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List of works by Tamir Tuller

A code for transcription elongation speed.

scientific article published on 22 November 2017

A comparative genomics study on the effect of individual amino acids on ribosome stalling.

scientific article published on 2 October 2015

A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics

scientific article published on 23 August 2017

A model for competition for ribosomes in the cell

scientific article published on March 2016

A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon

scientific article published on 24 September 2020

Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware

scientific article published on 23 November 2021

Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae

scientific article

Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease

scientific article

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

scientific article

Analysis of coevolving gene families using mutually exclusive orthologous modules

scientific article published on 17 April 2011

Association between translation efficiency and horizontal gene transfer within microbial communities

scientific article (publication date: June 2011)

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

scholarly article by Benny Chor published in July 2007

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

scientific article published on 15 May 2020

Challenges and obstacles related to solving the codon bias riddles

scientific article published on February 2014

ChimeraUGEM: unsupervised gene expression modeling in any given organism

scientific article published on 01 September 2019

Clone clusters in autoreactive CD4 T-cell lines from probable multiple sclerosis patients form disease-characteristic signatures

scientific article

Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics ⬇️

scientific article published on November 1, 2011

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

scientific article (publication date: 2009)

Codon bias, tRNA pools, and horizontal gene transfer ⬇️

scientific article published on May 1, 2011

Common and specific signatures of gene expression and protein-protein interactions in autoimmune diseases

scientific article published on 29 November 2012

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

scientific article

Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling

scientific article published on 22 February 2016

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

scientific article published on 3 November 2011

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

scientific article published on 31 March 2017

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

scientific article published on 3 April 2018

Computational discovery and modeling of novel gene expression rules encoded in the mRNA

scientific article published on 14 July 2020

Conservation of the relative tRNA composition in healthy and cancerous tissues

scientific article published on 22 February 2012

Controlling mRNA Translation

scientific article published on 23 May 2017

Correction: On the Ribosomal Density that Maximizes Protein Translation Rate

scientific article

Determinants of protein abundance and translation efficiency in S. cerevisiae

scientific article

Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells

scientific article

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

scientific article

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

scientific article

Efficient algorithms for reconstructing gene content by co-evolution

scientific article

Efficient manipulations of synonymous mutations for controlling translation rate: an analytical approach

scientific article published in February 2012

Efficient parsimony-based methods for phylogenetic network reconstruction

scientific article published in January 2007

Enhancing Heterologous Expression in Chlamydomonas reinhardtii by Transcript Sequence Optimization

scientific article published on 30 January 2018

Entrainment to periodic initiation and transition rates in a computational model for gene translation

scientific article

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

scientific article published on 10 May 2016

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

scientific article published on 27 June 2016

Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda

scientific article published on 28 February 2017

Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels

scientific article published on 20 December 2021

Evolutionary rate and gene expression across different brain regions

scientific article published on January 2008

Explicit expression for the steady-state translation rate in the infinite-dimensional homogeneous ribosome flow model

scientific article

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

scientific article published on 29 November 2014

Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae

scientific article

Forbidden penta-peptides

scientific article

Generation and comparative genomics of synthetic dengue viruses

scientific article

Genome scale analysis ofEscherichia coliwith a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation

scientific article published on 17 November 2017

Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model

scientific article published in Scientific Reports

Genome-scale analysis of translation elongation with a ribosome flow model

scientific article

Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium

scientific article published in Scientific Reports

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

scientific article published on 08 May 2007

Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions

scientific article published on 15 June 2011

Higher-order genomic organization of cellular functions in yeast

scientific article published on February 2009

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

scientific article published on 02 January 2019

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

scientific article published on 22 May 2015

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

scientific article published on 18 January 2008

Inferring phylogenetic networks by the maximum parsimony criterion: a case study

scientific article published on 26 October 2006

Laquinimod suppress antigen presentation in relapsing-remitting multiple sclerosis: in-vitro high-throughput gene expression study

scientific article published on 27 March 2010

Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins

scientific article published on 28 May 2013

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

scientific article published in November 2014

Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach

scientific article

Maximum likelihood of evolutionary trees: hardness and approximation

scientific article published in June 2005

Maximum likelihood of phylogenetic networks

scientific article

Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data

scientific article

Metabolic modeling of endosymbiont genome reduction on a temporal scale ⬇️

scientific article published on March 2011

Modeling three-dimensional genomic organization in evolution and pathogenesis

scientific article published on 27 July 2018

Modelling and measuring intracellular competition for finite resources during gene expression.

scientific article

Modelling the efficiency of codon-tRNA interactions based on codon usage bias

scientific article

Most associations between transcript features and gene expression are monotonic

scientific article published on 28 March 2014

Multiple roles of the coding sequence 5' end in gene expression regulation

scientific article

New universal rules of eukaryotic translation initiation fidelity

scientific article

Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics

article

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

scientific article

On the Ribosomal Density that Maximizes Protein Translation Rate ⬇️

scientific article

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

article

Optimal Down Regulation of mRNA Translation

scientific article published on 25 January 2017

Parsimony score of phylogenetic networks: hardness results and a linear-time heuristic

scientific article published in July 2009

Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts

scientific article published on 01 April 2019

Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells

scientific article

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

scientific article published on 02 September 2016

Properties and determinants of codon decoding time distributions

scientific article published on 17 October 2014

Properties of untranslated regions of the S. cerevisiae genome

scientific article

Quantifying the effect of ribosomal density on mRNA stability

scientific article

RFMapp: ribosome flow model application

article

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

scientific article published on 15 July 2015

Reconstructing ancestral gene content by coevolution

scientific article (publication date: 2010)

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples

scientific article published in September 2010

Reconstruction of ancestral genomic sequences using likelihood

scientific article

Ribosomal mutations affecting the translation of genes that use non-optimal codons

scientific article published on 8 August 2014

Ribosome Flow Model on a Ring

scientific article published in November 2015

Ribosome flow model with extended objects

scientific article published in October 2017

Ribosome flow model with positive feedback

scientific article published on 29 May 2013

Selection for reduced translation costs at the intronic 5' end in fungi

scientific article

Selection for translation efficiency on synonymous polymorphisms in recent human evolution

scientific article

Sensitivity of mRNA Translation

scientific article published on 4 August 2015

Sequence features of E. coli mRNAs affect their degradation

scientific article

Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis

scientific article published on 13 November 2017

Stability Analysis of the Ribosome Flow Model

article

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

scientific article published on March 2012

TP53 Cancerous Mutations Exhibit Selection for Translation Efficiency

The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

scientific article published on 01 August 2019

The Effect of Dysregulation of tRNA Genes and Translation Efficiency Mutations in Cancer and Neurodegeneration ⬇️

scientific article published on October 12, 2012

The NET-HMM approach: phylogenetic network inference by combining maximum likelihood and Hidden Markov Models

scientific article published in August 2009

The RNA polymerase flow model of gene transcription

scientific article

The average common substring approach to phylogenomic reconstruction

scientific article

The effect of tRNA levels on decoding times of mRNA codons

scientific article

The extent of ribosome queuing in budding yeast.

scientific article

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

scientific article published on 16 December 2014

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

scientific article

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

scientific article

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

scientific article

Translation efficiency is determined by both codon bias and folding energy

scientific article

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

scientific article

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

scientific article

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

scientific article published on 10 July 2020

Widespread non-modular overlapping codes in the coding regions

scientific article published on 08 April 2020

Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

scientific article published on 2 October 2015

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

scientific article published on 22 October 2016

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