Tamir Tuller

Hadas Zur, Tamir Tuller: RFMapp: ribosome flow model application. Bioinformatics 28(12): 1663-1664 (2012)

Alexandra Dana, Tamir Tuller: Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. Journal of Computational Biology 19(2): 200-231 (2012)

Michael Margaliot, Tamir Tuller: Stability Analysis of the Ribosome Flow Model. IEEE/ACM Trans. Comput. Biology Bioinform. 9(5): 1545-1552 (2012)

Michael Margaliot, Tamir Tuller: On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. IEEE/ACM Trans. Comput. Biology Bioinform. 9(6): 1724-1736 (2012)

Hadas Birin, Tamir Tuller: Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinformatics 12(S-9): S12 (2011)

Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller: Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. PLoS Computational Biology 7(9) (2011)

Tamir Tuller, Elchanan Mossel: Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics. IEEE/ACM Trans. Comput. Biology Bioinform. 8(6): 1667-1670 (2011)

Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller: A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). RECOMB 2011: 358-360

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 Bioinformatics 11(S-1): 38 (2010)

Tamir Tuller, Yifat Felder, Martin Kupiec: Discovering local patterns of co - evolution: computational aspects and biological examples. BMC Bioinformatics 11: 43 (2010)

Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin: Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples. Journal of Computational Biology 17(9): 1327-1344 (2010)

Tamir Tuller, Elchanan Mossel: Co-evolution is Incompatible with the Markov Assumption in Phylogenetics. CoRR abs/1008.0322 (2010)

Sagi Snir, Tamir Tuller: The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. J. Bioinformatics and Computational Biology 7(4): 625-644 (2009)

Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevich, Eytan Ruppin, Martin Kupiec: Higher-Order Genomic Organization of Cellular Functions in Yeast. Journal of Computational Biology 16(2): 303-316 (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. Biology Bioinform. 6(3): 495-505 (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: 164-180

Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller: Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. Bioinformatics 24(6): 826-832 (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: 273-277

Yifat Felder, Tamir Tuller: Discovering Local Patterns of Co-evolution. RECOMB-CG 2008: 55-71

Sagi Snir, Tamir Tuller: Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. WABI 2008: 354-368

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23(2): 123-128 (2007)

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 23(8): 1046-1047 (2007)

Isaac Elias, Tamir Tuller: Reconstruction of Ancestral Genomic Sequences Using Likelihood. Journal of Computational Biology 14(2): 216-237 (2007)

Benny Chor, Tamir Tuller: Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. Journal of Computational Biology 14(6): 817-838 (2007)

Tamir Tuller, Martin Kupiec, Eytan Ruppin: Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae. PLoS Computational Biology 3(12) (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: 61-72

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

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21): 2604-2611 (2006)

Benny Chor, Tamir Tuller: Finding a maximum likelihood tree is hard. J. ACM 53(5): 722-744 (2006)

Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor: The Average Common Substring Approach to Phylogenomic Reconstruction. Journal of Computational Biology 13(2): 336-350 (2006)

Benny Chor, Tamir Tuller: Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB 2006: 30-44

Benny Chor, Tamir Tuller: Maximum likelihood of evolutionary trees: hardness and approximation. ISMB (Supplement of Bioinformatics) 2005: 97-106

David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor: Information Theoretic Approaches to Whole Genome Phylogenies. RECOMB 2005: 283-295

Benny Chor, Tamir Tuller: Maximum Likelihood of Evolutionary Trees Is Hard. RECOMB 2005: 296-310

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

Benny Chor, Tamir Tuller: Adding Hidden Nodes to Gene Networks (Extended Abstract). WABI 2004: 123-134