Tamir Tuller

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. doi request reprint Common and specific signatures of gene expression and protein-protein interactions in autoimmune diseases
    T Tuller
    School of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Genes Immun 14:67-82. 2013
  2. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
  3. pmc Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
    Adi Mano
    Dept, of Computer Science, Technion Israel Institute of Technology, Haifa 32000, Israel
    BMC Bioinformatics 11:S38. 2010
  4. doi request reprint Co-evolution is incompatible with the Markov assumption in phylogenetics
    Tamir Tuller
    Faculty of Mathematics and Computer Science, Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel
    IEEE/ACM Trans Comput Biol Bioinform 8:1667-70. 2011
  5. pmc Co-evolutionary networks of genes and cellular processes across fungal species
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 10:R48. 2009
  6. pmc Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells
    Michael Gurevich
    Multiple Sclerosis Center, Sheba Medical Center, Tel Hashomer, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    BMC Med Genomics 2:46. 2009
  7. pmc Properties of untranslated regions of the S. cerevisiae genome
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    BMC Genomics 10:391. 2009
  8. pmc Translation efficiency is determined by both codon bias and folding energy
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:3645-50. 2010
  9. pmc Reconstructing ancestral gene content by coevolution
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    Genome Res 20:122-32. 2010
  10. pmc Discovering local patterns of co-evolution: computational aspects and biological examples
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    BMC Bioinformatics 11:43. 2010

Collaborators

Detail Information

Publications45

  1. doi request reprint Common and specific signatures of gene expression and protein-protein interactions in autoimmune diseases
    T Tuller
    School of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Genes Immun 14:67-82. 2013
    ..The relevant genes and pathways reported in this study are discussed at length, and may be helpful in the diagnoses and understanding of autoimmunity and/or specific autoimmune diseases...
  2. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
    ....
  3. pmc Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
    Adi Mano
    Dept, of Computer Science, Technion Israel Institute of Technology, Haifa 32000, Israel
    BMC Bioinformatics 11:S38. 2010
    ..Second, we describe a new approach for comparing the evolution of metabolic pathways. This approach can be used for detecting co-evolutionary relationships between metabolic pathways...
  4. doi request reprint Co-evolution is incompatible with the Markov assumption in phylogenetics
    Tamir Tuller
    Faculty of Mathematics and Computer Science, Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel
    IEEE/ACM Trans Comput Biol Bioinform 8:1667-70. 2011
    ..Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution...
  5. pmc Co-evolutionary networks of genes and cellular processes across fungal species
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 10:R48. 2009
    ..The introduction of measures such as evolutionary rate and propensity for gene loss have significantly advanced our knowledge of the evolutionary history and selection forces acting upon individual genes and cellular processes...
  6. pmc Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells
    Michael Gurevich
    Multiple Sclerosis Center, Sheba Medical Center, Tel Hashomer, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    BMC Med Genomics 2:46. 2009
    ..Similar approach can be also useful for dealing with other autoimmune diseases that characterized by relapsing-remitting nature...
  7. pmc Properties of untranslated regions of the S. cerevisiae genome
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    BMC Genomics 10:391. 2009
    ..The distribution of genes along chromosomes and the length of intragenic regions are basic genomic features known to play a major role in the regulation of gene transcription and translation...
  8. pmc Translation efficiency is determined by both codon bias and folding energy
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:3645-50. 2010
    ....
  9. pmc Reconstructing ancestral gene content by coevolution
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    Genome Res 20:122-32. 2010
    ..Our analysis suggests that LUCA appears to have been bacterial-like and had a genome size similar to the genome sizes of many extant organisms...
  10. pmc Discovering local patterns of co-evolution: computational aspects and biological examples
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    BMC Bioinformatics 11:43. 2010
    ..Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local...
  11. doi request reprint Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions
    Tamir Tuller
    School of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Hum Mol Genet 20:3606-19. 2011
    ..Some of these genes may be useful biomarkers for diagnosing MS and predicting relapses in MS patients...
  12. doi request reprint Higher-order genomic organization of cellular functions in yeast
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    J Comput Biol 16:303-16. 2009
    ..coli. A network-based analysis further supports this notion and suggests that the eukaryotic genomic architecture is more organized than previously thought. See online Supplementary Material at (www.liebertonline.com)...
  13. pmc Evolutionary rate and gene expression across different brain regions
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    Genome Biol 9:R142. 2008
    ..The evolutionary rate of a protein is a basic measure of evolution at the molecular level. Previous studies have shown that genes expressed in the brain have significantly lower evolutionary rates than those expressed in somatic tissues...
  14. pmc Determinants of protein abundance and translation efficiency in S. cerevisiae
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 3:e248. 2007
    ..Our analysis shows that in parallel to the adaptation occurring at the tRNA level via the codon bias, proteins do undergo a complementary adaptation at the amino acid level to further increase their abundance...
  15. pmc Forbidden penta-peptides
    Tamir Tuller
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Protein Sci 16:2251-9. 2007
    ..g., eukaryotes, prokaryotes, and archaea). Our analysis provides the first steps toward understanding the "grammar" of the forbidden penta-peptides...
  16. doi request reprint Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples
    Tamir Tuller
    Faculty of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel
    J Comput Biol 17:1327-44. 2010
    ..In addition, we showed that our approach reconstructs missing values at the leaves of the Fungi evolutionary tree better than ML or MP...
  17. doi request reprint Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion
    Hadas Birin
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 24:826-32. 2008
    ..Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input...
  18. ncbi request reprint Biological networks: comparison, conservation, and evolution via relative description length
    Benny Chor
    School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    J Comput Biol 14:817-38. 2007
    ..These conserved regions appear to be biologically relevant, proving the viability of our approach...
  19. ncbi request reprint The average common substring approach to phylogenomic reconstruction
    Igor Ulitsky
    School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    J Comput Biol 13:336-50. 2006
    ..We describe here five different applications of the method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights...
  20. pmc Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells
    Alexandra Dana
    The Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 8:e1002755. 2012
    ..Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance...
  21. doi request reprint RFMapp: ribosome flow model application
    Hadas Zur
    The Blavatnik School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Bioinformatics 28:1663-4. 2012
    ..Thus, it has been shown that RFM outperforms traditional predictors when analyzing both heterologous and endogenous genes...
  22. doi request reprint An evolutionarily conserved mechanism for controlling the efficiency of protein translation
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 141:344-54. 2010
    ..We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression...
  23. pmc Sequence features of E. coli mRNAs affect their degradation
    Gal Lenz
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
    PLoS ONE 6:e28544. 2011
    ..Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes...
  24. doi request reprint Efficient manipulations of synonymous mutations for controlling translation rate: an analytical approach
    Alexandra Dana
    The Iby and Aladar Fleischman Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
    J Comput Biol 19:200-31. 2012
    ..We demonstrate how this heuristic can be used in biotechnology for engineering a heterologous gene before expressing it in a new host...
  25. pmc Genome-scale analysis of translation elongation with a ribosome flow model
    Shlomi Reuveni
    Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Ramat Aviv, Israel
    PLoS Comput Biol 7:e1002127. 2011
    ....
  26. pmc Selection for translation efficiency on synonymous polymorphisms in recent human evolution
    Yedael Y Waldman
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Genome Biol Evol 3:749-61. 2011
    ..Testifying to this potential, we describe two synonymous SNPs that may have clinical implications in phenylketonuria and in Best's macular dystrophy due to TE differences between alleles...
  27. pmc Association between translation efficiency and horizontal gene transfer within microbial communities
    Tamir Tuller
    Faculty of Mathematics and Computer Science, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Blavatnik School of Computer Science, School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 39:4743-55. 2011
    ..Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community...
  28. doi request reprint TP53 cancerous mutations exhibit selection for translation efficiency
    Yedael Y Waldman
    Department of Molecular Microbiology and Biotechnology, Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    Cancer Res 69:8807-13. 2009
    ..Taken together, these results show that TE plays an important role in the selection of TP53 cancerous mutations...
  29. ncbi request reprint Maximum likelihood of evolutionary trees: hardness and approximation
    Benny Chor
    School of Computer Science, Tel Aviv University Tel Aviv, Israel
    Bioinformatics 21:i97-106. 2005
    ..It was proved that reconstructing the ML tree is computationally intractable (NP-hard). In this work we explore three directions, which extend that result...
  30. pmc Clone clusters in autoreactive CD4 T-cell lines from probable multiple sclerosis patients form disease-characteristic signatures
    Mathilda Mandel
    Blood Centre, Sheba Medical Centre, Tel Hashomer, 52621, Israel
    Immunology 128:287-300. 2009
    ..Analyses of clonal-clustering patterns may potentially aid in subclassification of MS or in characterizing aetiological agents of this disease...
  31. doi request reprint On the steady-state distribution in the homogeneous ribosome flow model
    Michael Margaliot
    School of Electrical Engineering Systems, Tel Aviv University, Tel Aviv
    IEEE/ACM Trans Comput Biol Bioinform 9:1724-36. 2012
    ..We discuss the relationship between these theoretical results and biological findings on the translation process...
  32. pmc Efficient algorithms for reconstructing gene content by co-evolution
    Hadas Birin
    School of Computer Science, Tel Aviv University, Israel
    BMC Bioinformatics 12:S12. 2011
    ..To this end, we defined a new computational problem, the Ancestral Co-Evolutionary (ACE) problem, and developed algorithms for solving it...
  33. pmc Strong association between mRNA folding strength and protein abundance in S. cerevisiae
    Hadas Zur
    School of Computer Science, and Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
    EMBO Rep 13:272-7. 2012
    ..mF strength also strongly correlates with ribosomal density and mRNA levels, suggesting that this relation at least partially pertains to the efficiency of translation elongation, presumably by preventing aggregation of mRNA molecules...
  34. pmc Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages
    Yedael Y Waldman
    Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:2964-74. 2010
    ..Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms...
  35. pmc Metabolic modeling of endosymbiont genome reduction on a temporal scale
    Keren Yizhak
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 7:479. 2011
    ....
  36. pmc New universal rules of eukaryotic translation initiation fidelity
    Hadas Zur
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 9:e1003136. 2013
    ..With the new suggested rules we were able to obtain a twice higher correlation with ribosomal density and protein levels in comparison to the Kozak rule alone (e.g. for protein levels r=0.7 vs. r=0.31; p<10(-12))...
  37. doi request reprint Ribosome flow model with positive feedback
    Michael Margaliot
    School of Electrical Engineering Systems, Tel Aviv University, Tel Aviv 69978, Israel
    J R Soc Interface 10:20130267. 2013
    ..These results may perhaps be used to re-engineer the biological system in order to obtain a desired translation rate...
  38. pmc Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression
    Efrat Oron
    Department of Plant Sciences, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:108. 2007
    ..A null mutation in CSN subunit 4 and hypomorphic mutations in csn5 lead to more severe defects than seen in the csn5-null mutants strain, suggesting that CSN5 carries only some of the CSN function...
  39. doi request reprint Explicit expression for the steady-state translation rate in the infinite-dimensional homogeneous ribosome flow model
    Yoram Zarai
    Tel Aviv University, Tel Aviv
    IEEE/ACM Trans Comput Biol Bioinform 10:1322-8. 2013
    ..To demonstrate this, we apply our approach to estimate the mean initiation rate in M. musculus, finding it to be around 0.17 codons per second...
  40. doi request reprint Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins
    Tuval Ben-Yehezkel
    Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    Genomics 102:419-29. 2013
    ..Genomic analysis of S. cerevisiae further supports the scanning model: ATG codons downstream rather than upstream of the main ATG tend to have higher context scores. ..
  41. ncbi request reprint Stability analysis of the ribosome flow model
    Michael Margaliot
    School of Electrical Engineering and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
    IEEE/ACM Trans Comput Biol Bioinform 9:1545-52. 2012
    ..Our analysis is based on a contraction principle and the theory of monotone dynamical systems. These analysis tools may prove useful in studying other properties of the RFM as well as additional intracellular biological processes...
  42. ncbi request reprint Maximum likelihood of phylogenetic networks
    Guohua Jin
    Department of Computer Science, Rice University Houston, TX, USA
    Bioinformatics 22:2604-11. 2006
    ..In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative...
  43. ncbi request reprint Efficient parsimony-based methods for phylogenetic network reconstruction
    Guohua Jin
    Department of Computer Science, Rice University, Houston, TX, USA
    Bioinformatics 23:e123-8. 2007
    ..Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results...
  44. ncbi request reprint Reconstruction of ancestral genomic sequences using likelihood
    Isaac Elias
    Department of Numerical Analysis and Computer Science, KTH, Stockholm, Sweden
    J Comput Biol 14:216-37. 2007
    ..Supplementary material of this work is available at www.nada.kth.se/~isaac/publications/aml/aml.html...
  45. ncbi request reprint Inferring phylogenetic networks by the maximum parsimony criterion: a case study
    Guohua Jin
    Department of Computer Science, Rice University, Houston, Texas, USA
    Mol Biol Evol 24:324-37. 2007
    ..Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history...