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Items: 1 to 50 of 53

1.

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.

Zviran A, Mor N, Rais Y, Gingold H, Peles S, Chomsky E, Viukov S, Buenrostro JD, Scognamiglio R, Weinberger L, Manor YS, Krupalnik V, Zerbib M, Hezroni H, Jaitin DA, Larastiaso D, Gilad S, Benjamin S, Gafni O, Mousa A, Ayyash M, Sheban D, Bayerl J, Aguilera-Castrejon A, Massarwa R, Maza I, Hanna S, Stelzer Y, Ulitsky I, Greenleaf WJ, Tanay A, Trumpp A, Amit I, Pilpel Y, Novershtern N, Hanna JH.

Cell Stem Cell. 2018 Dec 10. pii: S1934-5909(18)30550-2. doi: 10.1016/j.stem.2018.11.014. [Epub ahead of print]

PMID:
30554962
2.

Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity.

Gil N, Ulitsky I.

Cell Syst. 2018 Nov 28;7(5):537-547.e3. doi: 10.1016/j.cels.2018.10.009. Epub 2018 Nov 14.

PMID:
30447999
3.

Regulation of Neuroregeneration by Long Noncoding RNAs.

Perry RB, Hezroni H, Goldrich MJ, Ulitsky I.

Mol Cell. 2018 Nov 1;72(3):553-567.e5. doi: 10.1016/j.molcel.2018.09.021. Epub 2018 Oct 25.

PMID:
30401432
4.

Predicting microRNA targeting efficacy in Drosophila.

Agarwal V, Subtelny AO, Thiru P, Ulitsky I, Bartel DP.

Genome Biol. 2018 Oct 4;19(1):152. doi: 10.1186/s13059-018-1504-3.

5.

Altered p53 functionality in cancer-associated fibroblasts contributes to their cancer-supporting features.

Arandkar S, Furth N, Elisha Y, Nataraj NB, van der Kuip H, Yarden Y, Aulitzky W, Ulitsky I, Geiger B, Oren M.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6410-6415. doi: 10.1073/pnas.1719076115. Epub 2018 Jun 4.

6.

Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies.

Haimon Z, Volaski A, Orthgiess J, Boura-Halfon S, Varol D, Shemer A, Yona S, Zuckerman B, David E, Chappell-Maor L, Bechmann I, Gericke M, Ulitsky I, Jung S.

Nat Immunol. 2018 Jun;19(6):636-644. doi: 10.1038/s41590-018-0110-6. Epub 2018 May 18.

7.

Interactions between short and long noncoding RNAs.

Ulitsky I.

FEBS Lett. 2018 Sep;592(17):2874-2883. doi: 10.1002/1873-3468.13085. Epub 2018 May 23. Review.

PMID:
29749606
8.

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells.

Lubelsky Y, Ulitsky I.

Nature. 2018 Mar 1;555(7694):107-111. doi: 10.1038/nature25757. Epub 2018 Jan 24.

9.

SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA.

Tichon A, Perry RB, Stojic L, Ulitsky I.

Genes Dev. 2018 Jan 1;32(1):70-78. doi: 10.1101/gad.309138.117. Epub 2018 Jan 31.

10.

The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element.

Marín-Béjar O, Mas AM, González J, Martinez D, Athie A, Morales X, Galduroz M, Raimondi I, Grossi E, Guo S, Rouzaut A, Ulitsky I, Huarte M.

Genome Biol. 2017 Oct 27;18(1):202. doi: 10.1186/s13059-017-1331-y.

11.

Analysis of blood-based gene expression in idiopathic Parkinson disease.

Shamir R, Klein C, Amar D, Vollstedt EJ, Bonin M, Usenovic M, Wong YC, Maver A, Poths S, Safer H, Corvol JC, Lesage S, Lavi O, Deuschl G, Kuhlenbaeumer G, Pawlack H, Ulitsky I, Kasten M, Riess O, Brice A, Peterlin B, Krainc D.

Neurology. 2017 Oct 17;89(16):1676-1683. doi: 10.1212/WNL.0000000000004516. Epub 2017 Sep 15.

12.

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

Hezroni H, Ben-Tov Perry R, Meir Z, Housman G, Lubelsky Y, Ulitsky I.

Genome Biol. 2017 Aug 30;18(1):162. doi: 10.1186/s13059-017-1293-0.

13.

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB.

Sci Rep. 2017 Aug 17;7(1):8637. doi: 10.1038/s41598-017-08320-3.

14.

Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation.

Haimov O, Sinvani H, Martin F, Ulitsky I, Emmanuel R, Tamarkin-Ben-Harush A, Vardy A, Dikstein R.

Mol Cell Biol. 2017 Jul 14;37(15). pii: e00150-17. doi: 10.1128/MCB.00150-17. Print 2017 Aug 1.

15.

Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress.

Tamarkin-Ben-Harush A, Vasseur JJ, Debart F, Ulitsky I, Dikstein R.

Elife. 2017 Feb 8;6. pii: e21907. doi: 10.7554/eLife.21907.

16.

The functions of long noncoding RNAs in development and stem cells.

Perry RB, Ulitsky I.

Development. 2016 Nov 1;143(21):3882-3894. Review.

17.

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.

Ulitsky I.

Nat Rev Genet. 2016 Oct;17(10):601-14. doi: 10.1038/nrg.2016.85. Epub 2016 Aug 30. Review.

PMID:
27573374
18.

LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer.

Sas-Chen A, Aure MR, Leibovich L, Carvalho S, Enuka Y, Körner C, Polycarpou-Schwarz M, Lavi S, Nevo N, Kuznetsov Y, Yuan J, Azuaje F; Oslo Breast Cancer Research Consortium (OSBREAC)SauerTorillGeislerJürgenHofvindSolveigBathenTone FBorgenElinEngebråtenOlavFodstadØysteinGarredØysteinGeitvikGry AarumKåresenRolfNaumeBjørnMælandsmoGunhild MariRussnesHege GSchlichtingEllenSørlieThereseLingjærdeOle ChristianSahlbergKristine KleiviSkjervenHelle KristineFritzmanBritt, Ulitsky I, Diederichs S, Wiemann S, Yakhini Z, Kristensen VN, Børresen-Dale AL, Yarden Y.

EMBO Mol Med. 2016 Sep 1;8(9):1052-64. doi: 10.15252/emmm.201606198. Print 2016 Sep.

19.

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells.

Tichon A, Gil N, Lubelsky Y, Havkin Solomon T, Lemze D, Itzkovitz S, Stern-Ginossar N, Ulitsky I.

Nat Commun. 2016 Jul 13;7:12209. doi: 10.1038/ncomms12209.

20.

Nuclear Retention of mRNA in Mammalian Tissues.

Bahar Halpern K, Caspi I, Lemze D, Levy M, Landen S, Elinav E, Ulitsky I, Itzkovitz S.

Cell Rep. 2015 Dec 29;13(12):2653-62. doi: 10.1016/j.celrep.2015.11.036. Epub 2015 Dec 17.

21.

Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor.

Enuka Y, Lauriola M, Feldman ME, Sas-Chen A, Ulitsky I, Yarden Y.

Nucleic Acids Res. 2016 Feb 18;44(3):1370-83. doi: 10.1093/nar/gkv1367. Epub 2015 Dec 10.

22.

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.

23.

Recurrent inactivating RASA2 mutations in melanoma.

Arafeh R, Qutob N, Emmanuel R, Keren-Paz A, Madore J, Elkahloun A, Wilmott JS, Gartner JJ, Di Pizio A, Winograd-Katz S, Sindiri S, Rotkopf R, Dutton-Regester K, Johansson P, Pritchard AL, Waddell N, Hill VK, Lin JC, Hevroni Y, Rosenberg SA, Khan J, Ben-Dor S, Niv MY, Ulitsky I, Mann GJ, Scolyer RA, Hayward NK, Samuels Y.

Nat Genet. 2015 Dec;47(12):1408-10. doi: 10.1038/ng.3427. Epub 2015 Oct 26.

24.

Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.

25.

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs.

Housman G, Ulitsky I.

Biochim Biophys Acta. 2016 Jan;1859(1):31-40. doi: 10.1016/j.bbagrm.2015.07.017. Epub 2015 Aug 8. Review.

PMID:
26265145
26.

Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I.

Cell Rep. 2015 May 19;11(7):1110-22. doi: 10.1016/j.celrep.2015.04.023. Epub 2015 May 7.

27.

lincRNAs: genomics, evolution, and mechanisms.

Ulitsky I, Bartel DP.

Cell. 2013 Jul 3;154(1):26-46. doi: 10.1016/j.cell.2013.06.020. Review.

28.

Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing.

Auyeung VC, Ulitsky I, McGeary SE, Bartel DP.

Cell. 2013 Feb 14;152(4):844-58. doi: 10.1016/j.cell.2013.01.031.

29.

Extensive alternative polyadenylation during zebrafish development.

Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP.

Genome Res. 2012 Oct;22(10):2054-66. doi: 10.1101/gr.139733.112. Epub 2012 Jun 21.

30.

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.

Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP.

Cell. 2011 Dec 23;147(7):1537-50. doi: 10.1016/j.cell.2011.11.055. Erratum in: Cell. 2012 Oct 26;151(3):684-6.

31.

A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression.

Marom L, Ulitsky I, Cabilly Y, Shamir R, Elroy-Stein O.

PLoS One. 2011;6(10):e26992. doi: 10.1371/journal.pone.0026992. Epub 2011 Oct 31.

32.

Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear.

Elkan-Miller T, Ulitsky I, Hertzano R, Rudnicki A, Dror AA, Lenz DR, Elkon R, Irmler M, Beckers J, Shamir R, Avraham KB.

PLoS One. 2011 Apr 5;6(4):e18195. doi: 10.1371/journal.pone.0018195.

33.

Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture.

Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ, Ku S, Martynova M, Semechkin R, Galat V, Gottesfeld J, Izpisua Belmonte JC, Murry C, Keirstead HS, Park HS, Schmidt U, Laslett AL, Muller FJ, Nievergelt CM, Shamir R, Loring JF.

Cell Stem Cell. 2011 Jan 7;8(1):106-18. doi: 10.1016/j.stem.2010.12.003.

34.

SPIKE: a database of highly curated human signaling pathways.

Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.

Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167. Epub 2010 Nov 19.

35.

DEGAS: de novo discovery of dysregulated pathways in human diseases.

Ulitsky I, Krishnamurthy A, Karp RM, Shamir R.

PLoS One. 2010 Oct 19;5(10):e13367. doi: 10.1371/journal.pone.0013367.

36.

Towards computational prediction of microRNA function and activity.

Ulitsky I, Laurent LC, Shamir R.

Nucleic Acids Res. 2010 Aug;38(15):e160. doi: 10.1093/nar/gkq570. Epub 2010 Jun 24.

37.

A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.

Aguilar PS, Fröhlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A, Braberg H, Shamir R, Walter P, Mann M, Ejsing CS, Krogan NJ, Walther TC.

Nat Struct Mol Biol. 2010 Jul;17(7):901-8. doi: 10.1038/nsmb.1829. Epub 2010 Jun 6.

38.

Different sets of QTLs influence fitness variation in yeast.

Romano GH, Gurvich Y, Lavi O, Ulitsky I, Shamir R, Kupiec M.

Mol Syst Biol. 2010;6:346. doi: 10.1038/msb.2010.1. Epub 2010 Feb 16.

39.

Expander: from expression microarrays to networks and functions.

Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.

Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230. Epub 2010 Jan 28.

PMID:
20134430
40.

Propagation of human embryonic and induced pluripotent stem cells in an indirect co-culture system.

Abraham S, Sheridan SD, Laurent LC, Albert K, Stubban C, Ulitsky I, Miller B, Loring JF, Rao RR.

Biochem Biophys Res Commun. 2010 Mar 5;393(2):211-6. doi: 10.1016/j.bbrc.2010.01.101. Epub 2010 Feb 1.

41.

Towards accurate imputation of quantitative genetic interactions.

Ulitsky I, Krogan NJ, Shamir R.

Genome Biol. 2009;10(12):R140. doi: 10.1186/gb-2009-10-12-r140. Epub 2009 Dec 10.

42.

Identifying functional modules using expression profiles and confidence-scored protein interactions.

Ulitsky I, Shamir R.

Bioinformatics. 2009 May 1;25(9):1158-64. doi: 10.1093/bioinformatics/btp118. Epub 2009 Mar 17.

PMID:
19297352
43.

Allegro: analyzing expression and sequence in concert to discover regulatory programs.

Halperin Y, Linhart C, Ulitsky I, Shamir R.

Nucleic Acids Res. 2009 Apr;37(5):1566-79. doi: 10.1093/nar/gkn1064. Epub 2009 Jan 16.

44.

Regulatory networks define phenotypic classes of human stem cell lines.

Müller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF.

Nature. 2008 Sep 18;455(7211):401-5. doi: 10.1038/nature07213. Epub 2008 Aug 24.

45.

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.

46.

Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence.

Laurent LC, Chen J, Ulitsky I, Mueller FJ, Lu C, Shamir R, Fan JB, Loring JF.

Stem Cells. 2008 Jun;26(6):1506-16. doi: 10.1634/stemcells.2007-1081. Epub 2008 Apr 10.

47.

SPIKE--a database, visualization and analysis tool of cellular signaling pathways.

Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R.

BMC Bioinformatics. 2008 Feb 20;9:110. doi: 10.1186/1471-2105-9-110.

48.

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data.

Ulitsky I, Gat-Viks I, Shamir R.

Genome Biol. 2008 Jan 2;9(1):R1. doi: 10.1186/gb-2008-9-1-r1.

49.

Detecting pathways transcriptionally correlated with clinical parameters.

Ulitsky I, Shamir R.

Comput Syst Bioinformatics Conf. 2008;7:249-58.

50.

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