Tomer Shlomi's Lab
Departments of Computer Science and Biology,
Technion
Home › Publications
Subcellular compartmentalized-fluxomics elucidates the interplay between mitochondrial and cytosolic metabolism
W.D. Lee, D. Mukha, T. Shlomi
Journal: Submitted


Constraint-based Isotope Tracing (CBIT): Inferring flux constraints from isotope tracing data
M. Balber, T. Lavy, T. Shlomi
Journal: Submitted


Temporal-fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle
E. Ahn, P. Kumar, D. Mukha, A. Tzur, T. Shlomi
Journal: Molecular Systems Biology, 2017 (in press)


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: Nature Chemical Biology, 12(7), 2016



Targeted Inhibition of Glutamine-Dependent Glutathione Metabolism Overcomes Death Resistance Induced by Chronic Cycling Hypoxia
J. Matschke , H. Riffkin , D. Klein , R. Handrick , L. Ludemann , E. Metzen , T. Shlomi , M. Stuschke , V. Jendrossek
Journal: Antioxid Redox Signal, 25(2), 2016



Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
D. Davidi , E. Noor , W. Liebermeister , A. Bar-Even , A. Flamholz , K. Tummler , U. Barenholz , M. Goldenfeld , T. Shlomi , R. Milo
Journal: Proc. Natl. Acad. Sci. USA., 113(12), 2016



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.