Tamir Tuller - RankMe

73 papers B 4C 4Journal 51Unranked 13

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Novel Driver Mutations in GCB Lymphoma Patients that Affect Transcription Factors Binding. RECOMB-CG Ofek Shami-Schnitzer, Tamir Tuller
2025	J	`jnl`	The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3. Briefings Bioinform. Rami Zakh, Alexander Churkin, Marina Parr, Tamir Tuller, Ohad Etzion, Harel Dahari, Danny Barash
2024	J	`jnl`	Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding. PLoS Comput. Biol. Tal Gutman, Tamir Tuller
2024	—	`conf`	Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. RECOMB-CG Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller
2024	—	`conf`	Revisiting the Effects of MDR1 Variants Using Computational Approaches. RECOMB-CG Tal Gutman, Tamir Tuller
2024	J	`jnl`	Strong association between genomic 3D structure and CRISPR cleavage efficiency. PLoS Comput. Biol. Shaked Bergman, Tamir Tuller
2022	—	`conf`	Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a Microbiome. RECOMB-CG Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller
2021	J	`jnl`	New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region. Bioinform. Shaked Bergman, Alon Diament, Tamir Tuller
2020	J	`jnl`	CSN: unsupervised approach for inferring biological networks based on the genome alone. BMC Bioinform. Maya Galili, Tamir Tuller
2020	J	`jnl`	Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins. Genom. Proteom. Bioinform. Arup Panda, Tamir Tuller
2020	—	`conf`	Novel Driver Synonymous Mutations in the Coding Regions of GCB Lymphoma Patients Improve the Transcription Levels of BCL2. ISMCO Ofek Shami-Schnitzer, Zohar Zafrir, Tamir Tuller
2020	J	`jnl`	Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics. PLoS Comput. Biol. Doron Levin, Tamir Tuller
2019	J	`jnl`	ChimeraUGEM: unsupervised gene expression modeling in any given organism. Bioinform. Alon Diament, Iddo Weiner, Noam Shahar, Shira Landman, Yael Feldman, Shimshi Atar, Meital Avitan, Shira Schweitzer, Iftach Yacoby, Tamir Tuller
2019	J	`jnl`	Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. PLoS Comput. Biol. Yoram Zarai, Tamir Tuller
2019	J	`jnl`	The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. Bioinform. Tamir Tuller, Alon Diament, Avital Yahalom, Assaf Zemach, Shimshi Atar, Daniel A. Chamovitz
2018	J	`jnl`	Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. PLoS Comput. Biol. Yoram Zarai, Tamir Tuller
2018	J	`jnl`	Controllability Analysis and Control Synthesis for the Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
2018	J	`jnl`	Generation and comparative genomics of synthetic dengue viruses. BMC Bioinform. Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller
2018	J	`jnl`	The extent of ribosome queuing in budding yeast. PLoS Comput. Biol. Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller
2018	J	`jnl`	Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. Bioinform. Eli Goz, Zohar Zafrir, Tamir Tuller
2017	—	`conf`	Generation and Comparative Genomics of Synthetic Dengue Viruses. RECOMB-CG Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller
2017	J	`jnl`	Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinform. Zohar Zafrir, Tamir Tuller
2017	J	`jnl`	stAIcalc: tRNA adaptation index calculator based on species-specific weights. Bioinform. Renana Sabi, Renana Volvovitch Daniel, Tamir Tuller
2016	J	`jnl`	Contraction after small transients. Autom. Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
2016	—	`conf`	Controlling the ribosomal density profile in mRNA translation. CDC Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller
2016	J	`jnl`	Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. J. Comput. Biol. Eli Goz, Tamir Tuller
2015	J	`jnl`	Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge. Bioinform. Hadas Zur, Tamir Tuller
2015	J	`jnl`	Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PLoS Comput. Biol. Alon Diament, Tamir Tuller
2015	J	`jnl`	Ribosome Flow Model on a Ring. IEEE ACM Trans. Comput. Biol. Bioinform. Alon Raveh, Yoram Zarai, Michael Margaliot, Tamir Tuller
2014	J	`jnl`	Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case. IEEE ACM Trans. Comput. Biol. Bioinform. Yoram Zarai, Michael Margaliot, Tamir Tuller
2014	—	`conf`	On three generalizations of contraction. CDC Eduardo D. Sontag, Michael Margaliot, Tamir Tuller
2014	J	`jnl`	The RNA Polymerase Flow Model of Gene Transcription. IEEE Trans. Biomed. Circuits Syst. Shlomit Edri, Eran Gazit, Eyal Cohen, Tamir Tuller
2013	J	`jnl`	Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. Yoram Zarai, Michael Margaliot, Tamir Tuller
2013	J	`jnl`	New Universal Rules of Eukaryotic Translation Initiation Fidelity. PLoS Comput. Biol. Hadas Zur, Tamir Tuller
2013	J	`jnl`	Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. BMC Bioinform. Hadas Zur, Tamir Tuller
2012	J	`jnl`	Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells. PLoS Comput. Biol. Alexandra Dana, Tamir Tuller
2012	J	`jnl`	Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. J. Comput. Biol. Alexandra Dana, Tamir Tuller
2012	J	`jnl`	On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. Michael Margaliot, Tamir Tuller
2012	J	`jnl`	RFMapp: ribosome flow model application. Bioinform. Hadas Zur, Tamir Tuller
2012	J	`jnl`	Stability Analysis of the Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. Michael Margaliot, Tamir Tuller
2011	B	`conf`	A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). RECOMB Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller
2011	J	`jnl`	Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. Tamir Tuller, Elchanan Mossel
2011	J	`jnl`	Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinform. Hadas Birin, Tamir Tuller
2011	J	`jnl`	Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. PLoS Comput. Biol. Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller
2010	J	`jnl`	Co-evolution is Incompatible with the Markov Assumption in Phylogenetics CoRR Tamir Tuller, Elchanan Mossel
2010	J	`jnl`	Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinform. Adi Mano, Tamir Tuller, Oded Béjà, Ron Y. Pinter
2010	J	`jnl`	Discovering local patterns of co - evolution: computational aspects and biological examples. BMC Bioinform. Tamir Tuller, Yifat Felder, Martin Kupiec
2010	J	`jnl`	Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. J. Comput. Biol. Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
2009	—	`conf`	Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. RECOMB-CG Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
2009	J	`jnl`	Higher-Order Genomic Organization of Cellular Functions in Yeast. J. Comput. Biol. Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevich, Eytan Ruppin, Martin Kupiec
2009	J	`jnl`	Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE ACM Trans. Comput. Biol. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2009	J	`jnl`	The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. J. Bioinform. Comput. Biol. Sagi Snir, Tamir Tuller
2008	—	`conf`	Discovering Local Patterns of Co-evolution. RECOMB-CG Yifat Felder, Tamir Tuller
2008	—	`conf`	Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases. BIBM Udi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, Tamir Tuller
2008	J	`jnl`	Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. Bioinform. Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
2008	C	`conf`	Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. WABI Sagi Snir, Tamir Tuller
2007	—	`conf`	A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	J	`jnl`	Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. J. Comput. Biol. Benny Chor, Tamir Tuller
2007	J	`jnl`	Determinants of Protein Abundance and Translation Efficiency in PLoS Comput. Biol. Tamir Tuller, Martin Kupiec, Eytan Ruppin
2007	J	`jnl`	Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	C	`conf`	Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. WABI Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
2007	J	`jnl`	Maximum likelihood of phylogenetic networks. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	J	`jnl`	Reconstruction of Ancestral Genomic Sequences Using Likelihood. J. Comput. Biol. Isaac Elias, Tamir Tuller
2006	B	`conf`	Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB Benny Chor, Tamir Tuller
2006	—	`—`	Computational aspects of molecular evolution Tamir Tuller
2006	J	`jnl`	Finding a maximum likelihood tree is hard. J. ACM Benny Chor, Tamir Tuller
2006	J	`jnl`	Maximum likelihood of phylogenetic networks. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2006	J	`jnl`	The Average Common Substring Approach to Phylogenomic Reconstruction. J. Comput. Biol. Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor
2005	B	`conf`	Information Theoretic Approaches to Whole Genome Phylogenies. RECOMB David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor
2005	B	`conf`	Maximum Likelihood of Evolutionary Trees Is Hard. RECOMB Benny Chor, Tamir Tuller
2005	—	`conf`	Maximum likelihood of evolutionary trees: hardness and approximation. ISMB (Supplement of Bioinformatics) Benny Chor, Tamir Tuller
2005	C	`conf`	Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. WABI Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor
2004	C	`conf`	Adding Hidden Nodes to Gene Networks (Extended Abstract). WABI Benny Chor, Tamir Tuller