Welcome!

Selected Publications


Tal Gutman, Guy Goren, Omri Efroni, and Tamir Tuller. Estimating the predictive power of silent mutations on cancer classification and prognosis. NPJ Genom Med. 2021. .



Hadas Zur, Rachel Cohen-Kupiec, Sophie Vinokour, Tamir Tuller. Algorithms for ribosome traffic engineering and their potential in improving host cells' titer and growth rate. Scientific reports. 2020. .



Michael Peeri, Tamir Tuller. High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life. Genome Biology. 2020. .



Iddo Weiner, Noam Shahar, Pini Marcu, Iftach Yacoby, Tamir Tuller. Solving the riddle of the evolution of Shine-Dalgarno based translation in chloroplasts. Molecular Biology and Evolution. 2019. . Cover figure:



Renana Sabi, Tamir Tuller. Novel Insights into Gene Expression Regulation during Meiosis Revealed by Translation Elongation Dynamics. Nature Systems Biology and Applications. 2019. .



A. Diament, I. Weiner, N. Shahar, S. Landman, Y. Feldman, S. Atar, M. Avitan, S. Schweitzer, I. Yacoby, T. Tuller. ChimeraUGEM: unsupervised gene expression modeling in any given organism. Bioinformatics. 2019. .



Eli Goz, Zohar Zafrir, and Tamir Tuller. Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. Bioinformatics. 2018. .



Alon Diament*, Anna Feldman*, Elisheva Schochet, Martin Kupiec, Yoav Arava, and Tamir Tuller. The extent of ribosome queuing in budding yeast. PLoS Comput Biol. 2018. .



Alon Diament and Tamir Tuller. Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. Nucleic Acids Res. 2017. .



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 (2014 - 2021)


David Shallom, Danny Naiger, Shlomo Weiss, Tamir Tuller. Accelerating whole cell simulations of mRNA translation using a dedicated hardware. To appear ACS Synthetic Biology. 2021.



Rami Zakh, Alexander Churkin, Franziska Totzeck, Marina Parr, Tamir Tuller, Ohad Etzion, Harel Dahari, Dmitrij Frishman, and Danny Barash. A mathematical analysis of HDV genotypes: from molecules to cells. To appear in Mathematics. 2021.



Shir Bahiri, Rachel Cohen-Kupiec, Dana Yacobi, Larissa Fine, Boaz Apt, Alon Diament, and Tamir Tuller. Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts. To appear in RNA biol. 2021.



Tal Gutman, Guy Goren, Omri Efroni, Tamir Tuller. Estimating the Predictive Power of Silent Mutations on Cancer Classification and Prognosis. To appear in nature npj Genome Medicine. 2021.



Shir Bahiri and Tamir Tuller. Codon-based indexes for modeling gene expression and transcript evolution. ?To appear in Computational and Structural Biotechnology Journal. 2021.



Alexander Churkin, Franziska Totzeck, Marina Parr, Tamir Tuller, Dmitrij Frishman, and Danny Barash. A mathematical analysis of the RNA structure in viruses (RNASIV) database. To appear in Mathematics. 2021.



Michael Margaliot, Wasim Huleihel, Tamir Tuller. Variability in mRNA Translation: A Random Matrix Theory Approach . To appear in Scientific Reports 2021



Hadas Zur, Rachel Cohen-Kupiec, Sophie Vinokour, Tamir Tuller. Algorithms for Ribosome Traffic Engineering and their Potential in Improving Host Cells' Titer and Growth Rate. To appear in Scientific Reports 2020



Shaked Bergman , Alon Diamant, Tamir Tuller. New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region. To appear in Bioinformatics 2020



Michal Perach#, Zohar Zafrir#, Tamir Tuller*, Oded Lewinson*. Identifying evolutionarily selected slow codons in gene families from the entire genomes of E. coli and B. subtilis. To appear in RNA Biology 2020



Lia Baron*, Shimshi Atar*, Hadas Zur*, Modi Roopin*, Eli Goz, Tamir Tuller. Computational based design, generation, and tracking of 500 synthetic silent variants of Porcine circovirus reveals the relations between silent genomic information and viral fitness. To appear in Scientific Reports. 2020.



Lena Danielli, Ximing Li, Tamir Tuller, Ramiz Daniel. Quantifying distribution of protein oligomerization degree reflects cellular information capacity. To appear in Scientific Reports. 2020.



Yonatan Chemla#, Michael Peeri#, Mathias Heltberg, Mogens HOgh Jensen, Tamir Tuller*, Lital Alfonta*. mRNA secondary structure stability regulates bacterial translation insulation and re-initiation. To appear in Nature communication. 2020.



Yoram Zarai, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Modi Ruppin, Justin Julander and Tamir Tuller. Evolutionary Selection against Short Nucleotide Sequences in Viruses and their Related Hosts. To appear in DNA Research. 2020.



Doron Levin, Tamir Tuller. Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics. To appear in PLoS Compt. Biol. 2020.



Shir Bahiri-Elitzur and Tamir Tuller. Computational discovery and modeling of novel gene expression rules encoded in the mRNA. To Appear in Biochemical Society Transactions. 2020.



Maya Galili, Tamir Tuller. CSN: Unsupervised Approach for Inferring Biological Networks based on the Genome Alone. To Appear in BMC Bioinformatics. 2020.



Noam Shahar, Shira Landman, Iddo Weiner*, Tamar Elman, Eyal Dafni, Yael Feldman, Tamir Tuller, Iftach Yacoby. The integration of multiple nuclear-encoded transgenes in the green alga Chlamydomonas reinhardtii results in higher transcription levels. To Appear in Frontiers in Plant Science. 2019.



Michael Peeri, Tamir Tuller. High resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life. To appear in Genome Biology. 2019.



Shaked Bergman, Tamir Tuller. Widespread non-modular overlapping codes in the coding regions. To appear in Physical Biology. 2019.



Iddo Weiner#, Yael Feldman#, Noam Shahar, Iftach Yacoby, Tamir Tuller. CSO -- a sequence optimization software for engineering chloroplast expression in Chlamydomonas reinhardtii. To appear in Algal Research. 2019.



Iddo Weiner, Noam Shahar, Pini Marcu, Iftach Yacoby, Tamir Tuller. Solving the riddle of the evolution of Shine-Dalgarno based translation in chloroplasts. To appear in Molecular Biology and Evolution. 2019.



Renana Sabi, Tamir Tuller. Novel Insights into Gene Expression Regulation during Meiosis Revealed by Translation Elongation Dynamics. To appear in Nature Systems Biology and Applications. 2019.



Noam Shahar#, Iddo Weiner#, Lior Stotsky, Tamir Tuller*, Iftach Yacoby*. Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts. To appear in Nucleic Acids Res. 2019.



Arup Panda, Tamir Tuller. Exploring the Evidences of Local Selection in Naturally Occurring Intrinsically Disordered Proteins. to appear in Genomics Proteomics and Bioinformatics. 2019



A. Diament, I. Weiner, N. Shahar, S. Landman, Y. Feldman, S. Atar, M. Avitan, S. Schweitzer, I. Yacoby, T. Tuller. ChimeraUGEM: unsupervised gene expression modeling in any given organism. to appear in Bioinformatics. 2019



T. Tuller, A. Diament, A. Yahalom, A. Zemach, S. Atar, D.A. Chamovitz . The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. to appear in Bioinformatics. 2018



Eyal Dafni, Iddo Weiner, Tamir Tuller*, Iftach Yacoby* . Image processing algorithm for high throughput quantification of colony luminescence. to appear in mSphere. 2018



R. Sabi and T. Tuller. Modeling and measuring intracellular competition for finite resources during gene expression. To appear in J. R. Soc. Interface. 2018.



I. Nanikashvili, Y. Zarai, A. Ovseevich, T. Tuller* and M. Margaliot. Networks of ribosome flow models for modeling and analyzing intracellular traffic. To appear in Scientific Rep. 2018.



E. Leopold, T. Tuller and M. Scheinowitz. Prediction of the Wingate anaerobic mechanical power outputs from a maximal incremental cardiopulmonary exercise stress test using machine-learning approach. To appear in PLoS-1. 2018.



A. Panda, M. Drancourt, T. Tuller and P. Pontarotti. Genome wide analysis of horizontally acquired genes in the genus Mycobacterium. To appear in Scientific Rep. 2018.



D. Levin, T. Tuller. Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model. To appear in Scientific Rep. 2018.



I. Weiner, N. Shahar, Y. Feldman, S. Landman, Y. Milrad, O. Ben-Zvi, M. Avitan, E. Dafni, S. Schweitzer, H. Eilenberg, S. Atar, A. Diament, T. Tuller*, I. Yacoby*. Overcoming the expression barrier of the ferredoxin-hydrogenase chimera in Chlamydomonas reinhardtii supports a linear increment in photosynthetic hydrogen output. To appear in Algal Research. 2018.



E. Goz, Z. Zafrir, T. Tuller. Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. To appear in Bioinformatics. 2018.



A. Diament and T. Tuller. Modeling three-dimensional genomic organization in evolution and pathogenesis. To appear in Seminars in Cell and Developmental Biology. 2018.



Y. Zarai and T. Tuller. Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. To appear in PLoS Comput Biol. 2018.



E. Goz*, Y. Tsalenchuck*, R. Oren Benaroya, Z. Zafrir, S. Atar, T. Altman , J. Julander, T. Tuller. Generation of a synthetic Dengue virus and comparison to the wild type strains. To appear in BMC Bioinformatics. 2018.



I. Weiner#, S. Atar#, S. Schweitzer#, H. Eilenberg, Y. Feldman, M. Avitan, A. Danon, T. Tuller*, I. Yacoby*. Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization. To appear in The plant journal. 2017.



A. Diament*, A. Feldman*, E. Schochet, M. Kupiec, Y. Arava, and T. Tuller. The extent of ribosome queuing in budding yeast. To appear in PLoS Comput Biol. 2017.



G. Shaham and T. Tuller. Genome scale analysis of E. coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation. To appear in DNA Research. 2017.



E. Cohen* Z. Zafrir* and T. Tuller. A Code for Transcription Elongation Speed. To appear in RNA Biology. 2017.



O. Mioduser*, E. Goz*, T. Tuller. Significant differences in terms of codon usage bias between bacteriophage early and late genes: A comparative genomics analysis. To appear in BMC Genomics. 2017.



Y. Zarai, M. Margaliot and T. Tuller. Ribosome Flow Model with Extended Objects. To appear in J. R. Soc. Interface. 2017.



Y. Zarai, M. Margaliot and T. Tuller. A Deterministic Mathematical Model for Bidirectional Excluded Flow with Langmuir Kinetics. To appear in PLoS-1. 2017.



A. Diament and T. Tuller. Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. To appear in Nucleic Acids Res. 2017.



R. Sabi and T. Tuller. Nascent peptide-mediated ribosome stalling and its evolution. To appear in RNA. 2017.



Y. Zarai, M. Margaliot, E.D. Sontag, T. Tuller. Controlling mRNA Translation. To appear IEEE/ACM Trans Comput Biol Bioinform. 2017.



Y. Zarai, M. Margaliot, T. Tuller. Optimal Down Regulation of mRNA Translation. To appear in Scientific reports. 2016.



E. Goz*, O. Mioduser*, A. Diament, T. Tuller. Evidence of Translation Efficiency Adaptation of the Coding Regions of the Bacteriophage Lambda. To appear in DNA Research. 2016.



Z. Zafrir and T. Tuller. Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression prediction. To appear in BMC Bioinformatics. 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.


You can find a full list of my publication here.