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Items: 1 to 50 of 96

1.

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors.

Laudadio I, Formichetti S, Gioiosa S, Klironomos F, Rajewsky N, Macino G, Carissimi C, Fulci V.

Int J Genomics. 2018 Apr 26;2018:1243858. doi: 10.1155/2018/1243858. eCollection 2018.

2.

A Single-Cell Transcriptome Atlas of the Mouse Glomerulus.

Karaiskos N, Rahmatollahi M, Boltengagen A, Liu H, Hoehne M, Rinschen M, Schermer B, Benzing T, Rajewsky N, Kocks C, Kann M, Müller RU.

J Am Soc Nephrol. 2018 May 24. pii: ASN.2018030238. doi: 10.1681/ASN.2018030238. [Epub ahead of print]

PMID:
29794128
3.

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.

Plass M, Solana J, Wolf FA, Ayoub S, Misios A, Glažar P, Obermayer B, Theis FJ, Kocks C, Rajewsky N.

Science. 2018 May 25;360(6391). pii: eaaq1723. doi: 10.1126/science.aaq1723. Epub 2018 Apr 19.

PMID:
29674432
4.

Post-transcriptional Regulation by 3' UTRs Can Be Masked by Regulatory Elements in 5' UTRs.

Theil K, Herzog M, Rajewsky N.

Cell Rep. 2018 Mar 20;22(12):3217-3226. doi: 10.1016/j.celrep.2018.02.094.

5.

Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as.

Kocks C, Boltengagen A, Piwecka M, Rybak-Wolf A, Rajewsky N.

Methods Mol Biol. 2018;1724:77-96. doi: 10.1007/978-1-4939-7562-4_7.

PMID:
29322442
6.

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex.

Verduci L, Ferraiuolo M, Sacconi A, Ganci F, Vitale J, Colombo T, Paci P, Strano S, Macino G, Rajewsky N, Blandino G.

Genome Biol. 2017 Dec 20;18(1):237. doi: 10.1186/s13059-017-1368-y.

7.

Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo.

Maschmeyer P, Petkau G, Siracusa F, Zimmermann J, Zügel F, Kühl AA, Lehmann K, Schimmelpfennig S, Weber M, Haftmann C, Riedel R, Bardua M, Heinz GA, Tran CL, Hoyer BF, Hiepe F, Herzog S, Wittmann J, Rajewsky N, Melchers FG, Chang HD, Radbruch A, Mashreghi MF.

J Autoimmun. 2018 May;89:41-52. doi: 10.1016/j.jaut.2017.11.005. Epub 2017 Dec 1.

8.

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.

Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M.

Genome Biol. 2017 Oct 31;18(1):209. doi: 10.1186/s13059-017-1329-5.

9.

RNA localization is a key determinant of neurite-enriched proteome.

Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M.

Nat Commun. 2017 Sep 19;8(1):583. doi: 10.1038/s41467-017-00690-6.

10.

The Drosophila embryo at single-cell transcriptome resolution.

Karaiskos N, Wahle P, Alles J, Boltengagen A, Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP.

Science. 2017 Oct 13;358(6360):194-199. doi: 10.1126/science.aan3235. Epub 2017 Aug 31.

PMID:
28860209
11.

A map of human circular RNAs in clinically relevant tissues.

Maass PG, Glažar P, Memczak S, Dittmar G, Hollfinger I, Schreyer L, Sauer AV, Toka O, Aiuti A, Luft FC, Rajewsky N.

J Mol Med (Berl). 2017 Nov;95(11):1179-1189. doi: 10.1007/s00109-017-1582-9. Epub 2017 Aug 25.

12.

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.

Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N.

Science. 2017 Sep 22;357(6357). pii: eaam8526. doi: 10.1126/science.aam8526. Epub 2017 Aug 10.

PMID:
28798046
13.

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF.

J Biotechnol. 2017 Nov 10;261:76-84. doi: 10.1016/j.jbiotec.2017.05.019. Epub 2017 May 26. Review.

14.

Cell fixation and preservation for droplet-based single-cell transcriptomics.

Alles J, Karaiskos N, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N.

BMC Biol. 2017 May 19;15(1):44. doi: 10.1186/s12915-017-0383-5.

15.

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis.

Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, Santini T, Andronache A, Wade M, Laneve P, Rajewsky N, Bozzoni I.

Mol Cell. 2017 Apr 6;66(1):22-37.e9. doi: 10.1016/j.molcel.2017.02.017. Epub 2017 Mar 23.

16.

Translation of CircRNAs.

Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S.

Mol Cell. 2017 Apr 6;66(1):9-21.e7. doi: 10.1016/j.molcel.2017.02.021. Epub 2017 Mar 23.

17.

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.

Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120.

18.

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.

Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad AD, Ardakani FB, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter AS, Sieverling L; DEEP Consortium, Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz MH, Schultze JL, Radbruch A, Walter J, Hamann A, Polansky JK.

Immunity. 2016 Nov 15;45(5):1148-1161. doi: 10.1016/j.immuni.2016.10.022.

19.

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.

Elife. 2016 Aug 9;5. pii: e16797. doi: 10.7554/eLife.16797.

20.

Epigenetic dynamics of monocyte-to-macrophage differentiation.

Wallner S, Schröder C, Leitão E, Berulava T, Haak C, Beißer D, Rahmann S, Richter AS, Manke T, Bönisch U, Arrigoni L, Fröhler S, Klironomos F, Chen W, Rajewsky N, Müller F, Ebert P, Lengauer T, Barann M, Rosenstiel P, Gasparoni G, Nordström K, Walter J, Brors B, Zipprich G, Felder B, Klein-Hitpass L, Attenberger C, Schmitz G, Horsthemke B.

Epigenetics Chromatin. 2016 Jul 29;9:33. doi: 10.1186/s13072-016-0079-z. eCollection 2016.

21.

The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway.

Hasler D, Lehmann G, Murakawa Y, Klironomos F, Jakob L, Grässer FA, Rajewsky N, Landthaler M, Meister G.

Mol Cell. 2016 Jul 7;63(1):110-24. doi: 10.1016/j.molcel.2016.05.026. Epub 2016 Jun 23.

22.

MiR-150 Controls B Cell Differentiation by Targeting the Transcription Factor c-Myb.

Xiao C, Calado DP, Galler G, Thai TH, Patterson HC, Wang J, Rajewsky N, Bender TP, Rajewsky K.

Cell. 2016 May 5;165(4):1027. doi: 10.1016/j.cell.2016.04.056. No abstract available.

23.

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood.

Memczak S, Papavasileiou P, Peters O, Rajewsky N.

PLoS One. 2015 Oct 20;10(10):e0141214. doi: 10.1371/journal.pone.0141214. eCollection 2015.

24.

Extensive identification and analysis of conserved small ORFs in animals.

Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B.

Genome Biol. 2015 Sep 14;16:179. doi: 10.1186/s13059-015-0742-x.

25.

Translational regulation shapes the molecular landscape of complex disease phenotypes.

Schafer S, Adami E, Heinig M, Rodrigues KE, Kreuchwig F, Silhavy J, van Heesch S, Simaite D, Rajewsky N, Cuppen E, Pravenec M, Vingron M, Cook SA, Hubner N.

Nat Commun. 2015 May 26;6:7200. doi: 10.1038/ncomms8200.

26.

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed.

Rybak-Wolf A, Stottmeister C, Glažar P, Jens M, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, Herzog M, Schreyer L, Papavasileiou P, Ivanov A, Öhman M, Refojo D, Kadener S, Rajewsky N.

Mol Cell. 2015 Jun 4;58(5):870-85. doi: 10.1016/j.molcel.2015.03.027. Epub 2015 Apr 23.

27.

Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function.

Jia S, Ivanov A, Blasevic D, Müller T, Purfürst B, Sun W, Chen W, Poy MN, Rajewsky N, Birchmeier C.

EMBO J. 2015 May 12;34(10):1417-33. doi: 10.15252/embj.201490819. Epub 2015 Mar 31.

28.

microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes.

Blevins R, Bruno L, Carroll T, Elliott J, Marcais A, Loh C, Hertweck A, Krek A, Rajewsky N, Chen CZ, Fisher AG, Merkenschlager M.

PLoS Genet. 2015 Feb 25;11(2):e1005020. doi: 10.1371/journal.pgen.1005020. eCollection 2015.

29.

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals.

Ivanov A, Memczak S, Wyler E, Torti F, Porath HT, Orejuela MR, Piechotta M, Levanon EY, Landthaler M, Dieterich C, Rajewsky N.

Cell Rep. 2015 Jan 13;10(2):170-7. doi: 10.1016/j.celrep.2014.12.019. Epub 2014 Dec 31.

30.

Competition between target sites of regulators shapes post-transcriptional gene regulation.

Jens M, Rajewsky N.

Nat Rev Genet. 2015 Feb;16(2):113-26. doi: 10.1038/nrg3853. Epub 2014 Dec 9. Review.

PMID:
25488579
31.

miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim.

Haftmann C, Stittrich AB, Zimmermann J, Fang Z, Hradilkova K, Bardua M, Westendorf K, Heinz GA, Riedel R, Siede J, Lehmann K, Weinberger EE, Zimmel D, Lauer U, Häupl T, Sieper J, Backhaus M, Neumann C, Hoffmann U, Porstner M, Chen W, Grün JR, Baumgrass R, Matz M, Löhning M, Scheffold A, Wittmann J, Chang HD, Rajewsky N, Jäck HM, Radbruch A, Mashreghi MF.

Eur J Immunol. 2015 Apr;45(4):1192-205. doi: 10.1002/eji.201444633. Epub 2015 Jan 22.

32.

Paternal diet defines offspring chromatin state and intergenerational obesity.

Öst A, Lempradl A, Casas E, Weigert M, Tiko T, Deniz M, Pantano L, Boenisch U, Itskov PM, Stoeckius M, Ruf M, Rajewsky N, Reuter G, Iovino N, Ribeiro C, Alenius M, Heyne S, Vavouri T, Pospisilik JA.

Cell. 2014 Dec 4;159(6):1352-64. doi: 10.1016/j.cell.2014.11.005.

33.

Modules, networks and systems medicine for understanding disease and aiding diagnosis.

Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M.

Genome Med. 2014 Oct 17;6(10):82. doi: 10.1186/s13073-014-0082-6. eCollection 2014.

34.

A variety of dicer substrates in human and C. elegans.

Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N.

Cell. 2014 Nov 20;159(5):1153-1167. doi: 10.1016/j.cell.2014.10.040.

35.

DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D160-7. doi: 10.1093/nar/gku1180. Epub 2014 Nov 21.

36.

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.

Maaskola J, Rajewsky N.

Nucleic Acids Res. 2014 Dec 1;42(21):12995-3011. doi: 10.1093/nar/gku1083. Epub 2014 Nov 11.

37.

circRNA biogenesis competes with pre-mRNA splicing.

Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S.

Mol Cell. 2014 Oct 2;56(1):55-66. doi: 10.1016/j.molcel.2014.08.019. Epub 2014 Sep 18.

38.

circBase: a database for circular RNAs.

Glažar P, Papavasileiou P, Rajewsky N.

RNA. 2014 Nov;20(11):1666-70. doi: 10.1261/rna.043687.113. Epub 2014 Sep 18.

39.

Mixed messages: Re-initiation factors regulate translation of animal mRNAs.

Obermayer B, Rajewsky N.

Cell Res. 2014 Dec;24(12):1383-4. doi: 10.1038/cr.2014.114. Epub 2014 Aug 22.

40.

RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.

Maatz H, Jens M, Liss M, Schafer S, Heinig M, Kirchner M, Adami E, Rintisch C, Dauksaite V, Radke MH, Selbach M, Barton PJ, Cook SA, Rajewsky N, Gotthardt M, Landthaler M, Hubner N.

J Clin Invest. 2014 Aug;124(8):3419-30. doi: 10.1172/JCI74523. Epub 2014 Jun 24.

41.

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism.

Stoeckius M, Grün D, Kirchner M, Ayoub S, Torti F, Piano F, Herzog M, Selbach M, Rajewsky N.

EMBO J. 2014 Aug 18;33(16):1751-66. doi: 10.15252/embj.201488769. Epub 2014 Jun 23.

42.

Paternal RNA contributions in the Caenorhabditis elegans zygote.

Stoeckius M, Grün D, Rajewsky N.

EMBO J. 2014 Aug 18;33(16):1740-50. doi: 10.15252/embj.201488117. Epub 2014 Jun 3.

43.

Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.

Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E, Rajewsky N.

Mol Cell. 2014 Jun 19;54(6):1042-1054. doi: 10.1016/j.molcel.2014.03.049. Epub 2014 May 22.

44.

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.

Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ.

EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4.

45.

Conservation of mRNA and protein expression during development of C. elegans.

Grün D, Kirchner M, Thierfelder N, Stoeckius M, Selbach M, Rajewsky N.

Cell Rep. 2014 Feb 13;6(3):565-77. doi: 10.1016/j.celrep.2014.01.001. Epub 2014 Jan 23.

46.

The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation.

Solana J, Gamberi C, Mihaylova Y, Grosswendt S, Chen C, Lasko P, Rajewsky N, Aboobaker AA.

PLoS Genet. 2013;9(12):e1004003. doi: 10.1371/journal.pgen.1004003. Epub 2013 Dec 19.

47.

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation.

Graf R, Munschauer M, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M.

RNA Biol. 2013 Jul;10(7):1146-59. doi: 10.4161/rna.25194. Epub 2013 May 29.

48.

Circular RNAs are a large class of animal RNAs with regulatory potency.

Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N.

Nature. 2013 Mar 21;495(7441):333-8. doi: 10.1038/nature11928. Epub 2013 Feb 27.

PMID:
23446348
49.

Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells.

Onal P, Grün D, Adamidi C, Rybak A, Solana J, Mastrobuoni G, Wang Y, Rahn HP, Chen W, Kempa S, Ziebold U, Rajewsky N.

EMBO J. 2012 Jun 13;31(12):2755-69. doi: 10.1038/emboj.2012.110. Epub 2012 Apr 27.

50.

The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation.

von Eyss B, Maaskola J, Memczak S, Möllmann K, Schuetz A, Loddenkemper C, Tanh MD, Otto A, Muegge K, Heinemann U, Rajewsky N, Ziebold U.

EMBO J. 2012 Feb 15;31(4):972-85. doi: 10.1038/emboj.2011.451. Epub 2011 Dec 13.

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