Tomer Shlomi's Lab
Departments of Computer Science and Biology,
Home › Publications
Conservation of cellular metabolite concentrations and free energies
J. O. Park, S. A. Rubin, Y. Xu, D. Amador-Noguez, J. Fan, T. Shlomi, J. D. Rabinowitz.
Journal: Submitted

Efficient Modeling of MS/MS Data for Metabolic Flux Analysis
N. Tepper, T. Shlomi
Journal: PLoS One, 10(7), 2015

Quantitation of cellular metabolic fluxes of methionine
T. Shlomi, J. Fan, B. Tang, W. D. Kruger, J. D. Rabinowitz
Journal: Analytical Chemistry, 86(3), 2014

High throughput synthetic lethality screen reveals a tumorigenic role of adenylate cyclase in fumarate hydratase-deficient cancer cells
M. Boettcher, A. Lawson, V. Ladenburger, J. Fredebohm, J. Wolf, J. D. Hoheisel, C. Frezza, T. Shlomi
Journal: BMC Genomics, 15:158, 2014

Quantitative flux analysis identifies folate-dependent NADPH production.
J. Fan, J. Ye, J. Kamphorst, T. Shlomi, C. Thompson, J. D. Rabinowitz.
Journal: Nature 2014

An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments
N. Tepper and T. Shlomi
Journal: Bioinformatics, Bioinformatics, 29 (23), 2013

Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia
J. Fan, J. J. Kamphorst, R. Mathew, C. K. Hill, E. White, T. Shlomi*, J. D. Rabinowitz*. (*Equal contribution)
Journal: Molecular Systems Biology, Molecular Systems Biology, 9:712, 2013

Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive IDH flux.
J. Fan, J. Kamphorst, J. D. Rabinowitz, T. Shlomi.
Journal: Journal of Biological Chemistry, 288 (43), 2013

An interplay between molecular occupancy and enzyme cost shapes intracellular metabolite concentrations
N. Tepper, E. Noor, D. Amador-Noguez, H. Haraldsdóttir, R. Milo, J. Rabinowitz, .W. Liebermeister, T. Shlomi
Journal: PLoS One, 8 (9), 2013

A key role for mitochondrial gatekeeper pyruvate dehydrogenase in oncogene-induced senescence
J. Kaplon, L. Zheng, K. Meissl, B. Chaneton, V. A. Selivanov, G. MacKay, S.H van der Burg, E. M E Verdegaal, M. Cascante, T. Shlomi, E. Gottlieb*, D.S. Peeper* (*Equal contribution)
Journal: Nature, doi: 10.1038/nature12154, 2013

Cancer metabolism mistunes methylation.
T. Shlomi and J. D. Rabinowitz
Journal: Nature Chemical Biology (News and Views), 9, 2013

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
E. Vitkin, T. Shlomi
Journal: Genome Biology 13:R111, 2012

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
Journal: PLoS Computational Biology 8(7), 2012

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
S. Mintz-Oron, S. Meir, S. Malitsky, E. Ruppin, A. Aharoni, T. Shlomi
Journal: Proc Natl Acad Sci U S A. 109(1):339-44, 2012

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

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

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.

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.

Constraint-based Modeling of Perturbed Organisms: A ROOM for Improvement.
T. Shlomi, O. Berkman and E. Ruppin.
Proceedings: ISMB 2004.