Tamir Tuller

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 25

Top Topics

Arabidopsis Thaliana

Comparative Genomics

Gene Expression

Top Venues

PLoS Comput. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller
Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. RECOMB-CG (2024)
Tal Gutman, Tamir Tuller
Revisiting the Effects of MDR1 Variants Using Computational Approaches. RECOMB-CG (2024)
Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller
Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a Microbiome. RECOMB-CG (2022)
Shaked Bergman, Alon Diament, Tamir Tuller
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region. Bioinform. 36 (22-23) (2021)
Doron Levin, Tamir Tuller
Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics. PLoS Comput. Biol. 16 (7) (2020)
Ofek Shami-Schnitzer, Zohar Zafrir, Tamir Tuller
Novel Driver Synonymous Mutations in the Coding Regions of GCB Lymphoma Patients Improve the Transcription Levels of BCL2. ISMCO (2020)
Maya Galili, Tamir Tuller
CSN: unsupervised approach for inferring biological networks based on the genome alone. BMC Bioinform. 21 (1) (2020)
Arup Panda, Tamir Tuller
Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins. Genom. Proteom. Bioinform. 18 (5) (2020)
Alon Diament, Iddo Weiner, Noam Shahar, Shira Landman, Yael Feldman, Shimshi Atar, Meital Avitan, Shira Schweitzer, Iftach Yacoby, Tamir Tuller
ChimeraUGEM: unsupervised gene expression modeling in any given organism. Bioinform. 35 (18) (2019)
Yoram Zarai, Tamir Tuller
Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. PLoS Comput. Biol. 15 (7) (2019)
Tamir Tuller, Alon Diament, Avital Yahalom, Assaf Zemach, Shimshi Atar, Daniel A. Chamovitz
The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. Bioinform. 35 (16) (2019)
Yoram Zarai, Tamir Tuller
Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. PLoS Comput. Biol. 14 (4) (2018)
Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller
The extent of ribosome queuing in budding yeast. PLoS Comput. Biol. 14 (1) (2018)
Eli Goz, Zohar Zafrir, Tamir Tuller
Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. Bioinform. 34 (19) (2018)
Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller
Generation and comparative genomics of synthetic dengue viruses. BMC Bioinform. (6) (2018)
Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
Controllability Analysis and Control Synthesis for the Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller
Generation and Comparative Genomics of Synthetic Dengue Viruses. RECOMB-CG (2017)
Zohar Zafrir, Tamir Tuller
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinform. 18 (1) (2017)
Renana Sabi, Renana Volvovitch Daniel, Tamir Tuller
stAIcalc: tRNA adaptation index calculator based on species-specific weights. Bioinform. 33 (4) (2017)
Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
Controlling the ribosomal density profile in mRNA translation. CDC (2016)
Eli Goz, Tamir Tuller
Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. J. Comput. Biol. 23 (8) (2016)
Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
Contraction after small transients. Autom. 67 (2016)
Alon Raveh, Yoram Zarai, Michael Margaliot, Tamir Tuller
Ribosome Flow Model on a Ring. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Hadas Zur, Tamir Tuller
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge. Bioinform. 31 (8) (2015)
Alon Diament, Tamir Tuller
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PLoS Comput. Biol. 11 (5) (2015)
Shlomit Edri, Eran Gazit, Eyal Cohen, Tamir Tuller
The RNA Polymerase Flow Model of Gene Transcription. IEEE Trans. Biomed. Circuits Syst. 8 (1) (2014)
Eduardo D. Sontag, Michael Margaliot, Tamir Tuller
On three generalizations of contraction. CDC (2014)
Yoram Zarai, Michael Margaliot, Tamir Tuller
Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (6) (2014)
Hadas Zur, Tamir Tuller
Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. BMC Bioinform. 14 (S-15) (2013)
Yoram Zarai, Michael Margaliot, Tamir Tuller
Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Hadas Zur, Tamir Tuller
New Universal Rules of Eukaryotic Translation Initiation Fidelity. PLoS Comput. Biol. 9 (7) (2013)
Hadas Zur, Tamir Tuller
RFMapp: ribosome flow model application. Bioinform. 28 (12) (2012)
Alexandra Dana, Tamir Tuller
Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. J. Comput. Biol. 19 (2) (2012)
Michael Margaliot, Tamir Tuller
Stability Analysis of the Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (5) (2012)
Alexandra Dana, Tamir Tuller
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells. PLoS Comput. Biol. 8 (11) (2012)
Michael Margaliot, Tamir Tuller
On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (6) (2012)
Tamir Tuller, Elchanan Mossel
Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (6) (2011)
Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller
Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. PLoS Comput. Biol. 7 (9) (2011)
Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller
A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). RECOMB (2011)
Hadas Birin, Tamir Tuller
Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinform. 12 (S-9) (2011)
Tamir Tuller, Elchanan Mossel
Co-evolution is Incompatible with the Markov Assumption in Phylogenetics CoRR (2010)
Adi Mano, Tamir Tuller, Oded Béjà, Ron Y. Pinter
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinform. 11 (S-1) (2010)
Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. J. Comput. Biol. 17 (9) (2010)
Tamir Tuller, Yifat Felder, Martin Kupiec
Discovering local patterns of co - evolution: computational aspects and biological examples. BMC Bioinform. 11 (2010)
Sagi Snir, Tamir Tuller
The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. J. Bioinform. Comput. Biol. 7 (4) (2009)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (3) (2009)
Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. RECOMB-CG (2009)
Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevich, Eytan Ruppin, Martin Kupiec
Higher-Order Genomic Organization of Cellular Functions in Yeast. J. Comput. Biol. 16 (2) (2009)
Yifat Felder, Tamir Tuller
Discovering Local Patterns of Co-evolution. RECOMB-CG (2008)
Udi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, Tamir Tuller
Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases. BIBM (2008)
Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. Bioinform. 24 (6) (2008)
Sagi Snir, Tamir Tuller
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. WABI (2008)
Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. WABI (2007)
Tamir Tuller, Martin Kupiec, Eytan Ruppin
. PLoS Comput. Biol. 3 (12) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. 23 (2) (2007)
Isaac Elias, Tamir Tuller
Reconstruction of Ancestral Genomic Sequences Using Likelihood. J. Comput. Biol. 14 (2) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Maximum likelihood of phylogenetic networks. Bioinform. 23 (8) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA (2007)
Benny Chor, Tamir Tuller
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. J. Comput. Biol. 14 (6) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Maximum likelihood of phylogenetic networks. Bioinform. 22 (21) (2006)
Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor
The Average Common Substring Approach to Phylogenomic Reconstruction. J. Comput. Biol. 13 (2) (2006)
Benny Chor, Tamir Tuller
Finding a maximum likelihood tree is hard. J. ACM 53 (5) (2006)
Benny Chor, Tamir Tuller
Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB (2006)
Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor
Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. WABI (2005)
Benny Chor, Tamir Tuller
Maximum Likelihood of Evolutionary Trees Is Hard. RECOMB (2005)
Benny Chor, Tamir Tuller
Maximum likelihood of evolutionary trees: hardness and approximation. ISMB (Supplement of Bioinformatics) (2005)
David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor
Information Theoretic Approaches to Whole Genome Phylogenies. RECOMB (2005)
Benny Chor, Tamir Tuller
Adding Hidden Nodes to Gene Networks (Extended Abstract). WABI (2004)