Tumor reliance on cytosolic versus mitochondrial one-carbon flux depends on folate availability
W.D Lee, A.C Pirona, B. Sarvin, A. Stern, K. Di-Nur, E. Besser, S. Lagziel, D. Mukha, S. Raz, E. Aizenshtein, T. Shlomi
Cell Metabolism 33(1), 2021
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Mind your media
S. Lagziel, E. Gottlieb, T. Shlomi
Nature Metabolism, 2(21), 2020
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Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample specific ion distributions
B. Sarvin, S. Lagziel, N. Sarvin, D. Mukha, P. Kumar, E. Aizenshtein, T. Shlomi
Nature Communications, 11 (3186), 2020
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Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches
S. Lagziel, T. Shlomi
BMC Biology, 17 (1), 2019
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Inferring cancer dependencies on metabolic genes from large-scale genetic screens
S. Lagziel, W.D Lee, T. Shlomi
BMC Biology, 17 (37), 2019
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Intra-Tumoral Metabolic Zonation and Resultant Phenotypic Diversification Are Dictated by Blood Vessel Proximity
S. Kumar, H. Sharife, T. Kreisel, M. Mogilevsky, L. Bar-Lev, M. Grunewald, E. Aizenshtein, R. Karni, I. Paldor, T. Shlomi, E. Keshet
Cell Metabolism, 30(1), 2019
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Blimp1+ cells generate functional mouse sebaceous gland organoids in vitro
Feldman, D. Mukha, II Maor, E. Sedov, E. Koren, Y. Yosefzon, T. Shlomi, Y. Fuchs
Nature Communications, 10(1):2348, 2019
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Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells
W.D. Lee, D. Mukha, E. Aizenshtein, T. Shlomi
Nature Communications, 10(1):1351, 2019
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Sensitivity of pituitary gonadotropes to hyperglycemia leads to epigenetic aberrations and reduced follicle-stimulating hormone levels
A. Feldman, A. Saleh, L. Pnueli, S. Qiao, T. Shlomi, U. Boehm, P. Melamed
FASEB 33(1), 2019
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A new ESI-LC/MS approach for comprehensive metabolic profiling of phytocannabinoids in Cannabis
P. Berman, K, Futoran, G.M Lewitus, D. Mukha, M. Benami, T. Shlomi, D. Meiri
Sci Rep., 8 (11), 2018
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Transfer of miRNA in Macrophage-Derived Exosomes Induces Drug Resistance in Pancreatic Adenocarcinoma
Y. Binenbaum, E. Fridman, Z. Yaari, N. Milman, A. Schroeder, G. Ben David, T. Shlomi, Z. Gil
Cancer Research 78 (18), 2018
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Temporal-fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle
E. Ahn, P. Kumar, D. Mukha, A. Tzur, T. Shlomi
Molecular Systems Biology, 13 (11), 2017
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Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
J. O. Park, S. A. Rubin, Y. Xu, D. Amador-Noguez, J. Fan, T. Shlomi, J. D. Rabinowitz.
Nature Chemical Biology, 12(7), 2016
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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
Antioxid Redox Signal, 25(2), 2016
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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
Proc. Natl. Acad. Sci. USA., 113(12), 2016
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Efficient Modeling of MS/MS Data for Metabolic Flux Analysis
N. Tepper, T. Shlomi
PLoS One, 10(7), 2015
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Quantitation of cellular metabolic fluxes of methionine
T. Shlomi, J. Fan, B. Tang, W. D. Kruger, J. D. Rabinowitz
Analytical Chemistry, 86(3), 2014
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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
BMC Genomics, 15:158, 2014
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Quantitative flux analysis identifies folate-dependent NADPH production.
J. Fan, J. Ye, J. Kamphorst, T. Shlomi, C. Thompson, J. D. Rabinowitz.
Nature 2014
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An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments
N. Tepper and T. Shlomi
Bioinformatics 29 (23), 2013
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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)
Molecular Systems Biology, 9:712, 2013
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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 of Biological Chemistry, 288 (43), 2013
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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
PLoS One, 8 (9), 2013|
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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)
Nature, doi: 10.1038/nature12154, 2013
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Cancer metabolism mistunes methylation.
T. Shlomi and J. D. Rabinowitz
Nature Chemical Biology (News and Views), 9, 2013
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MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
E. Vitkin, T. Shlomi
Genome Biology 13:R111, 2012
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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
PLoS Computational Biology 8(7), 2012
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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
Proc Natl Acad Sci U S A. 109(1):339-44, 2012
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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).
Nature, 17;477, 2011
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Predicting Selective Drug Targets in Cancer through Metabolic Networks.
O. Folger, L. Jerby, C. Frezza, E. Gottlieb, E. Ruppin*, T. Shlomi* (*Equal contribution)
Molecular Systems Biology, 7:501, 2011
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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)
PLoS Computational Biology, 7 (3), 2011
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Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments.
N. Tepper, T. Shlomi
PLoS One, 6 (1), 2011
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iMAT: Integrative Metabolic Analysis Tool.
H. Zur, E. Ruppin, T. Shlomi
Bioinformatics, 15;26(24):3140-2, 2010
iMATWeb
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Computational Reconstruction of Tissue-specific Metabolic Models: Application to Human Liver Metabolism.
L. Jerby, T. Shlomi*, E. Ruppin* (*Equal contribution)
Molecular Systems Biology, Sep 7;6:401, 2010
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Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model.
K. Yizhak, T. Benyamini, W. Liebermeister, E. Ruppin, T. Shlomi
Bioinformatics, 26, 255-260, 2010 (ISMB 2010 – Outstanding Student Paper Award)
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Pathway-Based Functional Analysis of Metagenomes.
S. Bercovici, I. Sharon, R.Y. Pinter, T. Shlomi
RECOMB, 2010
JCB, 2011
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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
Genome Biology, 11: R43, 2010
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Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages.
Y. Waldman, T. Tuller, T. Shlomi, R. Sharan, E. Ruppin.
Nucleic Acids Research, 38(9), 2010
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Associating Genes and Protein Complexes with Disease via Network Propagation.
O. Vanunu, O. Magger, E. Ruppin, T. Shlomi, R. Sharan
PLoS Computational Biology, 6(1), 2010
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Predicting Metabolic Engineering Knockout Strategies for Chemical Production: Accounting for Competing Pathways.
Tepper, T. Shlomi
Bioinformatics, 2009, doi:10.1093
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Metabolic Network-based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism.
Shlomi.
Biotechnology and Genetic Engineering Reviews, Volume 26, ISBN: 9781904761914, 2009.
Metabolic Network-based Analysis of Yeast Gene-Nutrient Interactions.
Diamant, Y. Eldar, O. Rokhlenko, E. Ruppin, T. Shlomi.
Molecular BioSystems, DOI: 10.1039, 2009
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Network-based Prediction of Metabolic Enzymes Subcellular Localization.
Mintz, A. Aharoni, E. Ruppin, T. Shlomi.
Bioinformatics, 25(12): 247-252, 2009 (ISMB 2009)
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Predicting Metabolic Biomarkers of Human Inborn Errors of Metabolism.
Shlomi*, M. Cabili*, E. Ruppin. (*Equal contribution)
Molecular Systems Biology, 5:263, 2009
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Gene Translation Efficiency in Healthy and Cancerous Human Tissues.
Waldman*, T. Tuller*, T. Shlomi, S. Karni, R. Sharan and E. Ruppin. (*Equal contribution).
The 5th Annual RECOMB Satellite on Regulatory Genomics, MIT, MA, USA, Oct 29-Nov 2, 2008
Network-based Prediction of Human Tissue-specific Metabolism.
Shlomi*, M. Cabili*, M. Herrgard, B.Ø. Palsson , E. Ruppin. (*Equal contribution).
Nature Biotechnology, 26 (9), 1003-1010, 2008
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From E-MAPs to Module Maps: Dissecting Quantitative Genetic Interactions using Physical Interactions.
Ulitsky, T. Shlomi, M. Kupiec and R. Shamir.
Molecular Systems Biology, 4:209, 2008
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Systematic Condition-Dependent Annotation of Metabolic Genes.
Shlomi, M. Herrgard, V. Portnoy, E. Naim, B.Ø. Palsson, R. Sharan, and E. Ruppin.
Genome Research, 17(11):1626-1633, 2007
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Pepitope: Epitope mapping from affinity-selected peptides.
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.
Bioinformatics, 23(23):3244-3246, 2007
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Constraint-based Functional Similarity of Metabolic Genes: Going Beyond Network Topology.
Rokhlenko, T. Shlomi, R. Sharan, E. Ruppin, R.Y. Pinter.
Bioinformatics, 23(16):2139-2146 , 2007
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SPINE: A Framework for Signaling-Regulatory Pathway Inference from Cause-Effect Experiments.
Ourfali, T. Shlomi, T. Ideker, E. Ruppin, R. Sharan.
Bioinformatics, 23(13), 359-366, 2007 (ISMB 2007)
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A Genome-Scale Computational Study of the Interplay between Transcriptional Regulation and Metabolism.
Shlomi, Y. Eisenberg, R. Sharan, E. Ruppin.
RECOMB Satellite Workshop on Systems Biology, 2006
Molecular Systems Biology, 3:101, 2007
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QNet: A Tool for Querying Protein Interaction Networks.
Dost*, T. Shlomi*, N.Gupta, V. Bafna, and R. Sharan. (*Equal contribution)
Proceedings:Â RECOMB 2007
Journal of Computational Biology, 15 (7), 913-925, 2008
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Transcriptional Regulation of Protein Complexes within and across Species.
Tan, T. Shlomi, H. Feizi, T. Ideker, and R. Sharan.
Proc. Natl. Acad. Sci. USA., 104 (4), 1283-1288, 2007
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Evolutionary Conservation and Over-Representation of Functionally Enriched Network Patterns in the Yeast Regulatory Network
Meshi*, T. Shlomi*, E. Ruppin. (*Equal contribution)
BMC Systems Biology, 1:1, 2007
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Epitope Mapping using Combinatorial Phage-Display Libraries: A Graph-Based Algorithm.
Mayrose, T. Shlomi, N. D. Rubinstein, J. M. Gershoni, E. Ruppin, R. Sharan, and T. Pupko.
Nucleic Acids Research, 35 (1), 69-78, 2007
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Gene Loss Rate: A Probabilistic Measure for the Conservation of Eukaryotic Genes.
Borenstein*, T. Shlomi*, E. Ruppin, and R. Sharan. (*Equal contribution)
Nucleic Acids Research, 35 (1):e7, 2007
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Flux-based vs. Topology-based Similarity of Metabolic Genes.
Rokhlenko, T. Shlomi, R. Sharan, E. Ruppin, R. Pinter.
WABI 2006, Lecture Notes in Computer Science (LNCS), Vol. 4175, September 2006, pp. 274-285
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Conservation of Expression and Sequence of Metabolic Genes is Reflected by Activity Across Metabolic States.
Bilu, T. Shlomi, N. Barkai, and E. Ruppin.
PLoS Computational Biology, 2 (8), 932-938, 2006
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QPath: A Method for Querying Pathways in a Protein-Protein Interaction Network.Shlomi, D. Segal, E. Ruppin, and R. Sharan.
BMC Bioinformatics, 7:199, 2006.
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A Direct Comparison of Protein Interaction Confidence Assignment Schemes.
S. Suthram, T. Shlomi, E. Ruppin, R. Sharan and T. Idekrer.
First Annual RECOMB Satellite Workshop on Systems Biology, 2005
BMC Bioinformatics, 7:360, 2006
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Regulatory On/Off Minimization Of Metabolic Flux Changes After Genetic Perturbations.
T. Shlomi, O. Berkman and E. Ruppin.
Proc. Natl. Acad. Sci. USA. 102 (21), 7695-7700, 2005.
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Constraint-based Modeling of Perturbed Organisms: A ROOM for Improvement.
T. Shlomi, O. Berkman and E. Ruppin.
ISMB 2004.
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