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Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly.

Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C.

Nat Commun. 2018 Jan 30;9(1):327. doi: 10.1038/s41467-017-02395-2.


Putative functional genes in idiopathic dilated cardiomyopathy.

Nair NU, Das A, Amit U, Robinson W, Park SG, Basu M, Lugo A, Leor J, Ruppin E, Hannenhalli S.

Sci Rep. 2018 Jan 8;8(1):66. doi: 10.1038/s41598-017-18524-2.


Amphiphilic nanocarrier-induced modulation of PLK1 and miR-34a leads to improved therapeutic response in pancreatic cancer.

Gibori H, Eliyahu S, Krivitsky A, Ben-Shushan D, Epshtein Y, Tiram G, Blau R, Ofek P, Lee JS, Ruppin E, Landsman L, Barshack I, Golan T, Merquiol E, Blum G, Satchi-Fainaro R.

Nat Commun. 2018 Jan 2;9(1):16. doi: 10.1038/s41467-017-02283-9.


An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer.

Auslander N, Cunningham CE, Toosi BM, McEwen EJ, Yizhak K, Vizeacoumar FS, Parameswaran S, Gonen N, Freywald T, Bhanumathy KK, Freywald A, Vizeacoumar FJ, Ruppin E.

Mol Syst Biol. 2017 Dec 1;13(12):956. doi: 10.15252/msb.20177739.


Co-targeting the tumor endothelium and P-selectin-expressing glioblastoma cells leads to a remarkable therapeutic outcome.

Ferber S, Tiram G, Sousa-Herves A, Eldar-Boock A, Krivitsky A, Scomparin A, Yeini E, Ofek P, Ben-Shushan D, Vossen LI, Licha K, Grossman R, Ram Z, Henkin J, Ruppin E, Auslander N, Haag R, Calderón M, Satchi-Fainaro R.

Elife. 2017 Oct 4;6. pii: e25281. doi: 10.7554/eLife.25281.


Prediction and Subtyping of Hypertension from Pan-Tissue Transcriptomic and Genetic Analyses.

Basu M, Sharmin M, Das A, Nair NU, Wang K, Lee JS, Chang YC, Ruppin E, Hannenhalli S.

Genetics. 2017 Nov;207(3):1121-1134. doi: 10.1534/genetics.117.300280. Epub 2017 Sep 12.


Precision Oncology: The Road Ahead.

Senft D, Leiserson MDM, Ruppin E, Ronai ZA.

Trends Mol Med. 2017 Oct;23(10):874-898. doi: 10.1016/j.molmed.2017.08.003. Epub 2017 Sep 5. Review.


Detecting similar binding pockets to enable systems polypharmacology.

Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005522. doi: 10.1371/journal.pcbi.1005522. eCollection 2017 Jun.


Altered protein glycosylation predicts Alzheimer's disease and modulates its pathology in disease model Drosophila.

Frenkel-Pinter M, Stempler S, Tal-Mazaki S, Losev Y, Singh-Anand A, Escobar-Álvarez D, Lezmy J, Gazit E, Ruppin E, Segal D.

Neurobiol Aging. 2017 Aug;56:159-171. doi: 10.1016/j.neurobiolaging.2017.04.020. Epub 2017 May 3.


New Role for Interleukin-13 Receptor α1 in Myocardial Homeostasis and Heart Failure.

Amit U, Kain D, Wagner A, Sahu A, Nevo-Caspi Y, Gonen N, Molotski N, Konfino T, Landa N, Naftali-Shani N, Blum G, Merquiol E, Karo-Atar D, Kanfi Y, Paret G, Munitz A, Cohen HY, Ruppin E, Hannenhalli S, Leor J.

J Am Heart Assoc. 2017 May 20;6(5). pii: e005108. doi: 10.1161/JAHA.116.005108.


Insulin-like growth factor 1 receptor activation promotes mammary gland tumor development by increasing glycolysis and promoting biomass production.

Ter Braak B, Siezen CL, Lee JS, Rao P, Voorhoeve C, Ruppin E, van der Laan JW, van de Water B.

Breast Cancer Res. 2017 Feb 7;19(1):14. doi: 10.1186/s13058-017-0802-0.


Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy.

Cohen O, Oberhardt M, Yizhak K, Ruppin E.

PLoS One. 2016 Dec 20;11(12):e0168444. doi: 10.1371/journal.pone.0168444. eCollection 2016.


Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community.

Friedman N, Shriker E, Gold B, Durman T, Zarecki R, Ruppin E, Mizrahi I.

Environ Microbiol. 2017 Jan;19(1):174-184. doi: 10.1111/1462-2920.13551. Epub 2016 Dec 12.


Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction.

Auslander N, Wagner A, Oberhardt M, Ruppin E.

PLoS Comput Biol. 2016 Sep 27;12(9):e1005125. doi: 10.1371/journal.pcbi.1005125. eCollection 2016 Sep.


Therapeutic relevance of the protein phosphatase 2A in cancer.

Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KK, Lee JS, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M, Templeton SD, Shukla H, El Zawily AM, Boyd F, Alli N, Mousseau DD, Geyer R, Bonham K, Anderson DH, Yan J, Yu-Lee LY, Weaver BA, Uppalapati M, Ruppin E, Sablina A, Freywald A, Vizeacoumar FJ.

Oncotarget. 2016 Sep 20;7(38):61544-61561. doi: 10.18632/oncotarget.11399.


The Role of Temporal Trends in Growing Networks.

Mokryn O, Wagner A, Blattner M, Ruppin E, Shavitt Y.

PLoS One. 2016 Aug 3;11(8):e0156505. doi: 10.1371/journal.pone.0156505. eCollection 2016.


A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.

Auslander N, Yizhak K, Weinstock A, Budhu A, Tang W, Wang XW, Ambs S, Ruppin E.

Sci Rep. 2016 Jul 13;6:29662. doi: 10.1038/srep29662.


Metabolic Network Prediction of Drug Side Effects.

Shaked I, Oberhardt MA, Atias N, Sharan R, Ruppin E.

Cell Syst. 2016 Mar 23;2(3):209-13. doi: 10.1016/j.cels.2016.03.001. Epub 2016 Mar 23.


System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.

Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pontén F, Ruppin E, Barshack I, Geiger T.

Cell Syst. 2016 Mar 23;2(3):172-84. doi: 10.1016/j.cels.2016.02.001. Epub 2016 Mar 3.


Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.

Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M.

Nat Commun. 2016 Feb 3;7:8994. doi: 10.1038/ncomms9994.


Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.

Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E.

PLoS Comput Biol. 2016 Jan 28;12(1):e1004705. doi: 10.1371/journal.pcbi.1004705. eCollection 2016 Jan.


Functional Alignment of Metabolic Networks.

Mazza A, Wagner A, Ruppin E, Sharan R.

J Comput Biol. 2016 May;23(5):390-9. doi: 10.1089/cmb.2015.0203. Epub 2016 Jan 13.


Glutamine synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restricted glioblastoma.

Tardito S, Oudin A, Ahmed SU, Fack F, Keunen O, Zheng L, Miletic H, Sakariassen PØ, Weinstock A, Wagner A, Lindsay SL, Hock AK, Barnett SC, Ruppin E, Mørkve SH, Lund-Johansen M, Chalmers AJ, Bjerkvig R, Niclou SP, Gottlieb E.

Nat Cell Biol. 2015 Dec;17(12):1556-68. doi: 10.1038/ncb3272. Epub 2015 Nov 23.


Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis.

Rabinovich S, Adler L, Yizhak K, Sarver A, Silberman A, Agron S, Stettner N, Sun Q, Brandis A, Helbling D, Korman S, Itzkovitz S, Dimmock D, Ulitsky I, Nagamani SC, Ruppin E, Erez A.

Nature. 2015 Nov 19;527(7578):379-383. doi: 10.1038/nature15529. Epub 2015 Nov 11.


Harnessing the landscape of microbial culture media to predict new organism-media pairings.

Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, Ruppin E.

Nat Commun. 2015 Oct 13;6:8493. doi: 10.1038/ncomms9493.


Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival.

Megchelenbrink W, Katzir R, Lu X, Ruppin E, Notebaart RA.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12217-22. doi: 10.1073/pnas.1508573112. Epub 2015 Sep 14.


The role of branched chain amino acid and tryptophan metabolism in rat's behavioral diversity: Intertwined peripheral and brain effects.

Asor E, Stempler S, Avital A, Klein E, Ruppin E, Ben-Shachar D.

Eur Neuropsychopharmacol. 2015 Oct;25(10):1695-705. doi: 10.1016/j.euroneuro.2015.07.009. Epub 2015 Jul 31.


Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia.

Wagner A, Cohen N, Kelder T, Amit U, Liebman E, Steinberg DM, Radonjic M, Ruppin E.

Mol Syst Biol. 2015 Mar;11(3):791.


Modeling cancer metabolism on a genome scale.

Yizhak K, Chaneton B, Gottlieb E, Ruppin E.

Mol Syst Biol. 2015 Jun 30;11(6):817. doi: 10.15252/msb.20145307. Review.


Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media.

Ish-Am O, Kristensen DM, Ruppin E.

PLoS One. 2015 Apr 20;10(4):e0123785. doi: 10.1371/journal.pone.0123785. eCollection 2015.


Moving ahead on harnessing synthetic lethality to fight cancer.

Jerby-Arnon L, Ruppin E.

Mol Cell Oncol. 2015 Feb 25;2(2):e977150. doi: 10.4161/23723556.2014.977150. eCollection 2015 Apr-Jun.


Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.

Seaver SM, Bradbury LM, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS.

Front Plant Sci. 2015 Mar 10;6:142. doi: 10.3389/fpls.2015.00142. eCollection 2015.


Fumarate induces redox-dependent senescence by modifying glutathione metabolism.

Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, Johnson TI, Gaude E, King A, Leach JD, Edrada-Ebel R, Hedley A, Morrice NA, Kalna G, Blyth K, Ruppin E, Frezza C, Gottlieb E.

Nat Commun. 2015 Jan 23;6:6001. doi: 10.1038/ncomms7001.


Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.

Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, Avanzato D, Maione F, Hernandez-Fernaud JR, Mackay G, Zheng L, Reid S, Frezza C, Giraudo E, Fiorio Pla A, Anderson K, Ruppin E, Gottlieb E, Zanivan S.

Mol Cell Proteomics. 2015 Mar;14(3):621-34. doi: 10.1074/mcp.M114.045575. Epub 2015 Jan 8.


The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.

Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M.

Genomics. 2015 Jan;105(1):5-16. doi: 10.1016/j.ygeno.2014.10.013. Epub 2014 Nov 13.


Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.

Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E.

Elife. 2014 Nov 21;3. doi: 10.7554/eLife.03641.


Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.

Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, Seashore-Ludlow B, Weinstock A, Geiger T, Clemons PA, Gottlieb E, Ruppin E.

Cell. 2014 Aug 28;158(5):1199-1209. doi: 10.1016/j.cell.2014.07.027.


Integrating transcriptomics with metabolic modeling predicts biomarkers and drug targets for Alzheimer's disease.

Stempler S, Yizhak K, Ruppin E.

PLoS One. 2014 Aug 15;9(8):e105383. doi: 10.1371/journal.pone.0105383. eCollection 2014.


Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations.

Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E.

MBio. 2014 Aug 12;5(4). pii: e01526-14. doi: 10.1128/mBio.01526-14.


A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.

Yizhak K, Le Dévédec SE, Rogkoti VM, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E.

Mol Syst Biol. 2014 Aug 1;10:744. doi: 10.15252/msb.20134993. Erratum in: Mol Syst Biol. 2014 Nov;10(11):765.


Network-level architecture and the evolutionary potential of underground metabolism.

Notebaart RA, Szappanos B, Kintses B, Pál F, Györkei Á, Bogos B, Lázár V, Spohn R, Csörgő B, Wagner A, Ruppin E, Pál C, Papp B.

Proc Natl Acad Sci U S A. 2014 Aug 12;111(32):11762-7. doi: 10.1073/pnas.1406102111. Epub 2014 Jul 28.


A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.

Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003726. doi: 10.1371/journal.pcbi.1003726. eCollection 2014 Jul.


Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms.

Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Shtifman Segal E, Freilich S, Henry CS, Gophna U, Ruppin E.

PLoS One. 2014 May 27;9(5):e98372. doi: 10.1371/journal.pone.0098372. eCollection 2014.


p53 promotes the expression of gluconeogenesis-related genes and enhances hepatic glucose production.

Goldstein I, Yizhak K, Madar S, Goldfinger N, Ruppin E, Rotter V.

Cancer Metab. 2013 Feb 4;1(1):9. doi: 10.1186/2049-3002-1-9.


Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious.

Wagner A, Zarecki R, Reshef L, Gochev C, Sorek R, Gophna U, Ruppin E.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19166-71. doi: 10.1073/pnas.1312361110. Epub 2013 Nov 6.


Model-based identification of drug targets that revert disrupted metabolism and its application to ageing.

Yizhak K, Gabay O, Cohen H, Ruppin E.

Nat Commun. 2013;4:2632. doi: 10.1038/ncomms3632.


A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells.

Waldman YY, Geiger T, Ruppin E.

PLoS Genet. 2013;9(9):e1003806. doi: 10.1371/journal.pgen.1003806. Epub 2013 Sep 19.


Environmental stresses disrupt telomere length homeostasis.

Romano GH, Harari Y, Yehuda T, Podhorzer A, Rubinstein L, Shamir R, Gottlieb A, Silberberg Y, Pe'er D, Ruppin E, Sharan R, Kupiec M.

PLoS Genet. 2013;9(9):e1003721. doi: 10.1371/journal.pgen.1003721. Epub 2013 Sep 5.


Taming the complexity of large models.

Oberhardt M, Ruppin E.

EMBO Rep. 2013 Oct;14(10):848. doi: 10.1038/embor.2013.145. Epub 2013 Sep 6. No abstract available.


A method for inferring medical diagnoses from patient similarities.

Gottlieb A, Stein GY, Ruppin E, Altman RB, Sharan R.

BMC Med. 2013 Sep 2;11:194. doi: 10.1186/1741-7015-11-194.

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