zarai, M. Margaliot, and T. Tuller. A Convex Approach for Optimizing Protein. Translation Rate in the Inhomogeneous Ribosome Flow Model. J R Soc Interface. 2014.



A. Dana and T. Tuller. Properties and Determinants of Codons Decoding Time Distributions. To appear in BMC Genomics 2014 (special issue of RECOMB-CG 2014).



R. Singer, S. Atar, O. Atias, E. Oron, D. Segal, J. Hirsch, T. Tuller, A. Orian, D. Chamovitz. Drosophila COP9 Signalosome Subunit 7 interacts with multiple genomic loci to regulate development. Nucleic Acids Res. 2014.



A. Dana and T. Tuller. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res. 2014.



G. Pelchovich, N. Sigal, A. Dana, T. Tuller, I. G. Bravo, and U. Gophna. Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS Journal. 2014.



Y. Zarai, M. Margaliot and T. Tuller. Maximizing protein translation rate in the homogeneous ribosome flow model. IEEE/ACM Trans Comput Biol Bioinform. 2014.



R. Sabi and T. Tuller. Modeling the efficiency of codon-tRNA interactions based on codon usage bias. DNA Research, 2014.



I. Yofe*, Z. Zafrir* , R. Blau, M. Schuldiner*, T. Tuller *, E. Shapiro*, T. Ben Yehezkel*. Accurate, model-based tuning of synthetic gene expression using introns in S.cerevisiae. PLoS Genetics, 2014.



M. Margaliot, E. D. Sontag and T. Tuller. Entrainment to Periodic Initiation and Transition Rates in the Ribosome Flow Model. PLoS-1, 2014.



S. Edri, T. Tuller. Quantifying the Effect of Ribosomal Density on mRNA Stability. PLoS-1, 2014.



G. Shaham T. Tuller. Most Associations between Transcript Features Gene Expression are Monotone. Molecular BioSystems, 2014



G. Daras, S. Rigas, D. Tsitsekian, H. Zur, T. Tuller, and P. Hatzopoulos. Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease. Molecular Plant 2014.



S. Edri, E. Gazit, E. Cohen,T. Tuller. The RNA Polymerase Flow Model of Gene Transcription. IEEE Trans Biomed Circuits Syst. 2013



R. Norel, E. Bilal, N. Conrad-Chemineau, R. Bonneau, A. de la Fuente, I. Jurisica, D. Marbach, P. Meyer, J. J. Rice, T. Tuller and G. Stolovitzky. Sbv IMPROVER Diagnostics Signature Challenge Scoring Strategies. Systems Biomedicine 1:4, 1–9; October/November/December 2013



Y. Zarai, M. Margaliot and T. Tuller. Explicit expression for the steady state translation rate in the infinite-dimensional homogeneous ribosome flow model. IEEE/ACM Trans Comput Biol Bioinform. 2013.



H. Zur and T. Tuller. Transcript Features Alone Enable Accurate Prediction and Understanding of Gene Expression Evolution in S. cerevisiae. BMC Bioinfomatics. 2013 (special issue of RECOMB-CG 2013).



H. Zur and T. Tuller. New Universal Rules of Eukaryotic Translation Initiation Fidelity. PLoS Comput. Biol. 2013, 9(7):e1003136.



T Tuller. Challenges and Obstacles Related to Solving the Codon Bias Riddles. Biochemical Society Transactions. 2013.



M. Margaliot and T. Tuller . Ribosome Flow Model with Positive Feedback. J R Soc Interface. 2013. 10(85):20130267



T. Ben-Yehezkel*, H. Zur*, T. Marx, E. Shapiro, T Tuller. Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteinse. Genomics. 2013 May 28. doi:pii: S0888-7543(13)00110-9.



T. Tuller, S. Atar, E. Ruppin, M. Gurevich, A. Achiron. Common and Specific Signatures of Gene Expression and Protein-Protein Interactions in Autoimmune Diseases. Genes Immun. 2013 Mar;14(2):67-82.



T. Tuller. The effect of dysregulation of tRNA genes and translation efficiency mutations in cancer and neurodegeneration. Front Genet. 2012;3:201.



A. Dana and T. Tuller. Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol. 2012;8(11):e1002755.



M. Margaliot and T. Tuller. On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. IEEE/ACM Trans Comput Biol Bioinform. 2012; 9(6):1724-36.



H. Zur and T. Tuller. RFMapp: Ribosome Flow Model Application. Bioinformatics. 2012;28(12):1663-4.



M. Margaliot and T. Tuller. Stability Analysis of the Ribosome Flow Model. IEEE/ACM Trans Comput Biol Bioinform. 2012;9(5):1545-52.



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.


You can find a full list of my publication here.