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Items: 50

1.

Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle.

Ahn E, Kumar P, Mukha D, Tzur A, Shlomi T.

Mol Syst Biol. 2017 Nov 6;13(11):953. doi: 10.15252/msb.20177763.

2.

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage.

Park JO, Rubin SA, Xu YF, Amador-Noguez D, Fan J, Shlomi T, Rabinowitz JD.

Nat Chem Biol. 2016 Jul;12(7):482-9. doi: 10.1038/nchembio.2077. Epub 2016 May 2.

3.

Targeted Inhibition of Glutamine-Dependent Glutathione Metabolism Overcomes Death Resistance Induced by Chronic Cycling Hypoxia.

Matschke J, Riffkin H, Klein D, Handrick R, Lüdemann L, Metzen E, Shlomi T, Stuschke M, Jendrossek V.

Antioxid Redox Signal. 2016 Jul 10;25(2):89-107. doi: 10.1089/ars.2015.6589. Epub 2016 May 9.

PMID:
27021152
4.

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.

Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T, Milo R.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3401-6. doi: 10.1073/pnas.1514240113. Epub 2016 Mar 7.

5.

Correction: Efficient Modeling of MS/MS Data for Metabolic Flux Analysis.

Tepper N, Shlomi T.

PLoS One. 2015 Sep 14;10(9):e0138630. doi: 10.1371/journal.pone.0138630. eCollection 2015. No abstract available.

6.

Efficient Modeling of MS/MS Data for Metabolic Flux Analysis.

Tepper N, Shlomi T.

PLoS One. 2015 Jul 31;10(7):e0130213. doi: 10.1371/journal.pone.0130213. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0138630.

7.

Quantitative flux analysis reveals folate-dependent NADPH production.

Fan J, Ye J, Kamphorst JJ, Shlomi T, Thompson CB, Rabinowitz JD.

Nature. 2014 Jun 12;510(7504):298-302. doi: 10.1038/nature13236. Epub 2014 May 4. Erratum in: Nature. 2014 Sep 25;513(7519):574.

8.

High throughput synthetic lethality screen reveals a tumorigenic role of adenylate cyclase in fumarate hydratase-deficient cancer cells.

Boettcher M, Lawson A, Ladenburger V, Fredebohm J, Wolf J, Hoheisel JD, Frezza C, Shlomi T.

BMC Genomics. 2014 Feb 25;15:158. doi: 10.1186/1471-2164-15-158.

9.

Quantitation of cellular metabolic fluxes of methionine.

Shlomi T, Fan J, Tang B, Kruger WD, Rabinowitz JD.

Anal Chem. 2014 Feb 4;86(3):1583-91. doi: 10.1021/ac4032093. Epub 2014 Jan 16.

10.

Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia.

Fan J, Kamphorst JJ, Mathew R, Chung MK, White E, Shlomi T, Rabinowitz JD.

Mol Syst Biol. 2013 Dec 3;9:712. doi: 10.1038/msb.2013.65.

11.

An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments.

Tepper N, Shlomi T.

Bioinformatics. 2013 Dec 1;29(23):3045-52. doi: 10.1093/bioinformatics/btt516. Epub 2013 Oct 10.

PMID:
24123514
12.

Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load.

Tepper N, Noor E, Amador-Noguez D, Haraldsdóttir HS, Milo R, Rabinowitz J, Liebermeister W, Shlomi T.

PLoS One. 2013 Sep 26;8(9):e75370. doi: 10.1371/journal.pone.0075370. eCollection 2013.

13.

Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive isocitrate dehydrogenase (IDH) flux.

Fan J, Kamphorst JJ, Rabinowitz JD, Shlomi T.

J Biol Chem. 2013 Oct 25;288(43):31363-9. doi: 10.1074/jbc.M113.502740. Epub 2013 Sep 12.

14.

A key role for mitochondrial gatekeeper pyruvate dehydrogenase in oncogene-induced senescence.

Kaplon J, Zheng L, Meissl K, Chaneton B, Selivanov VA, Mackay G, van der Burg SH, Verdegaal EM, Cascante M, Shlomi T, Gottlieb E, Peeper DS.

Nature. 2013 Jun 6;498(7452):109-12. doi: 10.1038/nature12154. Epub 2013 May 19.

PMID:
23685455
15.

Metabolism: Cancer mistunes methylation.

Shlomi T, Rabinowitz JD.

Nat Chem Biol. 2013 May;9(5):293-4. doi: 10.1038/nchembio.1234. No abstract available.

16.
17.

Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters.

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

PLoS Comput Biol. 2012;8(7):e1002575. doi: 10.1371/journal.pcbi.1002575. Epub 2012 Jul 5.

18.

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity.

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

Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):339-44. doi: 10.1073/pnas.1100358109. Epub 2011 Dec 19.

19.

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.

Frezza C, Zheng L, Folger O, Rajagopalan KN, MacKenzie ED, Jerby L, Micaroni M, Chaneton B, Adam J, Hedley A, Kalna G, Tomlinson IP, Pollard PJ, Watson DG, Deberardinis RJ, Shlomi T, Ruppin E, Gottlieb E.

Nature. 2011 Aug 17;477(7363):225-8. doi: 10.1038/nature10363.

PMID:
21849978
20.

Predicting selective drug targets in cancer through metabolic networks.

Folger O, Jerby L, Frezza C, Gottlieb E, Ruppin E, Shlomi T.

Mol Syst Biol. 2011 Jun 21;7:501. doi: 10.1038/msb.2011.35. Erratum in: Mol Syst Biol. 2011;7. doi:10.1038/msb.2011.51.

21.

Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect.

Shlomi T, Benyamini T, Gottlieb E, Sharan R, Ruppin E.

PLoS Comput Biol. 2011 Mar;7(3):e1002018. doi: 10.1371/journal.pcbi.1002018. Epub 2011 Mar 10.

22.

Pathway-based functional analysis of metagenomes.

Sharon I, Bercovici S, Pinter RY, Shlomi T.

J Comput Biol. 2011 Mar;18(3):495-505. doi: 10.1089/cmb.2010.0260.

PMID:
21385050
23.

Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

Tepper N, Shlomi T.

PLoS One. 2011 Jan 21;6(1):e16274. doi: 10.1371/journal.pone.0016274.

24.

iMAT: an integrative metabolic analysis tool.

Zur H, Ruppin E, Shlomi T.

Bioinformatics. 2010 Dec 15;26(24):3140-2. doi: 10.1093/bioinformatics/btq602. Epub 2010 Nov 15.

PMID:
21081510
25.

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism.

Jerby L, Shlomi T, Ruppin E.

Mol Syst Biol. 2010 Sep 7;6:401. doi: 10.1038/msb.2010.56.

26.

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.

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

Bioinformatics. 2010 Jun 15;26(12):i255-60. doi: 10.1093/bioinformatics/btq183.

27.

Flux balance analysis accounting for metabolite dilution.

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

Genome Biol. 2010;11(4):R43. doi: 10.1186/gb-2010-11-4-r43. Epub 2010 Apr 16.

28.

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

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

Nucleic Acids Res. 2010 May;38(9):2964-74. doi: 10.1093/nar/gkq009. Epub 2010 Jan 21.

29.

Associating genes and protein complexes with disease via network propagation.

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

PLoS Comput Biol. 2010 Jan 15;6(1):e1000641. doi: 10.1371/journal.pcbi.1000641.

30.
31.

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways.

Tepper N, Shlomi T.

Bioinformatics. 2010 Feb 15;26(4):536-43. doi: 10.1093/bioinformatics/btp704. Epub 2009 Dec 23.

PMID:
20031969
32.

A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism.

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

Mol Biosyst. 2009 Dec;5(12):1732-9. doi: 10.1039/B823287N.

PMID:
19593469
33.

Network-based prediction of metabolic enzymes' subcellular localization.

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

Bioinformatics. 2009 Jun 15;25(12):i247-52. doi: 10.1093/bioinformatics/btp209.

34.

Predicting metabolic biomarkers of human inborn errors of metabolism.

Shlomi T, Cabili MN, Ruppin E.

Mol Syst Biol. 2009;5:263. doi: 10.1038/msb.2009.22. Epub 2009 Apr 28.

35.

Network-based prediction of human tissue-specific metabolism.

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E.

Nat Biotechnol. 2008 Sep;26(9):1003-10. doi: 10.1038/nbt.1487.

PMID:
18711341
36.

QNet: a tool for querying protein interaction networks.

Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R.

J Comput Biol. 2008 Sep;15(7):913-25. doi: 10.1089/cmb.2007.0172.

PMID:
18707533
37.

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions.

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

Mol Syst Biol. 2008;4:209. doi: 10.1038/msb.2008.42. Epub 2008 Jul 15.

38.

Pepitope: epitope mapping from affinity-selected peptides.

Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Freund NT, Bublil EM, Ruppin E, Sharan R, Gershoni JM, Martz E, Pupko T.

Bioinformatics. 2007 Dec 1;23(23):3244-6. Epub 2007 Oct 31.

PMID:
17977889
39.

Systematic condition-dependent annotation of metabolic genes.

Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BØ, Sharan R, Ruppin E.

Genome Res. 2007 Nov;17(11):1626-33. Epub 2007 Sep 25.

40.

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

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

Bioinformatics. 2007 Jul 1;23(13):i359-66.

PMID:
17646318
41.

Constraint-based functional similarity of metabolic genes: going beyond network topology.

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

Bioinformatics. 2007 Aug 15;23(16):2139-46. Epub 2007 Jun 22.

PMID:
17586548
42.

A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

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

Mol Syst Biol. 2007;3:101. Epub 2007 Apr 17.

44.

Transcriptional regulation of protein complexes within and across species.

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

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1283-8. Epub 2007 Jan 16.

45.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

Borenstein E, Shlomi T, Ruppin E, Sharan R.

Nucleic Acids Res. 2007;35(1):e7. Epub 2006 Dec 7.

46.

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T.

Nucleic Acids Res. 2007;35(1):69-78. Epub 2006 Dec 6.

47.

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states.

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

PLoS Comput Biol. 2006 Aug 18;2(8):e106. Epub 2006 Jul 6.

48.

A direct comparison of protein interaction confidence assignment schemes.

Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T.

BMC Bioinformatics. 2006 Jul 26;7:360.

49.

QPath: a method for querying pathways in a protein-protein interaction network.

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

BMC Bioinformatics. 2006 Apr 10;7:199.

50.

Regulatory on/off minimization of metabolic flux changes after genetic perturbations.

Shlomi T, Berkman O, Ruppin E.

Proc Natl Acad Sci U S A. 2005 May 24;102(21):7695-700. Epub 2005 May 16.

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