Tomer Shlomi's Research Group

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Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters.

R. Adadi, B. Volkmer, R. Milo, M. Heinemann, T. Shlomi

(submitted)

Functional genomics-based approach for metabolic network model reconstruction: Application for cyanobacteria networks.

E. Vitkin, T. Shlomi

(submitted)

Multi-level reconstruction of Arabidopsis metabolic network models: From subcellular compartmentalization to tissue-specificity.

S. Mintz-Oron, S. Meir, S. Malitsky, E. Ruppin, A. Aharoni, T. Shlomi

Journal: Proc. Natl. Acad. Sci. USA. (in press)

Metabolic synthetic lethality between fumarate hydratase and haem oxygenase: a new strategy to target fumarate hydratase-deficient cancer.

C. Frezza, L. Zheng, O. Folger, K. N. Rajagopalan, E. D. MacKenzie, L. Jerby, M. Micaroni, B. Chaneton, A. Hedley, G. Kalna, P. J. Pollard, I. P.M. Tomlinson, D. G. Watson, R. J. Deberardinis, T. Shlomi*, E. Ruppin*, E. Gottlieb (*Equal contribution).

Journal: Nature, 17;477, 2011

Predicting Selective Drug Targets in Cancer through Metabolic Networks.

O. Folger, L. Jerby, C. Frezza, E. Gottlieb, E. Ruppin*, T. Shlomi* (*Equal contribution)

Journal: Molecular Systems Biology, 7:501, 2011

Metabolic networks elucidate the role of proliferative adaptation in causing the Warburg effect.

T. Shlomi*, T. Benyamini*, E. Gottlieb, R. Sharan, E. Ruppin (*Equal contribution)

Journal: PLoS Computational Biology, 7 (3), 2011

Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments.

N. Tepper, T. Shlomi

Journal: PLoS One, 6 (1), 2011

iMAT: Integrative Metabolic Analysis Tool.

H. Zur, E. Ruppin, T. Shlomi

Journal: Bioinformatics, 15;26(24):3140-2, 2010

Computational Reconstruction of Tissue-specific Metabolic Models: Application to Human Liver Metabolism.

L. Jerby, T. Shlomi*, E. Ruppin* (*Equal contribution)

Journal: Molecular Systems Biology, Sep 7;6:401, 2010

Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model.

K. Yizhak, T. Benyamini, W. Liebermeister, E. Ruppin, T. Shlomi

Journal: Bioinformatics, 26, 255-260, 2010 (ISMB 2010 - Outstanding Student Paper Award)

Pathway-Based Functional Analysis of Metagenomes.

S. Bercovici, I. Sharon, R.Y. Pinter, T. Shlomi

Proceedings: RECOMB, 2010

Journal: JCB, 2011 (in press)

Flux balance analysis accounting for metabolite dilution

T. Benyamini, O. Folger, E. Ruppin, T. Shlomi

Proceedings: The 5th Annual RECOMB Satellite on Systems Biology, 2009

Journal: Genome Biology, 11: R43, 2010

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages.

Y. Waldman, T. Tuller, T. Shlomi, R. Sharan, E. Ruppin.

Journal: Nucleic Acids Research, 38(9), 2010

Associating Genes and Protein Complexes with Disease via Network Propagation.

O. Vanunu, O. Magger, E. Ruppin, T. Shlomi, R. Sharan

Journal: PLoS Computational Biology, 6(1), 2010

Predicting Metabolic Engineering Knockout Strategies for Chemical Production: Accounting for Competing Pathways.

N. Tepper, T. Shlomi

Journal: Bioinformatics, 2009, doi:10.1093

Metabolic Network-based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism.

T. Shlomi.

Journal: Biotechnology and Genetic Engineering Reviews, Volume 26, ISBN: 9781904761914, 2009.

Metabolic Network-based Analysis of Yeast Gene-Nutrient Interactions.

I. Diamant, Y. Eldar, O. Rokhlenko, E. Ruppin, T. Shlomi.

Journal: Molecular BioSystems, DOI: 10.1039, 2009

Network-based Prediction of Metabolic Enzymes’ Subcellular Localization.

S. Mintz, A. Aharoni, E. Ruppin, T. Shlomi.

Journal: Bioinformatics, 25(12): 247-252, 2009 (ISMB’09)

Predicting Metabolic Biomarkers of Human Inborn Errors of Metabolism.

T. Shlomi*, M. Cabili*, E. Ruppin. (*Equal contribution)

Journal: Molecular Systems Biology, 5:263, 2009

Gene Translation Efficiency in Healthy and Cancerous Human Tissues.

Y. Waldman*, T. Tuller*, T. Shlomi, S. Karni, R. Sharan and E. Ruppin. (*Equal contribution).

Proceedings: The 5th Annual RECOMB Satellite on Regulatory Genomics, MIT, MA, USA, Oct 29-Nov 2, 2008

Network-based Prediction of Human Tissue-specific Metabolism.

T. Shlomi*, M. Cabili*, M. Herrgard, B.Ø. Palsson , E. Ruppin. (*Equal contribution).

Journal: Nature Biotechnology, 26 (9), 1003-1010, 2008

From E-MAPs to Module Maps: Dissecting Quantitative Genetic Interactions using Physical Interactions.

I. Ulitsky, T. Shlomi, M. Kupiec and R. Shamir.

Journal: Molecular Systems Biology, 4:209, 2008

Systematic Condition-Dependent Annotation of Metabolic Genes.

T. Shlomi, M. Herrgard, V. Portnoy, E. Naim, B.Ø. Palsson, R. Sharan, and E. Ruppin.

Journal: Genome Research, 17(11):1626-1633, 2007

Pepitope: Epitope mapping from affinity-selected peptides.

I. Mayrose, O. Penn, E. Erez, N.D. Rubinstein, T. Shlomi, N.T. Freund, E.M. Bublil, E. Ruppin, R. Sharan, J.M. Gershoni, E. Martz, T. Pupko.

Journal: Bioinformatics, 23(23):3244-3246, 2007

Constraint-based Functional Similarity of Metabolic Genes: Going Beyond Network Topology.

O. Rokhlenko, T. Shlomi, R. Sharan, E. Ruppin, R.Y. Pinter.

Journal: Bioinformatics, 23(16):2139-2146 , 2007

SPINE: A Framework for Signaling-Regulatory Pathway Inference from Cause-Effect Experiments.

O. Ourfali, T. Shlomi, T. Ideker, E. Ruppin, R. Sharan.

Journal: Bioinformatics, 23(13), 359-366, 2007 (ISMB’07)

A Genome-Scale Computational Study of the Interplay between Transcriptional Regulation and Metabolism.

T. Shlomi, Y. Eisenberg, R. Sharan, E. Ruppin.

Proceedings: RECOMB Satellite Workshop on Systems Biology, 2006

Journal: Molecular Systems Biology, 3:101, 2007

QNet: A Tool for Querying Protein Interaction Networks.

B. Dost*, T. Shlomi*, N.Gupta, V. Bafna, and R. Sharan. (*Equal contribution)

Proceedings: RECOMB 2007

Journal: Journal of Computational Biology, 15 (7), 913-925, 2008

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Transcriptional Regulation of Protein Complexes within and across Species.

K. Tan, T. Shlomi, H. Feizi, T. Ideker, and R. Sharan.

Journal: Proc. Natl. Acad. Sci. USA., 104 (4), 1283-1288, 2007

Evolutionary Conservation and Over-Representation of Functionally Enriched Network Patterns in the Yeast Regulatory Network

O. Meshi*, T. Shlomi*, E. Ruppin. (*Equal contribution)

Journal: BMC Systems Biology, 1:1, 2007

Epitope Mapping using Combinatorial Phage-Display Libraries: A Graph-Based Algorithm.

I. Mayrose, T. Shlomi, N. D. Rubinstein, J. M. Gershoni, E. Ruppin, R. Sharan, and T. Pupko.

Journal: Nucleic Acids Research, 35 (1), 69-78, 2007

Gene Loss Rate: A Probabilistic Measure for the Conservation of Eukaryotic Genes.

E. Borenstein*, T. Shlomi*, E. Ruppin, and R. Sharan. (*Equal contribution)

Journal: Nucleic Acids Research, 35 (1):e7, 2007

Flux-based vs. Topology-based Similarity of Metabolic Genes.

O. Rokhlenko, T. Shlomi, R. Sharan, E. Ruppin, R. Pinter.

Proceedings: WABI 2006, Lecture Notes in Computer Science (LNCS), Vol. 4175, September 2006, pp. 274-285.

Conservation of Expression and Sequence of Metabolic Genes is Reflected by Activity Across Metabolic States.

Y. Bilu, T. Shlomi, N. Barkai, and E. Ruppin.

Journal: PLoS Computational Biology, 2 (8), 932-938, 2006

QPath: A Method for Querying Pathways in a Protein-Protein Interaction Network.

T. Shlomi, D. Segal, E. Ruppin, and R. Sharan.

Journal: BMC Bioinformatics, 7:199, 2006.

supplementary data

A Direct Comparison of Protein Interaction Confidence Assignment Schemes.

S. Suthram, T. Shlomi, E. Ruppin, R. Sharan and T. Idekrer.

Proceedings: First Annual RECOMB Satellite Workshop on Systems Biology, 2005

Journal: BMC Bioinformatics, 7:360, 2006

Regulatory On/Off Minimization Of Metabolic Flux Changes After Genetic Perturbations.

T. Shlomi, O. Berkman and E. Ruppin.

Journal: Proc. Natl. Acad. Sci. USA. 102 (21), 7695-7700, 2005.

supplementary data

Constraint-based Modeling of Perturbed Organisms: A ROOM for Improvement.

T. Shlomi, O. Berkman and E. Ruppin.

Proceedings: ISMB 2004.

supplementary data