Tamir Tuller

发表

sbv IMPROVER Diagnostic Signature Challenge

Igor Jurisica, Erhan Bilal, Raquel Norel, 2013 .

Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion

Tamir Tuller, Isaac Elias, Hadas Birin, 2007, WABI.

Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length

Tamir Tuller, Benny Chor, B. Chor, 2007, J. Comput. Biol..

Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Maximum likelihood of evolutionary trees: hardness and approximation

Tamir Tuller, Benny Chor, B. Chor, 2005, ISMB.

Image-Processing Software for High-Throughput Quantification of Colony Luminescence

Tamir Tuller, Eyal Dafni, Iddo Weiner, 2019, mSphere.

Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code

Tamir Tuller, Eli Goz, Zohar Zafrir, 2018, Bioinform..

Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Novel Driver Synonymous Mutations in the Coding Regions of GCB Lymphoma Patients Improve the Transcription Levels of BCL2

Tamir Tuller, Zohar Zafrir, Ofek Shami-Schnitzer, 2020, ISMCO.

Controllability Analysis and Control Synthesis for the Ribosome Flow Model

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Reconstruction of Ancestral Genomic Sequences Using Likelihood

Tamir Tuller, Isaac Elias, T. Tuller, 2007, J. Comput. Biol..

Finding a maximum likelihood tree is hard

Tamir Tuller, Benny Chor, B. Chor, 2006, JACM.

Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae

Eytan Ruppin, Tamir Tuller, Martin Kupiec, 2007, PLoS Comput. Biol..

Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach

Tamir Tuller, Alexandra Dana, T. Tuller, 2012, J. Comput. Biol..

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Tamir Tuller, Yoram Zarai, Y. Zarai, 2018, PLoS Comput. Biol..

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

Tamir Tuller, Alon Diament, T. Tuller, 2015, PLoS Comput. Biol..

New Universal Rules of Eukaryotic Translation Initiation Fidelity

Tamir Tuller, Hadas Zur, T. Tuller, 2013, PLoS Comput. Biol..

Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion

Tamir Tuller, Isaac Elias, Hadas Birin, 2008, Bioinform..

Networks of ribosome flow models for modeling and analyzing intracellular traffic

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2018, Scientific Reports.

CSN: unsupervised approach for inferring biological networks based on the genome alone

Tamir Tuller, Maya Galili, T. Tuller, 2020, BMC Bioinformatics.

Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions

Tamir Tuller, Eli Goz, T. Tuller, 2016, J. Comput. Biol..

Generation and comparative genomics of synthetic dengue viruses

Tamir Tuller, Eli Goz, Zohar Zafrir, 2017, BMC Bioinformatics.

Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples

Eytan Ruppin, Tamir Tuller, Hadas Birin, 2009, RECOMB-CG.

The Average Common Substring Approach to Phylogenomic Reconstruction

David Burstein, Tamir Tuller, Benny Chor, 2006, J. Comput. Biol..

Controlling mRNA Translation

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2016, 1602.02308.

Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge

Tamir Tuller, Hadas Zur, T. Tuller, 2015, Bioinform..

Information Theoretic Approaches to Whole Genome Phylogenies

David Burstein, Tamir Tuller, Benny Chor, 2005, RECOMB.

Biological Networks: Comparison, Conservation, and Evolutionary Trees

Tamir Tuller, Benny Chor, 2006, RECOMB.

Generation and Comparative Genomics of Synthetic Dengue Viruses

Tamir Tuller, Eli Goz, Yael Tsalenchuck, 2017, RECOMB-CG.

A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance

Sagi Snir, Luay Nakhleh, Guohua Jin, 2007, ISBRA.

stAIcalc: tRNA adaptation index calculator based on species-specific weights

Tamir Tuller, Renana Sabi, Renana Volvovitch Daniel, 2016, Bioinform..

Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics

Tamir Tuller, Doron Levin, T. Tuller, 2020, PLoS Comput. Biol..

Controlling the ribosomal density profile in mRNA translation

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2016, 2016 IEEE 55th Conference on Decision and Control (CDC).

Adding Hidden Nodes to Gene Networks (Extended Abstract)

Tamir Tuller, Benny Chor, 2004, WABI.

Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae

Tamir Tuller, Hadas Zur, 2013, BMC Bioinformatics.

The extent of ribosome queuing in budding yeast

Anna Feldman, Tamir Tuller, Martin Kupiec, 2018, PLoS Comput. Biol..

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways

Ron Y. Pinter, Tamir Tuller, Adi Mano, 2010, BMC Bioinformatics.

Higher-Order Genomic Organization of Cellular Functions in Yeast

Eytan Ruppin, Michael Gurevich, Tamir Tuller, 2009, J. Comput. Biol..

The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models

Sagi Snir, Tamir Tuller, T. Tuller, 2009, J. Bioinform. Comput. Biol..

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

Isaac Meilijson, Eytan Ruppin, Tamir Tuller, 2011, PLoS Comput. Biol..

Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking

Tamir Tuller, Zohar Zafrir, T. Tuller, 2017, BMC Bioinformatics.

Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases

Michael Gurevich, Tamir Tuller, Yifat Felder, 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.

Efficient algorithms for reconstructing gene content by co-evolution

Tamir Tuller, Hadas Birin, T. Tuller, 2011, BMC Bioinformatics.

Maximum likelihood of phylogenetic networks

Sagi Snir, Luay Nakhleh, Guohua Jin, 2007, Bioinform..

RFMapp: ribosome flow model application

Tamir Tuller, Hadas Zur, 2012, Bioinform..

A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract)

Isaac Meilijson, Eytan Ruppin, Tamir Tuller, 2011, RECOMB.

The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

Tamir Tuller, Alon Diament, Shimshi Atar, 2018, Bioinform..

On three generalizations of contraction

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2014, 53rd IEEE Conference on Decision and Control.

Contraction after small transients

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2015, Autom..

Discovering local patterns of co - evolution: computational aspects and biological examples

Tamir Tuller, Martin Kupiec, Yifat Felder, 2010, BMC Bioinformatics.

The RNA Polymerase Flow Model of Gene Transcription

Eran Gazit, Tamir Tuller, Eyal Cohen, 2014, IEEE Transactions on Biomedical Circuits and Systems.

Additional file 8

Tamir Tuller, Martin Kupiec, Yifat Felder, 2010 .

Efficient parsimony-based methods for phylogenetic network reconstruction

Sagi Snir, Luay Nakhleh, Guohua Jin, 2007, Bioinform..

Algorithms for ribosome traffic engineering and their potential in improving host cells' titer and growth rate

Tamir Tuller, Hadas Zur, Rachel Cohen-Kupiec, 2020, Scientific Reports.

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

Tamir Tuller, Alexandra Dana, T. Tuller, 2012, PLoS Comput. Biol..

Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics

Elchanan Mossel, Tamir Tuller, Elchanan Mossel, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

On the Steady-State Distribution in the Homogeneous Ribosome Flow Model

Michael Margaliot, Tamir Tuller, M. Margaliot, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Ribosome Flow Model on a Ring

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds

Daniel A. Chamovitz, Tamir Tuller, Benny Chor, 2005, WABI.

Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models

Sagi Snir, Tamir Tuller, T. Tuller, 2008, WABI.

Maximum Likelihood of Evolutionary Trees Is Hard

Tamir Tuller, Benny Chor, B. Chor, 2005, RECOMB.

ChimeraUGEM: unsupervised gene expression modeling in any given organism

Tamir Tuller, Iddo Weiner, Noam Shahar, 2019, Bioinform..

Maximum likelihood of phylogenetic networks

Sagi Snir, Luay Nakhleh, Guohua Jin, 2006, Bioinform..

Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Tamir Tuller, Yoram Zarai, 2019, PLoS Comput. Biol..

Stability Analysis of the Ribosome Flow Model

Michael Margaliot, Tamir Tuller, M. Margaliot, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic

Sagi Snir, Luay Nakhleh, Guohua Jin, 2009, IEEE ACM Trans. Comput. Biol. Bioinform..

Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples

Eytan Ruppin, Tamir Tuller, Hadas Birin, 2010, J. Comput. Biol..

New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region

Tamir Tuller, Alon Diament, Shaked Bergman, 2020, Bioinform..

Variability in mRNA translation: a random matrix theory approach

Michael Margaliot, Wasim Huleihel, Tamir Tuller, 2020, Scientific Reports.

A Mathematical Analysis of RNA Structural Motifs in Viruses

Dmitrij Frishman, Alexander Churkin, Danny Barash, 2021, Mathematics.

Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression

Tamir Tuller, Benny Chor, Daniel Yekutieli, 2007, Molecular systems biology.

Ribosome flow model with positive feedback

Michael Margaliot, Tamir Tuller, M. Margaliot, 2013, Journal of The Royal Society Interface.

Codon bias, tRNA pools, and horizontal gene transfer

Tamir Tuller, T. Tuller, 2011, Mobile genetic elements.

Entrainment to Periodic Initiation and Transition Rates in a Computational Model for Gene Translation

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2014, PloS one.

Mean of the Typical Decoding Rates: A New Translation Efficiency Index Based on the Analysis of Ribosome Profiling Data

Tamir Tuller, Alexandra Dana, T. Tuller, 2014, G3: Genes, Genomes, Genetics.

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic

Sagi Snir, Guohua Jin, Tamir Tuller, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence

Tamir Tuller, Alon Diament, T. Tuller, 2017, Nucleic acids research.

A model for competition for ribosomes in the cell

Michael Margaliot, Tamir Tuller, Eduardo D Sontag, 2015, Journal of The Royal Society Interface.

Composite effects of gene determinants on the translation speed and density of ribosomes

Michal Ziv-Ukelson, Eytan Ruppin, Tamir Tuller, 2011, Genome Biology.

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Tamir Tuller, Alon Diament, T. Tuller, 2014, Nature Communications.

Checkable Conditions for Contraction After Small Transients in Time and Amplitude

Michael Margaliot, Eduardo D. Sontag, Tamir Tuller, 2017 .

Translation efficiency is determined by both codon bias and folding energy

Eytan Ruppin, Tamir Tuller, Martin Kupiec, 2010, Proceedings of the National Academy of Sciences.

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

Tamir Tuller, Hadas Zur, T. Tuller, 2012, EMBO reports.

Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization

Tamir Tuller, Iddo Weiner, Iftach Yacoby, 2018, The Plant journal : for cell and molecular biology.

Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae.

Tamir Tuller, Renana Sabi, T. Tuller, 2017, RNA.

Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

Tamir Tuller, Renana Sabi, T. Tuller, 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

Metabolic modeling of endosymbiont genome reduction on a temporal scale

Eytan Ruppin, Tamir Tuller, Keren Yizhak, 2011, Molecular systems biology.

Conservation of the relative tRNA composition in healthy and cancerous tissues.

Michal Linial, Tamir Tuller, Shelly Mahlab, 2012, RNA.

On the Ribosomal Density that Maximizes Protein Translation Rate

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2016, PloS one.

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

Tamir Tuller, Alon Diament, T. Tuller, 2016, Biology Direct.

A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics

Michael Margaliot, Tamir Tuller, Yoram Zarai, 2016, PloS one.

Quantifying the Effect of Ribosomal Density on mRNA Stability

Tamir Tuller, Shlomit Edri, T. Tuller, 2014, PloS one.

The effect of tRNA levels on decoding times of mRNA codons

Tamir Tuller, Alexandra Dana, T. Tuller, 2014, Nucleic acids research.

Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development

Daniel A. Chamovitz, Tamir Tuller, Shimshi Atar, 2014, Nucleic acids research.

Efficient parsimony-based methods for phylogenetic network

Sagi Snir, Guohua Jin, Tamir Tuller, 2006 .

Co-evolutionary networks of genes and cellular processes across fungal species

Eytan Ruppin, Tamir Tuller, Martin Kupiec, 2009, Genome Biology.

Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

Eytan Ruppin, Tamir Tuller, Yedael Y. Waldman, 2011, Genome biology and evolution.

TP53 cancerous mutations exhibit selection for translation efficiency.

Roded Sharan, Eytan Ruppin, Tamir Tuller, 2009, Cancer research.

Overcoming the expression barrier of the ferredoxin‑hydrogenase chimera in Chlamydomonas reinhardtii supports a linear increment in photosynthetic hydrogen output

Tamir Tuller, Eyal Dafni, Iddo Weiner, 2018, Algal Research.

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

Roded Sharan, Eytan Ruppin, Tamir Tuller, 2010, Nucleic acids research.

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Tamir Tuller, Hadas Zur, T. Tuller, 2016, Nucleic acids research.

Forbidden penta‐peptides

Tamir Tuller, Benny Chor, Nathan Nelson, 2007, Protein science : a publication of the Protein Society.

Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae

Ehud Shapiro, Tamir Tuller, Zohar Zafrir, 2014, PLoS genetics.