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ORCIDTamir Tuller
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2020 – today
- 2024
[j48]Shaked Bergman
, Tamir Tuller:
Strong association between genomic 3D structure and CRISPR cleavage efficiency. PLoS Comput. Biol. 20(6): 1012214 (2024)- [c20]Tal Gutman, Tamir Tuller:
Revisiting the Effects of MDR1 Variants Using Computational Approaches. RECOMB-CG 2024: 226-247 - [c19]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: 248-270 - 2022
- [c18]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: 235-259 - 2021
- [j47]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): 5398-5404 (2021) - 2020
- [j46]Maya Galili, Tamir Tuller:
CSN: unsupervised approach for inferring biological networks based on the genome alone. BMC Bioinform. 21(1): 190 (2020) - [j45]Arup Panda, Tamir Tuller:
Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins. Genom. Proteom. Bioinform. 18(5): 549-564 (2020) - [j44]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) - [c17]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: 108-118
2010 – 2019
- 2019
- [j43]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): 2718-2723 (2019) - [j42]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): 3365-3371 (2019) - [j41]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) - 2018
- [j40]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): 3241-3248 (2018) - [j39]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. 19-S(6): 140:1-140:14 (2018) - [j38]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) - [j37]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) - [j36]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): 1351-1364 (2018) - 2017
- [j35]Renana Sabi, Renana Volvovitch Daniel, Tamir Tuller:
stAIcalc: tRNA adaptation index calculator based on species-specific weights. Bioinform. 33(4): 589-591 (2017) - [j34]Zohar Zafrir, Tamir Tuller:
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinform. 18(1): 77:1-77:10 (2017) - [c16]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: 31-52 - 2016
- [j33]Michael Margaliot, Eduardo D. Sontag, Tamir Tuller:
Contraction after small transients. Autom. 67: 178-184 (2016) - [j32]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): 641-650 (2016) - [c15]Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller:
Controlling the ribosomal density profile in mRNA translation. CDC 2016: 4184-4189 - 2015
- [j31]Hadas Zur, Tamir Tuller:
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge. Bioinform. 31(8): 1161-1168 (2015) - [j30]Alon Diament, Tamir Tuller:
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PLoS Comput. Biol. 11(5) (2015) - [j29]Alon Raveh, Yoram Zarai, Michael Margaliot, Tamir Tuller:
Ribosome Flow Model on a Ring. IEEE ACM Trans. Comput. Biol. Bioinform. 12(6): 1429-1439 (2015) - 2014
- [j28]Shlomit Edri, Eran Gazit, Eyal Cohen, Tamir Tuller:
The RNA Polymerase Flow Model of Gene Transcription. IEEE Trans. Biomed. Circuits Syst. 8(1): 54-64 (2014) - [j27]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): 1184-1195 (2014) - [c14]Eduardo D. Sontag, Michael Margaliot, Tamir Tuller:
On three generalizations of contraction. CDC 2014: 1539-1544 - 2013
- [j26]Hadas Zur, Tamir Tuller:
Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. BMC Bioinform. 14(S-15): S1 (2013) - [j25]Hadas Zur, Tamir Tuller:
New Universal Rules of Eukaryotic Translation Initiation Fidelity. PLoS Comput. Biol. 9(7) (2013) - [j24]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): 1322-1328 (2013) - 2012
- [j23]Hadas Zur, Tamir Tuller:
RFMapp: ribosome flow model application. Bioinform. 28(12): 1663-1664 (2012) - [j22]Alexandra Dana, Tamir Tuller:
Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. J. Comput. Biol. 19(2): 200-231 (2012) - [j21]Alexandra Dana, Tamir Tuller:
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells. PLoS Comput. Biol. 8(11) (2012) - [j20]Michael Margaliot, Tamir Tuller:
Stability Analysis of the Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1545-1552 (2012) - [j19]Michael Margaliot, Tamir Tuller:
On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1724-1736 (2012) - 2011
- [j18]Hadas Birin, Tamir Tuller:
Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinform. 12(S-9): S12 (2011) - [j17]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) - [j16]Tamir Tuller, Elchanan Mossel:
Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1667-1670 (2011) - [c13]Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller:
A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). RECOMB 2011: 358-360 - 2010
- [j15]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): 38 (2010) - [j14]Tamir Tuller, Yifat Felder, Martin Kupiec:
Discovering local patterns of co - evolution: computational aspects and biological examples. BMC Bioinform. 11: 43 (2010) - [j13]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): 1327-1344 (2010) - [i1]Tamir Tuller, Elchanan Mossel:
Co-evolution is Incompatible with the Markov Assumption in Phylogenetics. CoRR abs/1008.0322 (2010)
2000 – 2009
- 2009
- [j12]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): 625-644 (2009) - [j11]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): 303-316 (2009) - [j10]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): 495-505 (2009) - [c12]Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin:
Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. RECOMB-CG 2009: 164-180 - 2008
- [j9]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): 826-832 (2008) - [c11]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: 273-277 - [c10]Yifat Felder, Tamir Tuller:
Discovering Local Patterns of Co-evolution. RECOMB-CG 2008: 55-71 - [c9]Sagi Snir, Tamir Tuller:
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. WABI 2008: 354-368 - 2007
- [j8]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. 23(2): 123-128 (2007) - [j7]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Maximum likelihood of phylogenetic networks. Bioinform. 23(8): 1046-1047 (2007) - [j6]Isaac Elias, Tamir Tuller:
Reconstruction of Ancestral Genomic Sequences Using Likelihood. J. Comput. Biol. 14(2): 216-237 (2007) - [j5]Benny Chor, Tamir Tuller:
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. J. Comput. Biol. 14(6): 817-838 (2007) - [j4]Tamir Tuller, Martin Kupiec, Eytan Ruppin:
Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae. PLoS Comput. Biol. 3(12) (2007) - [c8]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: 61-72 - [c7]Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller:
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. WABI 2007: 111-123 - 2006
- [b1]Tamir Tuller:
Computational aspects of molecular evolution. Tel Aviv University, Israel, 2006 - [j3]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Maximum likelihood of phylogenetic networks. Bioinform. 22(21): 2604-2611 (2006) - [j2]Benny Chor, Tamir Tuller:
Finding a maximum likelihood tree is hard. J. ACM 53(5): 722-744 (2006) - [j1]Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor:
The Average Common Substring Approach to Phylogenomic Reconstruction. J. Comput. Biol. 13(2): 336-350 (2006) - [c6]Benny Chor, Tamir Tuller:
Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB 2006: 30-44 - 2005
- [c5]Benny Chor, Tamir Tuller:
Maximum likelihood of evolutionary trees: hardness and approximation. ISMB (Supplement of Bioinformatics) 2005: 97-106 - [c4]David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor:
Information Theoretic Approaches to Whole Genome Phylogenies. RECOMB 2005: 283-295 - [c3]Benny Chor, Tamir Tuller:
Maximum Likelihood of Evolutionary Trees Is Hard. RECOMB 2005: 296-310 - [c2]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: 53-64 - 2004
- [c1]Benny Chor, Tamir Tuller:
Adding Hidden Nodes to Gene Networks (Extended Abstract). WABI 2004: 123-134
Coauthor Index
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