Adding Hidden Nodes to Gene Networks (Extended Abstract). - Benny Chor; Tamir Tuller (WABI, 2004)

Maximum likelihood of evolutionary trees: hardness and approximation. - Benny Chor; Tamir Tuller (ISMB (Supplement of Bioinformatics), 2005)

Information Theoretic Approaches to Whole Genome Phylogenies. - David Burstein; Igor Ulitsky; Tamir Tuller; Benny Chor (RECOMB, 2005)

Maximum Likelihood of Evolutionary Trees Is Hard. - Benny Chor; Tamir Tuller (RECOMB, 2005)

Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. - Tamir Tuller; Efrat Oron; Erez Makavy; Daniel A. Chamovitz; Benny Chor (WABI, 2005)

Biological Networks: Comparison, Conservation, and Evolutionary Trees. - Benny Chor; Tamir Tuller (RECOMB, 2006)

Maximum likelihood of phylogenetic networks. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2006)

Finding a maximum likelihood tree is hard. - Benny Chor; Tamir Tuller (J. ACM, 2006)

The Average Common Substring Approach to Phylogenomic Reconstruction. - Igor Ulitsky; David Burstein; Tamir Tuller; Benny Chor (J. Comput. Biol., 2006)

Computational aspects of molecular evolution - Tamir Tuller (2006)

A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (ISBRA, 2007)

Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. - Hadas Birin; Zohar Gal-Or; Isaac Elias; Tamir Tuller (WABI, 2007)

Efficient parsimony-based methods for phylogenetic network reconstruction. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2007)

Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. - Benny Chor; Tamir Tuller (J. Comput. Biol., 2007)

Reconstruction of Ancestral Genomic Sequences Using Likelihood. - Isaac Elias; Tamir Tuller (J. Comput. Biol., 2007)

Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae. - Tamir Tuller; Martin Kupiec; Eytan Ruppin (PLoS Comput. Biol., 2007)

Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases. - Udi Rubinstein; Yifat Felder; Nana Ginzbourg; Michael Gurevich; Tamir Tuller (BIBM, 2008)

Discovering Local Patterns of Co-evolution. - Yifat Felder; Tamir Tuller (RECOMB-CG, 2008)

Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. - Sagi Snir; Tamir Tuller (WABI, 2008)

Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. - Hadas Birin; Zohar Gal-Or; Isaac Elias; Tamir Tuller (Bioinform., 2008)

Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. - Tamir Tuller; Hadas Birin; Martin Kupiec; Eytan Ruppin (RECOMB-CG, 2009)

The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. - Sagi Snir; Tamir Tuller (J. Bioinform. Comput. Biol., 2009)

Higher-Order Genomic Organization of Cellular Functions in Yeast. - Tamir Tuller; Udi Rubinstein; Dani Bar; Michael Gurevich; Eytan Ruppin; Martin Kupiec (J. Comput. Biol., 2009)

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. - Adi Mano; Tamir Tuller; Oded Béjà; Ron Y. Pinter (BMC Bioinform., 2010)

Discovering local patterns of co - evolution: computational aspects and biological examples. - Tamir Tuller; Yifat Felder; Martin Kupiec (BMC Bioinform., 2010)

Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. - Tamir Tuller; Hadas Birin; Martin Kupiec; Eytan Ruppin (J. Comput. Biol., 2010)

A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). - Shlomi Reuveni; Isaac Meilijson; Martin Kupiec; Eytan Ruppin; Tamir Tuller (RECOMB, 2011)

Efficient algorithms for reconstructing gene content by co-evolution. - Hadas Birin; Tamir Tuller (BMC Bioinform., 2011)

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. - Shlomi Reuveni; Isaac Meilijson; Martin Kupiec; Eytan Ruppin; Tamir Tuller (PLoS Comput. Biol., 2011)

Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. - Tamir Tuller; Elchanan Mossel (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

RFMapp: ribosome flow model application. - Hadas Zur; Tamir Tuller (Bioinform., 2012)

Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. - Alexandra Dana; Tamir Tuller (J. Comput. Biol., 2012)

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells. - Alexandra Dana; Tamir Tuller (PLoS Comput. Biol., 2012)

Stability Analysis of the Ribosome Flow Model. - Michael Margaliot; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. - Michael Margaliot; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. - Hadas Zur; Tamir Tuller (BMC Bioinform., 2013)

New Universal Rules of Eukaryotic Translation Initiation Fidelity. - Hadas Zur; Tamir Tuller (PLoS Comput. Biol., 2013)

Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model. - Yoram Zarai; Michael Margaliot; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

On three generalizations of contraction. - Eduardo D. Sontag; Michael Margaliot; Tamir Tuller (CDC, 2014)

The RNA Polymerase Flow Model of Gene Transcription. - Shlomit Edri; Eran Gazit; Eyal Cohen; Tamir Tuller (IEEE Trans. Biomed. Circuits Syst., 2014)

Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case. - Yoram Zarai; Michael Margaliot; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge. - Hadas Zur; Tamir Tuller (Bioinform., 2015)

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. - Alon Diament; Tamir Tuller (PLoS Comput. Biol., 2015)

Ribosome Flow Model on a Ring. - Alon Raveh; Yoram Zarai; Michael Margaliot; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Controlling the ribosomal density profile in mRNA translation. - Yoram Zarai; Michael Margaliot; Eduardo D. Sontag; Tamir Tuller (CDC, 2016)

Contraction after small transients. - Michael Margaliot; Eduardo D. Sontag; Tamir Tuller (Autom., 2016)

Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. - Eli Goz; Tamir Tuller (J. Comput. Biol., 2016)

Generation and Comparative Genomics of Synthetic Dengue Viruses. - Eli Goz; Yael Tsalenchuck; Rony Oren Benaroya; Shimshi Atar; Tahel Altman; Justin Julander; Tamir Tuller (RECOMB-CG, 2017)

stAIcalc: tRNA adaptation index calculator based on species-specific weights. - Renana Sabi; Renana Volvovitch Daniel; Tamir Tuller (Bioinform., 2017)

Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. - Zohar Zafrir; Tamir Tuller (BMC Bioinform., 2017)

Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. - Eli Goz; Zohar Zafrir; Tamir Tuller (Bioinform., 2018)

Generation and comparative genomics of synthetic dengue viruses. - Eli Goz; Yael Tsalenchuck; Rony Oren Benaroya; Zohar Zafrir; Shimshi Atar; Tahel Altman; Justin Julander; Tamir Tuller (BMC Bioinform., 2018)

The extent of ribosome queuing in budding yeast. - Alon Diament; Anna Feldman; Elisheva Schochet; Martin Kupiec; Yoav Arava; Tamir Tuller (PLoS Comput. Biol., 2018)

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. - Yoram Zarai; Tamir Tuller (PLoS Comput. Biol., 2018)

Controllability Analysis and Control Synthesis for the Ribosome Flow Model. - Yoram Zarai; Michael Margaliot; Eduardo D. Sontag; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

ChimeraUGEM: unsupervised gene expression modeling in any given organism. - Alon Diament; Iddo Weiner; Noam Shahar; Shira Landman; Yael Feldman; Shimshi Atar; Meital Avitan; Shira Schweitzer; Iftach Yacoby; Tamir Tuller (Bioinform., 2019)

The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. - Tamir Tuller; Alon Diament; Avital Yahalom; Assaf Zemach; Shimshi Atar; Daniel A. Chamovitz (Bioinform., 2019)

Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. - Yoram Zarai; Tamir Tuller (PLoS Comput. Biol., 2019)

Novel Driver Synonymous Mutations in the Coding Regions of GCB Lymphoma Patients Improve the Transcription Levels of BCL2. - Ofek Shami-Schnitzer; Zohar Zafrir; Tamir Tuller (ISMCO, 2020)

CSN: unsupervised approach for inferring biological networks based on the genome alone. - Maya Galili; Tamir Tuller (BMC Bioinform., 2020)

Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins. - Arup Panda; Tamir Tuller (Genom. Proteom. Bioinform., 2020)

Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics. - Doron Levin; Tamir Tuller (PLoS Comput. Biol., 2020)

New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region. - Shaked Bergman; Alon Diament; Tamir Tuller (Bioinform., 2021)

Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a Microbiome. - Liyam Chitayat Levi; Ido Rippin; Moran Ben Tulila; Rotem Galron; Tamir Tuller (RECOMB-CG, 2022)

Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. - Alma Davidson; Marina Parr; Franziska Totzeck; Alexander Churkin; Danny Barash; Dmitrij Frishman; Tamir Tuller (RECOMB-CG, 2024)

Revisiting the Effects of MDR1 Variants Using Computational Approaches. - Tal Gutman; Tamir Tuller (RECOMB-CG, 2024)

Strong association between genomic 3D structure and CRISPR cleavage efficiency. - Shaked Bergman; Tamir Tuller (PLoS Comput. Biol., 2024)

Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding. - Tal Gutman; Tamir Tuller (PLoS Comput. Biol., 2024)