Tamir Tuller
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Israeli researcher
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Computer Science Biology
Tamir Tuller's Degrees
- PhD Bioinformatics Tel Aviv University
- Masters Computer Science Tel Aviv University
- Bachelors Computer Science Tel Aviv University
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Why Is Tamir Tuller Influential?
(Suggest an Edit or Addition)According to Wikipedia, Tamir Tuller is an Israeli engineer, a computer scientist, and a systems and synthetic biologist. He is a professor and the director of Tel Aviv University's Laboratory of Computational Systems and Synthetic Biology. As of February 2022, Tuller has authored over 150 peer-reviewed scientific journal articles and hundreds of additional types of publications and patents. In addition, he is the founder and primary instructor of the International Genetically Engineered Machine program at Tel Aviv University and an entrepreneur.
Tamir Tuller's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation (2010) (771)
- Translation efficiency is determined by both codon bias and folding energy (2010) (515)
- The Average Common Substring Approach to Phylogenomic Reconstruction (2006) (208)
- The effect of tRNA levels on decoding times of mRNA codons (2014) (199)
- Composite effects of gene determinants on the translation speed and density of ribosomes (2011) (198)
- Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model (2011) (174)
- Multiple roles of the coding sequence 5′ end in gene expression regulation (2014) (164)
- Maximum likelihood of phylogenetic networks (2006) (129)
- Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae (2007) (127)
- Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells (2012) (115)
- Maximum likelihood of evolutionary trees: hardness and approximation (2005) (110)
- Strong association between mRNA folding strength and protein abundance in S. cerevisiae (2012) (101)
- Association between translation efficiency and horizontal gene transfer within microbial communities (2011) (98)
- New Universal Rules of Eukaryotic Translation Initiation Fidelity (2013) (96)
- A model for competition for ribosomes in the cell (2015) (94)
- Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias (2014) (92)
- Common and specific signatures of gene expression and protein–protein interactions in autoimmune diseases (2012) (88)
- Inferring phylogenetic networks by the maximum parsimony criterion: a case study. (2006) (88)
- Maximum Likelihood of Evolutionary Trees Is Hard (2005) (82)
- Entrainment to Periodic Initiation and Transition Rates in a Computational Model for Gene Translation (2014) (76)
- Stability Analysis of the Ribosome Flow Model (2012) (74)
- Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages (2010) (71)
- Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution (2016) (65)
- Laquinimod suppress antigen presentation in relapsing–remitting multiple sclerosis: In-vitro high-throughput gene expression study (2010) (65)
- A comparative genomics study on the effect of individual amino acids on ribosome stalling (2015) (61)
- Finding a maximum likelihood tree is hard (2006) (61)
- Estimation of ribosome profiling performance and reproducibility at various levels of resolution (2016) (60)
- Efficient parsimony-based methods for phylogenetic network reconstruction (2007) (58)
- stAIcalc: tRNA adaptation index calculator based on species-specific weights (2016) (57)
- Reconstructing ancestral gene content by coevolution. (2010) (57)
- Mean of the Typical Decoding Rates: A New Translation Efficiency Index Based on the Analysis of Ribosome Profiling Data (2014) (52)
- Properties of untranslated regions of the S. cerevisiae genome (2009) (52)
- Ribosome flow model with positive feedback (2013) (52)
- The extent of ribosome queuing in budding yeast (2018) (50)
- Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution (2011) (49)
- Conservation of the relative tRNA composition in healthy and cancerous tissues. (2012) (47)
- Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach (2014) (45)
- Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression (2007) (44)
- Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization (2018) (43)
- Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells (2009) (39)
- Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants (2015) (37)
- Quantifying the Effect of Ribosomal Density on mRNA Stability (2014) (37)
- Contraction after small transients (2015) (35)
- Sensitivity of mRNA Translation (2014) (35)
- Metabolic modeling of endosymbiont genome reduction on a temporal scale (2011) (35)
- On the Ribosomal Density that Maximizes Protein Translation Rate (2016) (34)
- Evolutionary rate and gene expression across different brain regions (2008) (34)
- Ribosome Flow Model on a Ring (2015) (34)
- Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways (2010) (34)
- Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic (2009) (31)
- Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function (2014) (31)
- Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model (2013) (31)
- Codon bias, tRNA pools, and horizontal gene transfer (2011) (30)
- Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease. (2014) (29)
- Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi (2015) (29)
- Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae (2014) (28)
- On the Steady-State Distribution in the Homogeneous Ribosome Flow Model (2012) (28)
- Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach (2012) (28)
- Sequence Features of E. coli mRNAs Affect Their Degradation (2011) (27)
- Forbidden penta‐peptides (2007) (26)
- Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae (2013) (26)
- Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes (2015) (25)
- Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae. (2017) (24)
- Reconstruction of Ancestral Genomic Sequences Using Likelihood (2007) (22)
- Co-evolutionary networks of genes and cellular processes across fungal species (2009) (21)
- Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions. (2011) (21)
- A code for transcription elongation speed (2018) (20)
- Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation (2017) (20)
- Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium (2018) (19)
- Modelling and measuring intracellular competition for finite resources during gene expression (2019) (19)
- Widespread non-modular overlapping codes in the coding regions (2020) (19)
- Optimal Down Regulation of mRNA Translation (2016) (19)
- Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling (2016) (19)
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life (2020) (18)
- Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development (2014) (18)
- The RNA Polymerase Flow Model of Gene Transcription (2014) (18)
- Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge (2015) (18)
- Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda (2017) (18)
- Properties and determinants of codon decoding time distributions (2014) (18)
- Overcoming the expression barrier of the ferredoxin‑hydrogenase chimera in Chlamydomonas reinhardtii supports a linear increment in photosynthetic hydrogen output (2018) (17)
- Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae (2012) (17)
- TP53 cancerous mutations exhibit selection for translation efficiency. (2009) (17)
- Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion (2008) (16)
- Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length (2007) (16)
- On three generalizations of contraction (2014) (16)
- Codon-based indices for modeling gene expression and transcript evolution (2021) (15)
- Checkable Conditions for Contraction After Small Transients in Time and Amplitude (2017) (15)
- Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis (2017) (15)
- Challenges and obstacles related to solving the codon bias riddles. (2014) (15)
- Networks of ribosome flow models for modeling and analyzing intracellular traffic (2018) (15)
- RFMapp: ribosome flow model application (2012) (14)
- Information Theoretic Approaches to Whole Genome Phylogenies (2005) (14)
- Ribosome flow model with extended objects (2017) (13)
- A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance (2007) (13)
- Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints (2015) (12)
- Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics (2019) (12)
- Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case (2014) (12)
- The Effect of Dysregulation of tRNA Genes and Translation Efficiency Mutations in Cancer and Neurodegeneration (2012) (12)
- Clone clusters in autoreactive CD4 T‐cell lines from probable multiple sclerosis patients form disease‐characteristic signatures (2009) (11)
- A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics (2016) (11)
- Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources (2018) (11)
- Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions (2016) (11)
- Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins. (2013) (11)
- Efficient parsimony-based methods for phylogenetic network (2006) (11)
- Genomic analysis of COP 9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression (2007) (10)
- Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code (2018) (10)
- Algorithms for ribosome traffic engineering and their potential in improving host cells' titer and growth rate (2020) (10)
- A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon (2020) (9)
- The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana (2018) (9)
- Higher-Order Genomic Organization of Cellular Functions in Yeast (2009) (9)
- Variability in mRNA translation: a random matrix theory approach (2020) (9)
- Controllability Analysis and Control Synthesis for the Ribosome Flow Model (2016) (9)
- Solving the riddle of the evolution of Shine-Dalgarno based translation in chloroplasts (2018) (9)
- Quantifying the distribution of protein oligomerization degree reflects cellular information capacity (2020) (9)
- Discovering local patterns of co - evolution: computational aspects and biological examples (2010) (8)
- Selection for reduced translation costs at the intronic 5′ end in fungi (2016) (8)
- The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models (2009) (8)
- The Integration of Multiple Nuclear-Encoded Transgenes in the Green Alga Chlamydomonas reinhardtii Results in Higher Transcription Levels (2020) (8)
- Discovering Local Patterns of Co-evolution (2008) (8)
- Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence (2017) (8)
- Modeling three-dimensional genomic organization in evolution and pathogenesis. (2019) (8)
- Ribosomal mutations affecting the translation of genes that use non‐optimal codons (2014) (7)
- Biological Networks: Comparison, Conservation, and Evolutionary Trees (2006) (7)
- ChimeraUGEM: unsupervised gene expression modeling in any given organism (2019) (7)
- Analysis of Coevolving Gene Families Using Mutually Exclusive Orthologous Modules (2011) (6)
- Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics (2020) (6)
- Controlling mRNA Translation (2016) (6)
- Modeling and Analyzing the Flow of Molecular Machines in Gene Expression (2018) (6)
- Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics (2010) (5)
- Three-dimensional Genomic Organization of Genes’ Function in Eukaryotes (2016) (5)
- Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics (2019) (5)
- Prediction of the Wingate anaerobic mechanical power outputs from a maximal incremental cardiopulmonary exercise stress test using machine-learning approach (2019) (4)
- The Effect of Codon Usage on the Success of Horizontal Gene Transfer (2013) (4)
- CSO – A sequence optimization software for engineering chloroplast expression in Chlamydomonas reinhardtii (2020) (4)
- Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts (2019) (4)
- Most associations between transcript features and gene expression are monotonic. (2014) (4)
- A Mathematical Analysis of RNA Structural Motifs in Viruses (2021) (4)
- SURVEY AND SUMMARY Multiple roles of the coding sequence 5 end in gene expression regulation (2015) (4)
- Estimating the predictive power of silent mutations on cancer classification and prognosis (2021) (4)
- sbv IMPROVER Diagnostic Signature Challenge (2013) (4)
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts (2020) (3)
- MPEPE, a predictive approach to improve protein expression in E. coli based on deep learning (2022) (3)
- New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region (2020) (3)
- Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins (2020) (3)
- Efficient algorithms for reconstructing gene content by co-evolution (2011) (3)
- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds (2005) (3)
- Evolutionary selection against short nucleotide sequences in viruses and their related hosts (2020) (3)
- Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking (2017) (3)
- Image-Processing Software for High-Throughput Quantification of Colony Luminescence (2019) (3)
- Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples (2010) (3)
- Controlling the ribosomal density profile in mRNA translation (2016) (3)
- Hidden Silent Codes in Viral Genomes (2017) (3)
- Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model (2018) (3)
- Adding Hidden Nodes to Gene Networks (Extended Abstract) (2004) (2)
- A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract) (2011) (2)
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data (2022) (2)
- mRNA secondary structure stability regulates bacterial translation insulation and re-initiation (2020) (2)
- Identification of conserved slow codons that are important for protein expression and function (2021) (2)
- Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples (2009) (2)
- Solving the Riddle of the Evolution of Shine-Dalgarno Based Translation in Chloroplasts. (2019) (2)
- A Mathematical Analysis of HDV Genotypes: From Molecules to Cells. (2021) (2)
- Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels (2021) (2)
- Estimation of ribosome profiling performance and reproducibility at various levels of resolution (2016) (1)
- Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts (2022) (1)
- Translation in the cell under fierce competition for shared resources: a mathematical model (2022) (1)
- Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae (2013) (1)
- Correction: On the Ribosomal Density that Maximizes Protein Translation Rate (2017) (1)
- Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness (2021) (1)
- Novel Driver Synonymous Mutations in the Coding Regions of GCB Lymphoma Patients Improve the Transcription Levels of BCL2 (2020) (1)
- Generation and comparative genomics of synthetic dengue viruses (2017) (1)
- Properties and determinants of codon decoding time distributions (2014) (1)
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life (2020) (1)
- Computational Modeling of Gene Translation and its Potential Applications in Individualized Medicine (2011) (1)
- Computational discovery and modeling of novel gene expression rules encoded in the mRNA. (2020) (1)
- Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models (2008) (1)
- CSN: unsupervised approach for inferring biological networks based on the genome alone (2020) (1)
- CSN: unsupervised approach for inferring biological networks based on the genome alone (2020) (0)
- Flow models for efficient simulation and engineering of transcription and translation elongation (2012) (0)
- Modulating Gene Expression within a Microbiome Based on Computational Models (2022) (0)
- Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes (2015) (0)
- Supplementary material-- A comprehensive sequence-based biophysical model of translation initiation and elongation in prokaryotes (2017) (0)
- Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity (2022) (0)
- Supplementary-Material for the work Maximum Likelihood of Phylogenetic Networks (2006) (0)
- Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware (2021) (0)
- Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium (2018) (0)
- Additional file 7 (2010) (0)
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis (2023) (0)
- Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources (2019) (0)
- Author Correction: Quantifying the distribution of protein oligomerization degree reflects cellular information capacity (2021) (0)
- Doppler-Based Algorithm for Mapping Cardiac Rotors by Induced Temperature Perturbations (2018) (0)
- Reconstructing ancestral gene content by coevolution Material Supplemental (2009) (0)
- Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins (2020) (0)
- Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking (2017) (0)
- Temporal mRNA Translation Efficiency Is Encoded In Viral Coding Regions (2017) (0)
- eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content (2022) (0)
- A comparative genomics study on the effect of individual amino acids on ribosome stalling (2015) (0)
- Generation and comparative genomics of synthetic dengue viruses (2018) (0)
- Additional file 9 (2010) (0)
- Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a Microbiome (2022) (0)
- Estimating the predictive power of silent mutations on cancer classification and prognosis (2021) (0)
- The Potential of Computational Genomics in the Design of Oncolytic Viruses (2021) (0)
- Ju n 20 14 On Three Generalizations of Contraction (2018) (0)
- Additional file 10 (2010) (0)
- 11.1 Identification of Gene Regulatory Networks by Gene Disruptions and Overexpressions (2002) (0)
- Determinants of Efficient Modulation of Ribosomal Traffic Jams (2021) (0)
- Networks of ribosome flow models for modeling and analyzing intracellular traffic (2019) (0)
- A Modulation Studies Spectrum Utilization Efficifncy of Power Utilization Signal-to-itoise Ratios (0)
- A computational predictor of the anaerobic mechanical power outputs from a clinical exercise stress test (2023) (0)
- Analysis of Gene Expression Data 3.1 Gapped Chips for Sbh 3.1.1 Motivation 3.1.2 an Upper Bound (2002) (0)
- Additional file 4 (2010) (0)
- Correction (2015) (0)
- Additional file 8 (2010) (0)
- Reply to Weak effects made to appear strong by inflated correlation coefficients : The correlation between 3 D genomic distance and codon usage frequencies is comparable to the maximal correlation expected (2016) (0)
- Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases (2008) (0)
- Coevolution of Gene Families: Models, Algorithms, and Systems Biology (2012) (0)
- Reconstructing ancestral gene content by coevolution Material (2009) (0)
- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion (2007) (0)
- Analysis of the steady state translation rate in the infinite-dimensional homogeneous ribosomeflowmodel ? (2013) (0)
- Biological Networks: Comparison, Conservation, and Evolutionary Trees (Extended Abstract) (2006) (0)
- Supplementary material from "Ribosome flow model with extended objects" (2017) (0)
- SURVEY AND SUMMARY Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution (2016) (0)
- Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis (2017) (0)
- Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model (2018) (0)
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