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2018

Spatiotemporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline.
Diag, A. and Schilling, M. and Klironomos, F. and Ayoub, S. and Rajewsky, N.
Developmental Cell 8 November 2018 (In Press)

Roles of long noncoding RNAs and circular RNAs in translation.
Chekulaeva, M. and Rajewsky, N.
Cold Spring Harbor Perspectives in Biology 6 August 2018 (In Press)

A single-cell transcriptome atlas of the mouse glomerulus.
Karaiskos, N. and Rahmatollahi, M. and Boltengagen, A. and Liu, H. and Hoehne, M. and Rinschen, M. and Schermer, B. and Benzing, T. and Rajewsky, N. and Kocks, C. and Kann, M. and Müller, R.U.
Journal of the American Society of Nephrology 29 (8): 2060-2068. August 2018

Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects underlying impaired adult neurogenesis.
Zywitza, V. and Misios, A. and Bunatyan, L. and Willnow, T.E. and Rajewsky, N.
bioRxiv : 365619. 9 July 2018

Regulation of spatial and temporal gene expression in an animal germline.
Diag, A. and Schilling, M. and Klironomos, F. and Ayoub, S. and Rajewsky, N.
bioRxiv : 348425. 15 June 2018

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.
Plass, M. and Solana, J. and Wolf, F.A. and Ayoub, S. and Misios, A. and Glažar, P. and Obermayer, B. and Theis, F.J. and Kocks, C. and Rajewsky, N.
Science 360 (6391): eaaq1723. 25 May 2018

Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo.
Maschmeyer, P. and Petkau, G. and Siracusa, F. and Zimmermann, J. and Zügel, F. and Kühl, A.A. and Lehmann, K. and Schimmelpfennig, S. and Weber, M. and Haftmann, C. and Riedel, R. and Bardua, M. and Heinz, G.A. and Tran, C.L. and Hoyer, B.F. and Hiepe, F. and Herzog, S. and Wittmann, J. and Rajewsky, N. and Melchers, F.G. and Chang, H.D. and Radbruch, A. and Mashreghi, M.F.
Journal of Autoimmunity 89 : 41-52. May 2018

Characterization of transcription termination-associated RNAs: new insights into their biogenesis, tailing, and expression in primary tumors.
Laudadio, I. and Formichetti, S. and Gioiosa, S. and Klironomos, F. and Rajewsky, N. and Macino, G. and Carissimi, C. and Fulci, V.
International Journal of Genomics 2018 : 1243858. 26 April 2018

Post-transcriptional regulation by 3' UTRs can be masked by regulatory elements in 5' UTRs.
Theil, K. and Herzog, M. and Rajewsky, N.
Cell Reports 22 (12): 3217-3226. 20 March 2018

Single-molecule fluorescence in situ hybridization (FISH) of circular RNA CDR1as.
Kocks, C. and Boltengagen, A. and Piwecka, M. and Rybak-Wolf, A. and Rajewsky, N.
Methods in Molecular Biology 1724 : 77-96. 2018

2017

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. and Ferraiuolo, M. and Sacconi, A. and Ganci, F. and Vitale, J. and Colombo, T. and Paci, P. and Strano, S. and Macino, G. and Rajewsky, N. and Blandino, G.
Genome Biology 18 (1): 237. 20 December 2017

RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation.
Backofen, R. and Engelhardt, J. and Erxleben, A. and Fallmann, J. and Grüning, B. and Ohler, U. and Rajewsky, N. and Stadler, P.F.
Journal of Biotechnology 261 : 76-84. 10 November 2017

A map of human circular RNAs in clinically relevant tissues.
Maass, P.G. and Glažar, P. and Memczak, S. and Dittmar, G. and Hollfinger, I. and Schreyer, L. and Sauer, A.V. and Toka, O. and Aiuti, A. and Luft, F.C. and Rajewsky, N.
Journal of Molecular Medicine 95 (11): 1179-1189. November 2017

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E. and Menegatti, J. and Franke, V. and Kocks, C. and Boltengagen, A. and Hennig, T. and Theil, K. and Rutkowski, A. and Ferrai, C. and Baer, L. and Kermas, L. and Friedel, C. and Rajewsky, N. and Akalin, A. and Dölken, L. and Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A. and Hamey, F. and Plass, M. and Solana, J. and Dahlin, J.S. and Gottgens, B. and Rajewsky, N. and Simon, L. and Theis, F.J.
bioRxiv : 208819. 25 October 2017

The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
Science 358 (6360): 194-199. 13 October 2017

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.
Piwecka, M. and Glažar, P. and Hernandez-Miranda, L.R. and Memczak, S. and Wolf, S.A. and Rybak-Wolf, A. and Filipchyk, A. and Klironomos, F. and Cerda Jara, C.A. and Fenske, P. and Trimbuch, T. and Zywitza, V. and Plass, M. and Schreyer, L. and Ayoub, S. and Kocks, C. and Kühn, R. and Rosenmund, C. and Birchmeier, C. and Rajewsky, N.
Science 357 (6357): eaam8526. 22 September 2017

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A. and van den Bruck, D. and Ciolli Mattioli, C. and Franke, V. and Imami, K. and McShane, E. and Moreno-Estelles, M. and Calviello, L. and Filipchyk, A. and Peguero-Sanchez, E. and Müller, T. and Woehler, A. and Birchmeier, C. and Merino, E. and Rajewsky, N. and Ohler, U. and Mazzoni, E.O. and Selbach, M. and Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B. and Yusuf, D. and Wurmus, R. and Rajewsky, N. and Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. and Karaiskos, N. and Praktiknjo, S.D. and Grosswendt, S. and Wahle, P. and Ruffault, P.L. and Ayoub, S. and Schreyer, L. and Boltengagen, A. and Birchmeier, C. and Zinzen, R. and Kocks, C. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. and Karaiskos, N. and Praktiknjo, S. and Grosswendt, S. and Wahle, P. and Ruffault, P.L. and Ayoub, S. and Schreyer, L. and Boltengagen, A. and Birchmeier, C. and Zinzen, R. and Kocks, C. and Rajewsky, N.
bioRxiv : 099473. 13 April 2017

Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis.
Legnini, I. and Di Timoteo, G. and Rossi, F. and Morlando, M. and Briganti, F. and Sthandier, O. and Fatica, A. and Santini, T. and Andronache, A. and Wade, M. and Laneve, P. and Rajewsky, N. and Bozzoni, I.
Molecular Cell 66 (1): 22-37.e9. 6 April 2017

Translation of circRNAs.
Pamudurti, NR. and Bartok, O. and Jens, M. and Ashwal-Fluss, R. and Stottmeister, C. and Ruhe, L. and Hanan, M. and Wyler, E. and Perez-Hernandez, D. and Ramberger, E. and Shenzis, S. and Samson, M. and Dittmar, G. and Landthaler, M. and Chekulaeva, M. and Rajewsky, N. and Kadener, S.
Molecular Cell 66 (1): 9-21. 6 April 2017

The Drosophila embryo at single cell transcriptome resolution.
Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
bioRxiv : 117382. 17 March 2017

Essentials of miRNA-dependent control of mRNA translation and decay, miRNA targeting principles, and methods for target identification.
Grosswendt, S. and Rajewsky, N.
In: Essentials of noncoding RNA in neuroscience: ontogenetics, plasticity of the vertebrate brain. Academic Press (U.K.), London, 19-38. ISBN 978-012804402-5 2017

2016

The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery.
Stunnenberg, H.G. and Hirst, M.
Cell 167 (7): 1145-1149. 17 November 2016

Epigenomic profiling of human CD4(+) T cells supports a linear differentiation model and highlights molecular regulators of memory development.
Durek, P. and Nordström, K. and Gasparoni, G. and Salhab, A. and Kressler, C. and de Almeida, M. and Bassler, K. and Ulas, T. and Schmidt, F. and Xiong, J. and Glažar, P. and Klironomos, F. and Sinha, A. and Kinkley, S. and Yang, X. and Arrigoni, L. and Amirabad, A.. and Ardakani, F.B. and Feuerbach, L. and Gorka, O. and Ebert, P. and Müller, F. and Li, N. and Frischbutter, S. and Schlickeiser, S. and Cendon, C. and Fröhler, S. and Felder, B. and Gasparoni, N. and Imbusch, C.D. and Hutter, B. and Zipprich, G. and Tauchmann, Y. and Reinke, S. and Wassilew, G. and Hoffmann, U. and Richter, A.S. and Sieverling, L. and Chang, H.D. and Syrbe, U. and Kalus, U. and Eils, J. and Brors, B. and Manke, T. and Ruland, J. and Lengauer, T. and Rajewsky, N. and Chen, W. and Dong, J. and Sawitzki, B. and Chung, H.R. and Rosenstiel, P. and Schulz, M.H. and Schultze, J.L. and Radbruch, A. and Walter, J. and Hamann, A. and Polansky, J.K.
Immunity 45 (5): 1148-1161. 15 November 2016

Conserved functional antagonism of CELF 1 and MBNL proteins controls stem cell-specific alternative splicing in planarians.
Solana, J. and Irimia, M. and Ayoub, S. and Orejuela, M.R. and Zywitza, V. and Jens, M. and Tapial, J. and Ray, D. and Morris, Q.D. and Hughes, T.R. and Blencowe, B.J. and Rajewsky, N.
eLife 5 : e16797. 9 August 2016

Epigenetic dynamics of monocyte-to-macrophage differentiation.
Wallner, S. and Schroeder, C. and Leitão, E. and Berulava, T. and Haak, C. and Beißer, D. and Rahmann, S. and Richter, A.S. and Manke, T. and Bönisch, U. and Arrigoni, L. and Fröhler, S. and Klironomos, F. and Chen, W. and Rajewsky, N. and Müller, F. and Ebert, P. and Lengauer, T. and Barann, M. and Rosenstiel, P. and Gasparoni, G. and Nordström, K. and Walter, J. and Brors, B. and Zipprich, G. and Felder, B. and Klein-Hitpass, L. and Attenberger, C. and Schmitz, G. and Horsthemke, B.
Epigenetics & Chromatin 9 : 33. 29 July 2016

The Lupus autoantigen La prevents Mis-channeling of tRNA fragments into the human microRNA pathway.
Hasler, D. and Lehmann, G. and Murakawa, Y. and Klironomos, F. and Jakob, L. and Grässer, F.A. and Rajewsky, N. and Landthaler, M. and Meister, G.
Molecular Cell 63 (1): 110-124. 7 July 2016

A pipeline for PAR-CLIP data analysis.
Jens, M.
Methods in Molecular Biology 1358 : 197-207. 2016

2015

Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood.
Memczak, S. and Papavasileiou, P. and Peters, O. and Rajewsky, N.
PLoS ONE 10 (10): e0141214. 20 October 2015

4-fragment gateway cloning format for MosSCI-compatible vectors integrating promoterome and 3'UTRome libraries of Caenorhabditis elegans.
Kogame, T.
Journal of Medical Investigation 62 (3.4): 161-166. 18 September 2015

Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak, S.D. and Zauber, H. and Bielow, C. and Thiel, D. and Kutz, K. and Calviello, L. and Mastrobuoni, G. and Rajewsky, N. and Kempa, S. and Selbach, M. and Obermayer, B.
Genome Biology 16 : 179. 14 September 2015

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed.
Rybak-Wolf, A. and Stottmeister, C. and Glažar, P. and Jens, M. and Pino, N. and Giusti, S. and Hanan, M. and Behm, M. and Bartok, O. and Ashwal-Fluss, R. and Herzog, M. and Schreyer, L. and Papavasileiou, P. and Ivanov, A. and Öhman, M. and Refojo, D. and Kadener, S. and Rajewsky, N.
Molecular Cell 58 (5): 870-885. 4 June 2015

Translational regulation shapes the molecular landscape of complex disease phenotypes.
Schafer, S. and Adami, E. and Heinig, M. and Costa Rodrigues, K.E. and Kreuchwig, F. and Silhavy, J. and van Heesch, S. and Simaite, D. and Rajewsky, N. and Cuppen, E. and Pravenec, M. and Vingron, M. and Cook, S.A. and Hubner, N.
Nature Communications 6 : 7200. 26 May 2015

Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function.
Jia, S. and Ivanov, A. and Blasevic, D. and Müller, T. and Purfürst, B. and Sun, W. and Chen, W. and Poy, M.N. and Rajewsky, N. and Birchmeier, C.
EMBO Journal 34 (10): 1417-1433. 12 May 2015

Comprehensive identification and characterization of conserved small ORFs in animals.
Mackowiak, S.D. and Zauber, H. and Bielow, C. and Thiel, D. and Kutz, K. and Calviello, L. and Mastrobuoni, G. and Rajewsky, N. and Kempa, S. and Selbach, M. and Obermayer, B.
bioRxiv : 017772. 9 April 2015

Lin41/Trim71 is essential for mouse development and specifically expressed in postnatal ependymal cells of the brain.
Cuevas, E. and Rybak-Wolf, A. and Rohde, A.M. and Nguyen, D.T.T. and Wulczyn, F.G.
Frontiers in Cell and Developmental Biology 3 : 20. 2 April 2015

miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim.
Haftmann, C. and Stittrich, A.B. and Zimmermann, J. and Fang, Z. and Hradilkova, K. and Bardua, M. and Westendorf, K. and Heinz, G.A. and Riedel, R. and Siede, J. and Lehmann, K. and Weinberger, E.E. and Zimmel, D. and Lauer, U. and Häupl, T. and Sieper, J. and Backhaus, M. and Neumann, C. and Hoffmann, U. and Porstner, M. and Chen, W. and Grün, J.R. and Baumgrass, R. and Matz, M. and Löhning, M. and Scheffold, A. and Wittmann, J. and Chang, H.D. and Rajewsky, N. and Jäck, H.M. and Radbruch, A. and Mashreghi, M.F.
European Journal of Immunology 45 (4): 1192-1205. April 2015

Specific microRNAs regulate heat stress responses in Caenorhabditis elegans.
Nehammer, C. and Podolska, A. and Mackowiak, S.D. and Kagias, K. and Pocock, R.
Scientific Reports 5 : 8866. 9 March 2015

microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes.
Blevins, R. and Bruno, L. and Carroll, T. and Elliott, J. and Marcais, A. and Loh, C. and Hertweck, A. and Krek, A. and Rajewsky, N. and Chen, C.Z. and Fisher, A.G. and Merkenschlager, M.
PLoS Genetics 11 (2): e1005020. 25 February 2015

Competition between target sites of regulators shapes post-transcriptional gene regulation.
Jens, M. and Rajewsky, N.
Nature Reviews Genetics 16 (2): 113-126. February 2015

DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.
Blin, K. and Dieterich, C. and Wurmus, R. and Rajewsky, N. and Landthaler, M. and Akalin, A.
Nucleic Acids Research 43 (Database issue): D160-D167. 28 January 2015

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals.
Ivanov, A. and Memczak, S. and Wyler, E. and Torti, F. and Porath, H.T. and Orejuela, M.R. and Piechotta, M. and Levanon, E.Y. and Landthaler, M. and Dieterich, C. and Rajewsky, N.
Cell Reports 10 (2): 170-177. 13 January 2015

2014

Paternal diet defines offspring chromatin state and intergenerational obesity.
Öst, A. and Lempradl, A. and Casas, E. and Weigert, M. and Tiko, T. and Deniz, M. and Pantano, L. and Boenisch, U. and Itskov, P.M. and Stoeckius, M. and Ruf, M. and Rajewsky, N. and Reuter, G. and Iovino, N. and Ribeiro, C. and Alenius, M. and Heyne, S. and Vavouri, T. and Pospisilik, J.A.
Cell 159 (6): 1352-1364. 4 December 2014

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.
Maaskola, J. and Rajewsky, N.
Nucleic Acids Research 42 (21): 12995-13011. 1 December 2014

Mixed messages: re-initiation factors regulate translation of animal mRNAs.
Obermayer, B. and Rajewsky, N.
Cell Research 24 (12): 1383-1384. December 2014

A variety of dicer substrates in human and C. elegans.
Rybak-Wolf, A. and Jens, M. and Murakawa, Y. and Herzog, M. and Landthaler, M. and Rajewsky, N.
Cell 159 (5): 1153-1167. 20 November 2014

Novel RNA modifications in the nervous system: form and function.
Satterlee, J.S. and Basanta-Sanchez, M. and Blanco, S. and Li, J.B. and Meyer, K. and Pollock, J. and Sadri-Vakili, G. and Rybak-Wolf, A.
Journal of Neuroscience 34 (46): 15170-15177. 12 November 2014

circBase: a database for circular RNAs.
Glažar, P. and Papavasileiou, P. and Rajewsky, N.
RNA 20 (11): 1666-1670. November 2014

Modules, networks and systems medicine for understanding disease and aiding diagnosis.
Gustafsson, M. and Nestor, C.E. and Zhang, H. and Barabási, A.L. and Baranzini, S. and Brunak, S. and Chung, K.F. and Federoff, H.J. and Gavin, A.C. and Meehan, R.R. and Picotti, P. and Pujana, M.À. and Rajewsky, N. and Smith, K.G.C. and Sterk, P.J. and Villoslada, P. and Benson, M.
Genome Medicine 6 (10): 82. 17 October 2014

circRNA biogenesis competes with pre-mRNA splicing.
Ashwal-Fluss, R. and Meyer, M. and Pamudurti, N.R. and Ivanov, A. and Bartok, O. and Hanan, M. and Evantal, N. and Memczak, S. and Rajewsky, N. and Kadener, S.
Molecular Cell 56 (1): 55-66. 2 October 2014

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism.
Stoeckius, M. and Grün, D. and Kirchner, M. and Ayoub, S. and Torti, F. and Piano, F. and Herzog, M. and Selbach, M. and Rajewsky, N.
EMBO Journal 33 (16): 1751-1766. 18 August 2014

Paternal RNA contributions in the Caenorhabditis elegans zygote.
Stoeckius, M. and Grün, D. and Rajewsky, N.
EMBO Journal 33 (16): 1740-1750. 18 August 2014

RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.
Maatz, H. and Jens, M. and Liss, M. and Schafer, S. and Heinig, M. and Kirchner, M. and Adami, E. and Rintisch, C. and Dauksaite, V. and Radke, M.H. and Selbach, M. and Barton, P.J.R. and Cook, S.A. and Rajewsky, N. and Gotthardt, M. and Landthaler, M. and Hubner, N.
Journal of Clinical Investigation 124 (8): 3419-3430. 1 August 2014

MicroRNA-138 is a potential regulator of memory performance in humans.
Schroeder, J. and Ansaloni, S. and Schilling, M. and Liu, T. and Radke, J. and Jaedicke, M. and Schjeide, B.M.M. and Mashychev, A. and Tegeler, C. and Radbruch, H. and Papenberg, G. and Duezel, S. and Demuth, I. and Bucholtz, N. and Lindenberger, U. and Li, S.C. and Steinhagen-Thiessen, E. and Lill, C.M. and Bertram, L.
Frontiers in Human Neuroscience 8 : 501. 11 July 2014

Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.
Grosswendt, S. and Filipchyk, A. and Manzano, M. and Klironomos, F. and Schilling, M. and Herzog, M. and Gottwein, E. and Rajewsky, N.
Molecular Cell 54 (6): 1042-1054. 19 June 2014

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.
Bazzini, A.A. and Johnstone, T.G. and Christiano, R. and Mackowiak, S.D. and Obermayer, B. and Fleming, E.S. and Vejnar, C.E. and Lee, M.T. and Rajewsky, N. and Walther, T.C. and Giraldez, A.J.
EMBO Journal 33 (9): 981-993. 2 May 2014

Conservation of mRNA and protein expression during development of C. elegans.
Grün, D. and Kirchner, M. and Thierfelder, N. and Stoeckius, M. and Selbach, M. and Rajewsky, N.
Cell Reports 6 (3): 565-577. 13 February 2014

Whole-mount in situ hybridization using DIG-labeled probes in planarian.
Rybak-Wolf, A. and Solana, J.
Methods in Molecular Biology 1211 : 41-51. 2014

2013

The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation.
Solana, J. and Gamberi, C. and Mihaylova, Y. and Grosswendt, S. and Chen, C. and Lasko, P. and Rajewsky, N. and Aboobaker, A.A.
PLoS Genetics 9 (12): e1004003. December 2013

Advanced topics in bioinformatics and computational biology.
Hao, B. and Zhang, C. and Li, Y. and Li, H. and Wei, L. and Kanehisa, M. and Lai, L. and Chen, R. and Rajewsky, N. and Zhang, M.Q. and Han, J. and Jiang, R. and Zhang, X. and Li, Y.
In: Basics of Bioinformatics. Springer (Germany), Heidelberg, 369-395. ISBN 978-3-642-38950-4 1 July 2013

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation.
Graf, R. and Munschauer, M. and Mastrobuoni, G. and Mayr, F. and Heinemann, U. and Kempa, S. and Rajewsky, N. and Landthaler, M.
RNA Biology 10 (7): 1146-1159. 1 July 2013

Circular RNAs are a large class of animal RNAs with regulatory potency.
Memczak, S. and Jens, M. and Elefsinioti, A. and Torti, F. and Krueger, J. and Rybak, A. and Maier, L. and Mackowiak, S.D. and Gregersen, L.H. and Munschauer, M. and Loewer, A. and Ziebold, U. and Landthaler, M. and Kocks, C. and le Noble, F. and Rajewsky, N.
Nature 495 (7441): 333-338. 21 March 2013

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
Li, N. and You, X. and Chen, T. and Mackowiak, S.D. and Friedlaender, M.R. and Weigt, M. and Du, H. and Gogol-Doering, A. and Chang, Z. and Dieterich, C. and Hu, Y. and Chen, W.
Nucleic Acids Research 41 (6): 3619-3634. 8 February 2013

Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis.
Solana, J.
EvoDevo 4 (1): 2. 8 January 2013

2012

Extracellularly delivered single-stranded viral RNA causes neurodegeneration dependent on TLR7.
Lehmann, S.M. and Rosenberger, K. and Krueger, C. and Habbel, P. and Derkow, K. and Kaul, D. and Rybak, A. and Brandt, C. and Schott, E. and Wulczyn, F.G. and Lehnardt, S.
Journal of Immunology 189 (3): 1448-1458. 1 August 2012

Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells.
Onal, P. and Gruen, D. and Adamidi, C. and Rybak, A. and Solana, J. and Mastrobuoni, G. and Wang, Y. and Rahn, H.P. and Chen, W. and Kempa, S. and Ziebold, U. and Rajewsky, N.
EMBO Journal 31 (12): 2755-2769. 27 April 2012

The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation.
von Eyss, B. and Maaskola, J. and Memczak, S. and Möllmann, K. and Schuetz, A. and Loddenkemper, C. and Tanh, M.D. and Otto, A. and Muegge, K. and Heinemann, U. and Rajewsky, N. and Ziebold, U.
EMBO Journal 31 (4): 972-985. 15 February 2012

Select microRNAs are essential for early development in the sea urchin.
Song, J.L. and Stoeckius, M. and Maaskola, J. and Friedlaender, M. and Stepicheva, N. and Juliano, C. and Lebedeva, S. and Thompson, W. and Rajewsky, N. and Wessel, G.M.
Developmental Biology 362 (1): 104-113. 1 February 2012

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Friedlaender, M.R. and Mackowiak, S.D. and Li, N. and Chen, W. and Rajewsky, N.
Nucleic Acids Research 40 (1): 37-52. 1 January 2012

doRiNA: a database of RNA interactions in post-transcriptional regulation.
Anders, G. and Mackowiak, S.D. and Jens, M. and Maaskola, J. and Kuntzagk, A. and Rajewsky, N. and Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

Genes involved in the metastatic cascade of medullary thyroid tumours.
Schreiber, C. and Vormbrock, K. and Ziebold, U.
Methods in Molecular Biology 878 : 217-228. 2012

2011

In vivo and transcriptome-wide identification of RNA binding protein target sites.
Jungkamp, A.C. and Stoeckius, M. and Mecenas, D. and Gruen, D. and Mastrobuoni, G. and Kempa, S. and Rajewsky, N.
Molecular Cell 44 (5): 828-840. 9 December 2011

Identification of novel and known miRNAs in deep-sequencing data with miRDeep2.
Mackowiak, S.D.
Current Protocols in Bioinformatics S36 : Unit12.10. December 2011

Large-scale de novo prediction of physical protein-protein association.
Elefsinioti, A. and Sarac, O.S. and Hegele, A. and Plake, C. and Hubner, N.C. and Poser, I. and Sarov, M. and Hyman, A. and Mann, M. and Schroeder, M. and Stelzl, U. and Beyer, A.
Molecular & Cellular Proteomics 10 (11): M111.010629. November 2011

Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.
Lebedeva, S. and Jens, M. and Theil, K. and Schwanhaeusser, B. and Selbach, M. and Landthaler, M. and Rajewsky, N.
Molecular Cell 43 (3): 340-352. 5 August 2011

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi, C. and Wang, Y. and Gruen, D. and Mastrobuoni, G. and You, X. and Tolle, D. and Dodt, M. and Mackowiak, S.D. and Gogol-Doering, A. and Oenal, P. and Rybak, A. and Ross, E. and Alvarado, A.S. and Kempa, S. and Dieterich, C. and Rajewsky, N. and Chen, W.
Genome Research 21 (7): 1193-1200. July 2011

microRNAs and the Operon paper.
Rajewsky, N.
Journal of Molecular Biology 409 (1): 70-75. 27 May 2011

The impact of miRNA target sites in coding sequences and in 3'UTRs.
Fang, Z. and Rajewsky, N.
PLoS ONE 6 (3): e18067. 22 March 2011

2010

Integrative analysis of the caenorhabditis elegans genome by the modENCODE project.
Gerstein, M.B. and Lu, Z.J. and Van Nostrand, E.L. and Cheng, C. and Arshinoff, B.I. and Liu, T. and Yip, K.Y. and Robilotto, R. and Rechtsteiner, A. and Ikegami, K. and Alves, P. and Chateigner, A. and Perry, M. and Morris, M. and Auerbach, R.K. and Feng, X. and Leng, J. and Vielle, A. and Niu, W. and Rhrissorrakrai, K. and Agarwal, A. and Alexander, R.P. and Barber, G. and Brdlik, C.M. and Brennan, J. and Brouillet, J.J. and Carr, A. and Cheung, M.S. and Clawson, H. and Contrino, S. and Dannenberg, L.O. and Dernburg, A.F. and Desai, A. and Dick, L. and Dose, A.C. and Du, J. and Egelhofer, T. and Ercan, S. and Euskirchen, G. and Ewing, B. and Feingold, E.A. and Gassmann, R. and Good, P.J. and Green, P. and Gullier, F. and Gutwein, M. and Guyer, M.S. and Habegger, L. and Han, T. and Henikoff, J.G. and Henz, S.R. and Hinrichs, A. and Holster, H. and Hyman, T. and Iniguez, A.L. and Janette, J. and Jensen, M. and Kato, M. and Kent, W.J. and Kephart, E. and Khivansara, V. and Khurana, E. and Kim, J.K. and Kolasinska-Zwierz, P. and Lai, E.C. and Latorre, I. and Leahey, A. and Lewis, S. and Lloyd, P. and Lochovsky, L. and Lowdon, R.F. and Lubling, Y. and Lyne, R. and Maccoss, M. and Mackowiak, S.D. and Mangone, M. and McKay, S. and Mecenas, D. and Merrihew, G. and Miller, D.M. and Muroyama, A. and Murray, J.I. and Ooi, S.L. and Pham, H. and Phippen, T. and Preston, E.A. and Rajewsky, N. and Raetsch, G. and Rosenbaum, H. and Rozowsky, J. and Rutherford, K. and Ruzanov, P. and Sarov, M. and Sasidharan, R. and Sboner, A. and Scheid, P. and Segal, E. and Shin, H. and Shou, C. and Slack, F.J. and Slightam, C. and Smith, R. and Spencer, W.C. and Stinson, E.O. and Taing, S. and Takasaki, T. and Vafeados, D. and Voronina, K. and Wang, G. and Washington, N.L. and Whittle, C.M. and Wu, B. and Yan, K.K. and Zeller, G. and Zha, Z. and Zhong, M. and Zhou, X. and Ahringer, J. and Strome, S. and Gunsalus, K.C. and Micklem, G. and Liu, X.S. and Reinke, V. and Kim, S.K. and Hillier, L.W. and Henikoff, S. and Piano, F. and Snyder, M. and Stein, L. and Lieb, J.D. and Waterston, R.H.
Science 330 (6012): 1775-1787. 24 December 2010

The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes.
Stittrich, A.B. and Haftmann, C. and Sgouroudis, E. and Kuehl, A.A. and Hegazy, A.N. and Panse, I. and Riedel, R. and Flossdorf, M. and Dong, J. and Fuhrmann, F. and Heinz, G.A. and Fang, Z. and Li, N. and Bissels, U. and Hatam, F. and Jahn, A. and Hammoud, B. and Matz, M. and Schulze, F.M. and Baumgrass, R. and Bosio, A. and Mollenkopf, H.J. and Gruen, J. and Thiel, A. and Chen, W. and Hoefer, T. and Loddenkemper, C. and Loehning, M. and Chang, H.D. and Rajewsky, N. and Radbruch, A. and Mashreghi, M.F.
Nature Immunology 11 (11): 1057-1062. November 2010

The Landscape of C. elegans 3'UTRs.
Mangone, M. and Manoharan, A.P. and Thierry-Mieg, D. and Thierry-Mieg, J. and Han, T. and Mackowiak, S. and Mis, E. and Zegar, C. and Gutwein, M.R. and Khivansara, V. and Attie, O. and Chen, K. and Salehi-Ashtiani, K. and Vidal, M. and Harkins, T.T. and Bouffard, P. and Suzuki, Y. and Sugano, S. and Kohara, Y. and Rajewsky, N. and Piano, F. and Gunsalus, K.C. and Kim, J.K.
Science 329 (5990): 432-435. 23 July 2010

Deciphering the porcine intestinal microRNA transcriptome.
Sharbati, S. and Friedlaender, M.R. and Sharbati, J. and Hoeke, L. and Chen, W. and Keller, A. and Stahler, P.F. and Rajewsky, N. and Einspanier, R.
BMC Genomics 11 (1): 275. 30 April 2010

Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.
Chen, K. and van Nimwegen, E. and Rajewsky, N. and Siegal, M.L.
Genome Biology and Evolution 2 (1): 697-707. 2010

2009

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.
Stoeckius, M. and Maaskola, J. and Colombo, T. and Rahn, H.P. and Friedlaender, M.R. and Li, N. and Chen, W. and Piano, F. and Rajewsky, N.
Nature Methods 6 (10): 745-751. October 2009

High-resolution profiling and discovery of planarian small RNAs.
Friedlaender, M.R. and Adamidi, C. and Han, T. and Lebedeva, S. and Isenbarger, T.A. and Hirst, M. and Marra, M. and Nusbaum, C. and Lee, W.L. and Jenkin, J.C. and Alvarado, A.S. and Kim, J.K. and Rajewsky, N.
Proceedings of the National Academy of Sciences of the United States of America 106 (28): 11546-11551. 14 July 2009

Reexamining microRNA site accessibility in Drosophila: a population genomics study.
Chen, K. and Maaskola, J. and Siegal, M.L. and Rajewsky, N.
PLoS ONE 4 (5): e5681. 25 May 2009

2008

A human snoRNA with microRNA-like functions.
Ender, C. and Krek, A. and Friedlaender, M.R. and Beitzinger, M. and Weinmann, L. and Chen, W. and Pfeffer, S. and Rajewsky, N. and Meister, G.
Molecular Cell 32 (4): 519-528. 21 November 2008

Widespread changes in protein synthesis induced by microRNAs.
Selbach, M. and Schwanhaeusser, B. and Thierfelder, N. and Fang, Z. and Khanin, R. and Rajewsky, N.
Nature 455 (7209): 58-63. 4 September 2008

Discovering microRNAs from deep sequencing data using miRDeep.
Friedlaender, M.R. and Chen, W. and Adamidi, C. and Maaskola, J. and Einspanier, R. and Knespel, S. and Rajewsky, N.
Nature Biotechnology 26 (4): 407-415. April 2008

Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage.
Koralov, S.B. and Muljo, S.A. and Galler, G.R. and Krek, A. and Chakraborty, T. and Kanellopoulou, C. and Jensen, K. and Cobb, B.S. and Merkenschlager, M. and Rajewsky, N. and Rajewsky, K.
Cell 132 (5): 860-874. 7 March 2008

Computational challenges in the study of small regulatory RNAS.
Betel, D. and Leslie, C. and Rajewsky, N.
In: Pacific Symposium on Biocomputing. 2008

2007

MiR-150 Controls B Cell Differentiation by Targeting the Transcription Factor c-Myb.
Xiao, C. and Calado, D.P. and Galler, G. and Thai, T.H. and Patterson, H.C. and Wang, J. and Rajewsky, N. and Bender, T.P. and Rajewsky, K.
Cell 131 (1): 146-159. 5 October 2007

Regulation of the germinal center response by microRNA-155.
Thai, T.H. and Calado, D.P. and Casola, S. and Ansel, K.M. and Xiao, C. and Xue, Y. and Murphy, A. and Frendewey, D. and Valenzuela, D. and Kutok, J.L. and Schmidt-Supprian, M. and Rajewsky, N. and Yancopoulos, G. and Rao, A. and Rajewsky, K.
Science 316 (5824): 604-608. 27 April 2007

The evolution of gene regulation by transcription factors and microRNAs.
Chen, K. and Rajewsky, N.
Nature Reviews Genetics 8 (2): 93-103. February 2007

Computational prediction of microRNA targets in vertebrates, fruitflies and nematodes.
Gruen, D. and Rajewsky, N.
In: MicroRNAs: From Basic Science to Disease Biology. Cambridge University Press (U.K.), Cambridge, 172-186. ISBN 9780521865982 2007

2006

Natural selection on human microRNA binding sites inferred from SNP data.
Chen, K. and Rajewsky, N.
Nature Genetics 38 (12): 1452-1456. 1 December 2006

L(ou)sy miRNA targets?
Rajewsky, N.
Nature Structural & Molecular Biology 13 (9): 754-755. September 2006

microRNA target predictions in animals.
Rajewsky, N.
Nature Genetics 38 (Suppl.): S8-S13. June 2006

A genome-wide map of conserved microRNA targets in C. elegans.
Lall, S. and Grun, D. and Krek, A. and Chen, K. and Wang, Y.L. and Dewey, C.N. and Sood, P. and Colombo, T. and Bray, N. and Macmenamin, P. and Kao, H.L. and Gunsalus, K.C. and Pachter, L. and Piano, F. and Rajewsky, N.
Current Biology 16 (5): 460-471. 7 March 2006

Cell type specific signatures of microRNAs on target mRNA expression.
Sood, P. and Krek, A. and Zavolan, M. and Macino, G. and Rajewsky, N.
Proceedings of the National Academy of Sciences of the United States of America 103 (8): 2746-2751. 21 February 2006

Deep conservation of microRNA-target relationships and 3'UTR motifs in vertebrates, flies, and nematodes.
Chen, K. and Rajewsky, N.
Cold Spring Harbor Symposia on Quantitative Biology 71 : 149-156. 2006

2005

Silencing of microRNAs in vivo with 'antagomirs'.
Krutzfeldt, J. and Rajewsky, N. and Braich, R. and Rajeev, K.G. and Tuschl, T. and Manoharan, M. and Stoffel, M.
Nature 438 (7068): 685-689. 1 December 2005

microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
Gruen, D. and Wang, Y.L. and Langenberger, D. and Gunsalus, K.C. and Rajewsky, N.
PLoS Computational Biology 1 (1): e13. June 2005

Combinatorial microRNA target predictions.
Krek, A. and Gruen, D. and Poy, M.N. and Wolf, R. and Rosenberg, L. and Epstein, E.J. and MacMenamin, P. and da Piedade, I. and Gunsalus, K.C. and Stoffel, M. and Rajewsky, N.
Nature Genetics 37 (5): 495-500. May 2005

MicroRNA profiling of the murine hematopoietic system.
Monticelli, S. and Ansel, K.M. and Xiao, C. and Socci, N.D. and Krichevsky, A.M. and Thai, T.H. and Rajewsky, N. and Marks, D.S. and Sander, C. and Rajewsky, K. and Rao, A. and Kosik, K.S.
Genome Biology 6 (8): R71. 2005

2004

A pancreatic islet-specific microRNA regulates insulin secretion.
Poy, M.N. and Eliasson, L. and Krutzfeldt, J. and Kuwajima, S. and Ma, X. and Macdonald, P.E. and Pfeffer, S. and Tuschl, T. and Rajewsky, N. and Rorsman, P. and Stoffel, M.
Nature 432 (7014): 226-230. 11 November 2004

Transcriptional control in the segmentation gene network of Drosophila.
Schroeder, M.D. and Pearce, M. and Fak, J. and Fan, H. and Unnerstall, U. and Emberly, E. and Rajewsky, N. and Siggia, E.D. and Gaul, U.
PLoS Biology 2 (9): E271. September 2004

Survival of resting mature B lymphocytes depends on BCR signaling via the Igalpha/beta heterodimer.
Kraus, M. and Alimzhanov, M.B. and Rajewsky, N. and Rajewsky, K.
Cell 117 (6): 787-800. 11 June 2004

A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer.
Yannoutsos, N. and Barreto, V. and Misulovin, Z. and Gazumyan, A. and Yu, W. and Rajewsky, N. and Peixoto, B.R. and Eisenreich, T. and Nussenzweig, M.C.
Nature Immunology 5 (4): 443-450. April 2004

Computational identification of microRNA targets.
Rajewsky, N. and Socci, N.D.
Developmental Biology 267 (2): 529-535. 15 March 2004

2003

Conservation of regulatory elements between two species of Drosophila.
Emberly, E. and Rajewsky, N. and Siggia, E.D.
BMC Bioinformatics 4 : 57. 20 November 2003

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.
Yang, E. and van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Schroeder, M. and Magnasco, M. and Darnell, J.E.
Genome Research 13 (8): 1863-1872. August 2003

SMASHing regulatory sites in DNA by human-mouse sequence comparisons.
Zavolan, M. and Socci, N.D. and Rajewsky, N. and Gaasterlamd, T.
Proceedings of the IEEE Computer Society Bioinformatics Conference 2 : 277-286. 2003

2002

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
Rajewsky, N. and Vergassola, M. and Gaul, U. and Siggia, E.D.
BMC Bioinformatics 3 : 30. 24 October 2002

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.
van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Siggia, E.D.
Proceedings of the National Academy of Sciences of the United States of America 99 (11): 7323-7328. 28 May 2002

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons.
Rajewsky, N. and Socci, N.D. and Zapotocky, M. and Siggia, E.D.
Genome Research 12 (2): 298-308. February 2002

2001

Circadian regulation of gene expression systems in the Drosophila head.
Claridge-Chang, A. and Wijnen, H. and Naef, F. and Boothroyd, C. and Rajewsky, N. and Young, M.W.
Neuron 32 (4): 657-671. 20 November 2001

2000

Spatial particle condensation for an exclusion process on a ring.
Rajewsky, N. and Sasamoto, T. and Speer, E.R.
Physica A: Statistical Mechanics and its Applications 279 (1-4): 123-142. 1 May 2000

A deterministic sandpile automaton revisited.
Luebeck, S. and Rajewsky, N. and Wolf, D.E.
European Physical Journal B 13 (4): 715-721. February 2000

1999

Exact solution of an exclusion process with three classes of particles and vacancies.
Mallick, K. and Mallick, S. and Rajewsky, N.
Journal of Physics A 32 (48): 8399-8410. 3 December 1999

Exact solution of a cellular automaton for traffic.
Evans, M.R. and Rajewsky, N. and Speer, E.R.
Journal of Statistical Physics 95 (1-2): 45-96. April 1999

1998

The asymmetric exclusion model with different types of update.
Rajewsky, N.
In: Traffic and Granular Flow '97. National University of Singapore, Singapore, 399-418. ISBN 978-9813083875 December 1998

The asymmetric exclusion process: Comparison of update procedures.
Rajewsky, N. and Santen, L. and Schadschneider, A. and Schreckenberg, M.
Journal of Statistical Physics 92 (1-2): 151-194. July 1998

1997

Exact results for one-dimensional cellular automata with different types of updates.
Rajewsky, N. and Schreckenberg, M.
Physica A: Statistical Mechanics and its Applications 245 (1-2): 139-144. 15 October 1997

1996

The asymmetric exclusion model with sequential update.
Rajewsky, N. and Schadschneider, A. and Schreckenberg, M.
Journal of Physics A 29 (12): L305-L309. 21 June 1996

The asymmetric exclusion model with time continous and time non-continous update.
Rajewsky, N. and Santen, L. and Schadschneider, A. and Schreckenberg, M.
In: 1996 Conference on Scientific Computing in Europe, 1996, Centre for Teaching Computing, Dublin City University. 1996

1995

A probabilistic cellular-automaton for evolution.
Rajewsky, N. and Schreckenberg, M.
Journal de Physique I 5 (9): 1129-1134. September 1995

1990

Anomalous roughening in 3-dimensional polynucleation growth.
Lehner, C. and Rajewsky, N. and Wolf, D.E. and Kertesz, J.
Physica A: Statistical Mechanics and its Applications 164 (1): 81-90. 15 March 1990

1987

Timing, genetic requirements and functional consequences of somatic hypermutation during B-cell development.
Allen, D. and Cumano, A. and Dildrop, R. and Kocks, C. and Rajewsky, K. and Rajewsky, N. and Roes, J. and Sablitzky, F. and Siekevitz, M.
Immunological Reviews 96 : 5-22. April 1987

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