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Items: 1 to 50 of 230

1.

Reply to: 'IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma'.

Auslander N, Lee JS, Ruppin E.

Nat Med. 2019 Dec;25(12):1836-1838. doi: 10.1038/s41591-019-0646-5. Epub 2019 Dec 5. No abstract available.

PMID:
31806908
2.

The landscape of tiered regulation of breast cancer cell metabolism.

Katzir R, Polat IH, Harel M, Katz S, Foguet C, Selivanov VA, Sabatier P, Cascante M, Geiger T, Ruppin E.

Sci Rep. 2019 Nov 28;9(1):17760. doi: 10.1038/s41598-019-54221-y.

3.

Translational reprogramming marks adaptation to asparagine restriction in cancer.

Pathria G, Lee JS, Hasnis E, Tandoc K, Scott DA, Verma S, Feng Y, Larue L, Sahu AD, Topisirovic I, Ruppin E, Ronai ZA.

Nat Cell Biol. 2019 Dec;21(12):1590-1603. doi: 10.1038/s41556-019-0415-1. Epub 2019 Nov 18.

PMID:
31740775
4.

Functional Genomic Complexity Defines Intratumor Heterogeneity and Tumor Aggressiveness in Liver Cancer.

Kwon SM, Budhu A, Woo HG, Chaisaingmongkol J, Dang H, Forgues M, Harris CC, Zhang G, Auslander N, Ruppin E, Mahidol C, Ruchirawat M, Wang XW.

Sci Rep. 2019 Nov 15;9(1):16930. doi: 10.1038/s41598-019-52578-8.

5.

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma.

Wolf Y, Bartok O, Patkar S, Eli GB, Cohen S, Litchfield K, Levy R, Jiménez-Sánchez A, Trabish S, Lee JS, Karathia H, Barnea E, Day CP, Cinnamon E, Stein I, Solomon A, Bitton L, Pérez-Guijarro E, Dubovik T, Shen-Orr SS, Miller ML, Merlino G, Levin Y, Pikarsky E, Eisenbach L, Admon A, Swanton C, Ruppin E, Samuels Y.

Cell. 2019 Sep 19;179(1):219-235.e21. doi: 10.1016/j.cell.2019.08.032. Epub 2019 Sep 12.

6.

Multiomics Prediction of Response Rates to Therapies to Inhibit Programmed Cell Death 1 and Programmed Cell Death 1 Ligand 1.

Lee JS, Ruppin E.

JAMA Oncol. 2019 Aug 22. doi: 10.1001/jamaoncol.2019.2311. [Epub ahead of print]

PMID:
31436822
7.

Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival.

Nair NU, Das A, Rogkoti VM, Fokkelman M, Marcotte R, de Jong CG, Koedoot E, Lee JS, Meilijson I, Hannenhalli S, Neel BG, de Water BV, Le Dévédec SE, Ruppin E.

Sci Rep. 2019 Jul 29;9(1):10989. doi: 10.1038/s41598-019-47440-w.

8.

Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer.

Magen A, Das Sahu A, Lee JS, Sharmin M, Lugo A, Gutkind JS, Schäffer AA, Ruppin E, Hannenhalli S.

Cell Rep. 2019 Jul 23;28(4):938-948.e6. doi: 10.1016/j.celrep.2019.06.067.

9.

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

Irizar PA, 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. 2019 May 31;10(1):2459. doi: 10.1038/s41467-019-10559-5.

10.

Mitochondrial Regulation of the Hippocampal Firing Rate Set Point and Seizure Susceptibility.

Styr B, Gonen N, Zarhin D, Ruggiero A, Atsmon R, Gazit N, Braun G, Frere S, Vertkin I, Shapira I, Harel M, Heim LR, Katsenelson M, Rechnitz O, Fadila S, Derdikman D, Rubinstein M, Geiger T, Ruppin E, Slutsky I.

Neuron. 2019 Jun 5;102(5):1009-1024.e8. doi: 10.1016/j.neuron.2019.03.045. Epub 2019 Apr 29.

11.

Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5-/- mice.

Li Y, Tinoco R, Elmén L, Segota I, Xian Y, Fujita Y, Sahu A, Zarecki R, Marie K, Feng Y, Khateb A, Frederick DT, Ashkenazi SK, Kim H, Perez EG, Day CP, Segura Muñoz RS, Schmaltz R, Yooseph S, Tam MA, Zhang T, Avitan-Hersh E, Tzur L, Roizman S, Boyango I, Bar-Sela G, Orian A, Kaufman RJ, Bosenberg M, Goding CR, Baaten B, Levesque MP, Dummer R, Brown K, Merlino G, Ruppin E, Flaherty K, Ramer-Tait A, Long T, Peterson SN, Bradley LM, Ronai ZA.

Nat Commun. 2019 Apr 2;10(1):1492. doi: 10.1038/s41467-019-09525-y.

12.

Correction: CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma.

Alon M, Arafeh R, Lee JS, Madan S, Kalaora S, Nagler A, Abgarian T, Greenberg P, Ruppin E, Samuels Y.

Oncotarget. 2019 Feb 12;10(13):1344. doi: 10.18632/oncotarget.26685. eCollection 2019 Feb 12.

13.

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy.

Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E.

Mol Syst Biol. 2019 Mar 11;15(3):e8323. doi: 10.15252/msb.20188323.

14.

A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK.

Feng X, Arang N, Rigiracciolo DC, Lee JS, Yeerna H, Wang Z, Lubrano S, Kishore A, Pachter JA, König GM, Maggiolini M, Kostenis E, Schlaepfer DD, Tamayo P, Chen Q, Ruppin E, Gutkind JS.

Cancer Cell. 2019 Mar 18;35(3):457-472.e5. doi: 10.1016/j.ccell.2019.01.009. Epub 2019 Feb 14.

PMID:
30773340
15.

Acid-Induced Downregulation of ASS1 Contributes to the Maintenance of Intracellular pH in Cancer.

Silberman A, Goldman O, Boukobza Assayag O, Jacob A, Rabinovich S, Adler L, Lee JS, Keshet R, Sarver A, Frug J, Stettner N, Galai S, Persi E, Halpern KB, Zaltsman-Amir Y, Pode-Shakked B, Eilam R, Anikster Y, Nagamani SCS, Ulitsky I, Ruppin E, Erez A.

Cancer Res. 2019 Feb 1;79(3):518-533. doi: 10.1158/0008-5472.CAN-18-1062. Epub 2018 Dec 20.

16.

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival.

Tang W, Zhou M, Dorsey TH, Prieto DA, Wang XW, Ruppin E, Veenstra TD, Ambs S.

Genome Med. 2018 Dec 3;10(1):94. doi: 10.1186/s13073-018-0602-x.

17.

Criticality in tumor evolution and clinical outcome.

Persi E, Wolf YI, Leiserson MDM, Koonin EV, Ruppin E.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11101-E11110. doi: 10.1073/pnas.1807256115. Epub 2018 Nov 7.

18.

Publisher Correction: Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma.

Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T, Tian T, Wei Z, Madan S, Sullivan RJ, Boland G, Flaherty K, Herlyn M, Ruppin E.

Nat Med. 2018 Dec;24(12):1942. doi: 10.1038/s41591-018-0247-8.

PMID:
30333558
19.

Targeting the Warburg effect via LDHA inhibition engages ATF4 signaling for cancer cell survival.

Pathria G, Scott DA, Feng Y, Sang Lee J, Fujita Y, Zhang G, Sahu AD, Ruppin E, Herlyn M, Osterman AL, Ronai ZA.

EMBO J. 2018 Oct 15;37(20). pii: e99735. doi: 10.15252/embj.201899735. Epub 2018 Sep 12.

20.

Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma.

Kalaora S, Wolf Y, Feferman T, Barnea E, Greenstein E, Reshef D, Tirosh I, Reuben A, Patkar S, Levy R, Quinkhardt J, Omokoko T, Qutob N, Golani O, Zhang J, Mao X, Song X, Bernatchez C, Haymaker C, Forget MA, Creasy C, Greenberg P, Carter BW, Cooper ZA, Rosenberg SA, Lotem M, Sahin U, Shakhar G, Ruppin E, Wargo JA, Friedman N, Admon A, Samuels Y.

Cancer Discov. 2018 Nov;8(11):1366-1375. doi: 10.1158/2159-8290.CD-17-1418. Epub 2018 Sep 12.

21.

CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma.

Alon M, Arafeh R, Lee JS, Madan S, Kalaora S, Nagler A, Abgarian T, Greenberg P, Ruppin E, Samuels Y.

Oncotarget. 2018 Jul 27;9(58):31264-31277. doi: 10.18632/oncotarget.25805. eCollection 2018 Jul 27. Erratum in: Oncotarget. 2019 Feb 12;10(13):1344.

22.

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma.

Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T, Tian T, Wei Z, Madan S, Sullivan RJ, Boland G, Flaherty K, Herlyn M, Ruppin E.

Nat Med. 2018 Oct;24(10):1545-1549. doi: 10.1038/s41591-018-0157-9. Epub 2018 Aug 20. Erratum in: Nat Med. 2018 Dec;24(12):1942.

23.

Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures.

Lee JS, Adler L, Karathia H, Carmel N, Rabinovich S, Auslander N, Keshet R, Stettner N, Silberman A, Agemy L, Helbling D, Eilam R, Sun Q, Brandis A, Malitsky S, Itkin M, Weiss H, Pinto S, Kalaora S, Levy R, Barnea E, Admon A, Dimmock D, Stern-Ginossar N, Scherz A, Nagamani SCS, Unda M, Wilson DM 3rd, Elhasid R, Carracedo A, Samuels Y, Hannenhalli S, Ruppin E, Erez A.

Cell. 2018 Sep 6;174(6):1559-1570.e22. doi: 10.1016/j.cell.2018.07.019. Epub 2018 Aug 9.

24.

Systems analysis of intracellular pH vulnerabilities for cancer therapy.

Persi E, Duran-Frigola M, Damaghi M, Roush WR, Aloy P, Cleveland JL, Gillies RJ, Ruppin E.

Nat Commun. 2018 Jul 31;9(1):2997. doi: 10.1038/s41467-018-05261-x.

25.

Harnessing synthetic lethality to predict the response to cancer treatment.

Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, McGarry L, James D, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E.

Nat Commun. 2018 Jun 29;9(1):2546. doi: 10.1038/s41467-018-04647-1.

26.

Reverting the molecular fingerprint of tumor dormancy as a therapeutic strategy for glioblastoma.

Tiram G, Ferber S, Ofek P, Eldar-Boock A, Ben-Shushan D, Yeini E, Krivitsky A, Blatt R, Almog N, Henkin J, Amsalem O, Yavin E, Cohen G, Lazarovici P, Lee JS, Ruppin E, Milyavsky M, Grossman R, Ram Z, Calderón M, Haag R, Satchi-Fainaro R.

FASEB J. 2018 Jun 1:fj201701568R. doi: 10.1096/fj.201701568R. [Epub ahead of print]

PMID:
29856660
27.

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. Erratum in: Nat Commun. 2019 May 31;10(1):2459.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

PMID:
28552182
36.

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.

37.

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.

38.

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.

39.

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.

PMID:
27696646
40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

PMID:
26759932
49.

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.

50.

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.

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