Publications

Journals

Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevitch, Eytan Ruppin and Martin Kupiec. Higher-order Genomic Organization of Cellular Functions in Yeast. To appear in JCB (RECOMB-SB-RG 2008 special issue).

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

Tamir Tuller, Martin Kupiec, Eytan Ruppin. Evolutionary Rate and Gene Expression Across Different Brain Regions. Genome Biol. 9(9):R142, 2008.

Hadas Birin, Zohar Gal-or, Isaac Elias and Tamir Tuller. Inferring Horizontal Transfers in the Presence of Rearrangements by the Minimum Evolution Criterion. Bioinformatics 2008 24(6):826-32.

Tamir Tuller, Martin Kupiec, Eytan Ruppin. Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae. PLoS Comput. Biol. 3(12):e248, 2007.

Tamir Tuller, Benny Chor, Nathan Nelson. Forbidden Penta-Peptides. Prot. Sci. 16(10):2251-2259, 2007.

Efrat Oron, Tamir Tuller, Li Ling, Nina Rozovsky, Daniel Yekutieli, Daniel Segal, Benny Chor, Bruce Edgar, Sigal Rencus, Daniel Chamovitz. Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol. Syst. Biol. 3:108, 2007.

Isaac Elias and Tamir Tuller. Reconstruction of Ancestral Genomic Sequences Using Likelihood. J. Comput. Biol. 14(2):216-37, 2007. (pdf).

Benny Chor and Tamir Tuller. Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. J. Comput. Biol. 14(6):617-38, 2007.

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. Bioinformatics 23 (2):123-128, 2007. (pdf).

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. Mol. Biol. Evol. 24 (1):324-37, 2007.

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

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

Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor. The Average Common Substring Approach to Phylogenomics. Journal of Computational Biology (JCB) 13(2):336-50, 2006. (pdf).

Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation. Bioinformatics 21(Suppl 1):i97-i106, 2005. (pdf).

Peer-Reviewed Conference Proceedings

Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevitch, Eytan Ruppin and Martin Kupiec. Higher-order Genomic Organization of Cellular Functions in Yeast. To appear in RECOMB-SB 2008.

Yedael Waldman*, Tamir Tuller*, Tomer Shlomi, Shaul Karni, Roded Sharan and Eytan Ruppin. Gene Translation Efficiency in Healthy and Cancerous Human Tissues. To appear in RECOMB-RG 2008.

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

Yifat Felder and Tamir Tuller. Discovering Local Patterns of Co - Evolution. To appear in RECOMB-CG 2008.

Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. To appear in WABI 2008.

Hadas Birin, Zohar Gal-or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations and Horizontal Transfers by the Minimum Evolution Criterion. The 7th workshop on Algorithms in Bioinformatics (WABI), University of Pennsylvania , USA , September 7-9, 2007.

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. International Symposium on Bioinformatics Research and Applications (ISBRA),Georgia State University in Atlanta, USA, May 7-10, 2007.

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. ECCB 2006, Eilat, Israel, January 21-24, 2007.

Tamir Tuller, Benny Chor. Biological Networks: Comparison, Conservation, and Evolutionary Trees. RECOMB 2006, Venice, Italy, 30-44, April 2-5, 2006. Abstract.

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, Mallorca, Spain, Ooctober 3-6, 2005. Abstract.

Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation. ISMB 2005, Detroit Marriot Renaissance Center, Michigan, USA, June 25-29, 2005. Proceedings p. 97.Abstract.

David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor. Information Theoretic Approaches to Whole Genome Phylogenomics. RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005. Proceedings p. 283. Abstract.

Benny Chor, Tamir Tuller. Maximum Likelihood of Evolutionary Trees is Hard. RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005. Proceedings p. 296. Abstract.

Benny Chor, Tamir Tuller. Adding hidden nodes to gene network. The 4th workshop on Algorithms in Bioinformatics (WABI), 2004, Bergen, Norway, September 17-21, 2004. Proceedings p. 123. Abstract.

Theses

Tamir Tuller. Approximation of communication channel by finite-state model, and universal decoding. Master's thesis under the supervision of Prof. Jacob Ziv , Faculty of Electrical Engineering, Technion, Israel, 2002.

Tamir Tuller. Computational Aspects of Molecular Evolution. Ph.D thesis under the supervision of Prof. Benny Chor and Prof. Nathan Nelson, School of Computer Science, Tel-Aviv University, Israel, 2006.

Selected Posters

Tamir Tuller, Ohad Greenshpan, Eran Cohen, Benny Chor. Regulation and Genomic Arrangement of microRNA Genes. RECOMB 2006.

Tamir Tuller, Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. RECOMB 2007.

Yifat Felder, Tamir Tuller, Nana Ginzbourg, Udi Rubinstein, Michael Gurevich, Anat Achiron. A new approach for inferring regulatory networks from literature and gene expression measurements. RECOMB 2007.

Tamir Tuller, Martin Kupiec, Eytan Ruppin. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. RECOMB-CG 2008.