Research Topics
Species | Tamir TullerSummaryAffiliation: Tel Aviv University Country: Israel Publications
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Detail Information
Publications
Common and specific signatures of gene expression and protein-protein interactions in autoimmune diseasesT 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...
Composite effects of gene determinants on the translation speed and density of ribosomesTamir Tuller
Department of Biomedical Engineering, Tel Aviv University, Israel
Genome Biol 12:R110. 2011....- Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathwaysAdi 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... - Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissionsTamir 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... - Co-evolutionary networks of genes and cellular processes across fungal speciesTamir 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... - Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cellsMichael 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... - Properties of untranslated regions of the S. cerevisiae genomeTamir 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... - Reconstructing ancestral gene content by coevolutionTamir 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... - Discovering local patterns of co-evolution: computational aspects and biological examplesTamir 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... - Translation efficiency is determined by both codon bias and folding energyTamir Tuller
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 107:3645-50. 2010.... - Higher-order genomic organization of cellular functions in yeastTamir 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)... - Evolutionary rate and gene expression across different brain regionsTamir 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... - Determinants of protein abundance and translation efficiency in S. cerevisiaeTamir 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... - Forbidden penta-peptidesTamir 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... - Co-evolution is incompatible with the Markov assumption in phylogeneticsTamir 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... - Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examplesTamir 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... - Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterionHadas 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... 
Biological networks: comparison, conservation, and evolution via relative description lengthBenny 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...- The average common substring approach to phylogenomic reconstructionIgor 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... - Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cellsAlexandra 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... - RFMapp: ribosome flow model applicationHadas Zur
The Blavatnik School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
Bioinformatics 28:1663-4. 2012..AVAILABILITY AND IMPLEMENTATION: Distributable cross-platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/RFM_Installers/install.htm... - An evolutionarily conserved mechanism for controlling the efficiency of protein translationTamir 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... - Sequence features of E. coli mRNAs affect their degradationGal 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... - Efficient manipulations of synonymous mutations for controlling translation rate: an analytical approachAlexandra 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... - Selection for translation efficiency on synonymous polymorphisms in recent human evolutionYedael 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... - Genome-scale analysis of translation elongation with a ribosome flow modelShlomi Reuveni
Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Ramat Aviv, Israel
PLoS Comput Biol 7:e1002127. 2011.... - Association between translation efficiency and horizontal gene transfer within microbial communitiesTamir 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... - Maximum likelihood of evolutionary trees: hardness and approximationBenny Chor
School of Computer Science, Tel-Aviv University Tel-Aviv, Israel
Bioinformatics 21:i97-106. 2005..We note that ML reconstruction for sparse inputs is still hard under this condition, and furthermore many real datasets satisfy it... - TP53 cancerous mutations exhibit selection for translation efficiencyYedael 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... - Efficient algorithms for reconstructing gene content by co-evolutionHadas 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... - Strong association between mRNA folding strength and protein abundance in S. cerevisiaeHadas 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... - Metabolic modeling of endosymbiont genome reduction on a temporal scaleKeren Yizhak
The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
Mol Syst Biol 7:479. 2011.... - Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stagesYedael 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... - Clone clusters in autoreactive CD4 T-cell lines from probable multiple sclerosis patients form disease-characteristic signaturesMathilda 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... - Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expressionEfrat 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... - Stability analysis of the ribosome flow modelMichael 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... - On the steady-state distribution in the homogeneous ribosome flow modelMichael 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... - Reconstruction of ancestral genomic sequences using likelihoodIsaac 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... - Efficient parsimony-based methods for phylogenetic network reconstructionGuohua 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... - Inferring phylogenetic networks by the maximum parsimony criterion: a case studyGuohua 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... - Maximum likelihood of phylogenetic networksGuohua Jin
Department of Computer Science, Rice University Houston, TX, USA
Bioinformatics 22:2604-11. 2006..AVAILABILITY: Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf..