Publications



2017

Maschmeyer P.; Petkau G.; Siracusa F.; Zimmermann J.; Zuegel F.; Kuehl A.A.; Lehmann K.; Schimmelpfennig S.; Weber M.; Haftmann C.; Riedel R.; Bardua M.; Heinz G.A.; Tran C.L.; Hoyer B.F.; Hiepe F.; Herzog S.; Wittmann J.; Rajewsky N.; Melchers F.G.; Chang H.D.; Radbruch A.; Mashreghi M.F.
Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo
Journal of Autoimmunity : (2017-12-01)



Backofen R.; Engelhardt J.; Erxleben A.; Fallmann J.; Gruening B.; Ohler U.; Rajewsky N.; Stadler P.F.
RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation
Journal of Biotechnology 261: 76-84 (2017-11-10)



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



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.; Doelken L.; Graesser F.; Landthaler M.
Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection
Genome Biology 18 (1): 209 (2017-10-31)



Karaiskos N.; Wahle P.; Alles J.; Boltengagen A.; Ayoub S.; Kipar C.; Kocks C.; Rajewsky N.; Zinzen R.P.
The Drosophila embryo at single-cell transcriptome resolution
Science 358 (6360): 194-199 (2017-10-13)



Piwecka M.; Glazar P.; Hernandez-Miranda L.R.; Memczak S.; Wolf S.A.; Rybak-Wolf A.; Filipchyk A.; Klironomos F.; Cerda Jara C.A.; Fenske P.; Trimbuch T.; Zywitza V.; Plass M.; Schreyer L.; Ayoub S.; Kocks C.; Kuehn R.; Rosenmund C.; Birchmeier C.; Rajewsky N.
Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function
Science 357 (6357): eaam8526 (2017-09-22)



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.; Mueller T.; Woehler A.; Birchmeier C.; Merino E.; Rajewsky N.; Ohler U.; Mazzoni E.O.; Selbach M.; Akalin A.; Chekulaeva M.
RNA localization is a key determinant of neurite-enriched proteome
Nature Communications 8 (1): 583 (2017-09-19)



Uyar B.; Yusuf D.; Wurmus R.; Rajewsky N.; Ohler U.; Akalin A.
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Nucleic Acids Research 45 (10): e91 (2017-06-02)



Alles J.; Karaiskos N.; Praktiknjo S.D.; Grosswendt S.; Wahle P.; Ruffault P.L.; Ayoub S.; Schreyer L.; Boltengagen A.; Birchmeier C.; Zinzen R.; Kocks C.; Rajewsky N.
Cell fixation and preservation for droplet-based single-cell transcriptomics
BMC Biology 15 (1): 44 (2017-05-19)



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.
Translation of circRNAs
Molecular Cell 66 (1): 9-21.e7 (2017-04-06)



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.
Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis
Molecular Cell 66 (1): 22-37.e9 (2017-04-06)



2016

Durek P.; Nordstroem K.; Gasparoni G.; Salhab A.; Kressler C.; de Almeida M.; Bassler K.; Ulas T.; Schmidt F.; Xiong J.; Glazar P.; Klironomos F.; Sinha A.; Kinkley S.; Yang X.; Arrigoni L.; Amirabad A..; Ardakani F.B.; Feuerbach L.; Gorka O.; Ebert P.; Mueller F.; Li N.; Frischbutter S.; Schlickeiser S.; Cendon C.; Froehler S.; Felder B.; Gasparoni N.; Imbusch C.D.; Hutter B.; Zipprich G.; Tauchmann Y.; Reinke S.; Wassilew G.; Hoffmann U.; Richter A.S.; Sieverling L.; Chang H.D.; Syrbe U.; Kalus U.; Eils J.; Brors B.; Manke T.; Ruland J.; Lengauer T.; Rajewsky N.; Chen W.; Dong J.; Sawitzki B.; Chung H.R.; Rosenstiel P.; Schulz M.H.; Schultze J.L.; Radbruch A.; Walter J.; Hamann A.; Polansky J.K.
Epigenomic profiling of human CD4+ T cells supports a linear differentiation model and highlights molecular regulators of memory development
Immunity 45 (5): 1148-1161 (2016-11-15)



Solana J.; Irimia M.; Ayoub S.; Orejuela M.R.; Zywitza V.; Jens M.; Tapial J.; Ray D.; Morris Q.D.; Hughes T.R.; Blencowe B.J.; Rajewsky N.
Conserved functional antagonism of CELF 1 and MBNL proteins controls stem cell-specific alternative splicing in planarians
eLife 5: e16797 (2016-08-09)



Wallner S.; Schroeder C.; Leitao E.; Berulava T.; Haak C.; Beisser D.; Rahmann S.; Richter A.S.; Manke T.; Boenisch U.; Arrigoni L.; Froehler S.; Klironomos F.; Chen W.; Rajewsky N.; Mueller F.; Ebert P.; Lengauer T.; Barann M.; Rosenstiel P.; Gasparoni G.; Nordstroem K.; Walter J.; Brors B.; Zipprich G.; Felder B.; Klein-Hitpass L.; Attenberger C.; Schmitz G.; Horsthemke B.
Epigenetic dynamics of monocyte-to-macrophage differentiation
Epigenetics & Chromatin 9: 33 (2016-07-29)



Hasler D.; Lehmann G.; Murakawa Y.; Klironomos F.; Jakob L.; Graesser F.A.; Rajewsky N.; Landthaler M.; Meister G.
The Lupus autoantigen La prevents Mis-channeling of tRNA fragments into the human microRNA pathway
Molecular Cell 63 (1): 110-124 (2016-07-07)



2015

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



Mackowiak S.D.; Zauber H.; Bielow C.; Thiel D.; Kutz K.; Calviello L.; Mastrobuoni G.; Rajewsky N.; Kempa S.; Selbach M.; Obermayer B.
Extensive identification and analysis of conserved small ORFs in animals
Genome Biology 16: 179 (2015-09-14)



Rybak-Wolf A.; Stottmeister C.; Glazar P.; Jens M.; Pino N.; Giusti S.; Hanan M.; Behm M.; Bartok O.; Ashwal-Fluss R.; Herzog M.; Schreyer L.; Papavasileiou P.; Ivanov A.; Oehman M.; Refojo D.; Kadener S.; Rajewsky N.
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed
Molecular Cell 58 (5): 870-885 (2015-06-04)



Schafer S.; Adami E.; Heinig M.; Costa Rodrigues K.E.; Kreuchwig F.; Silhavy J.; van Heesch S.; Simaite D.; Rajewsky N.; Cuppen E.; Pravenec M.; Vingron M.; Cook S.A.; Hubner N.
Translational regulation shapes the molecular landscape of complex disease phenotypes
Nature Communications 6: 7200 (2015-05-26)



Jia S.; Ivanov A.; Blasevic D.; Mueller T.; Purfuerst B.; Sun W.; Chen W.; Poy M.N.; Rajewsky N.; Birchmeier C.
Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic {beta}-cell function
EMBO Journal 34 (10): 1417-1433 (2015-05-12)



Haftmann C.; Stittrich A.B.; Zimmermann J.; Fang Z.; Hradilkova K.; Bardua M.; Westendorf K.; Heinz G.A.; Riedel R.; Siede J.; Lehmann K.; Weinberger E.E.; Zimmel D.; Lauer U.; Haeupl T.; Sieper J.; Backhaus M.; Neumann C.; Hoffmann U.; Porstner M.; Chen W.; Gruen J.R.; Baumgrass R.; Matz M.; Loehning M.; Scheffold A.; Wittmann J.; Chang H.D.; Rajewsky N.; Jaeck H.M.; Radbruch A.; Mashreghi M.F.
miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim
European Journal of Immunology 45 (4): 1192-1205 (2015-04)



Blevins R.; Bruno L.; Carroll T.; Elliott J.; Marcais A.; Loh C.; Hertweck A.; Krek A.; Rajewsky N.; Chen C.Z.; Fisher A.G.; Merkenschlager M.
microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes
PLoS Genetics 11 (2): e1005020 (2015-02-25)



Jens M.; Rajewsky N.
Competition between target sites of regulators shapes post-transcriptional gene regulation
Nature Reviews Genetics 16 (2): 113-126 (2015-02)



Blin K.; Dieterich C.; Wurmus R.; Rajewsky N.; Landthaler M.; Akalin A.
DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
Nucleic Acids Research 43 (Database issue): D160-D167 (2015-01-28)



Ivanov A.; Memczak S.; Wyler E.; Torti F.; Porath H.T.; Orejuela M.R.; Piechotta M.; Levanon E.Y.; Landthaler M.; Dieterich C.; Rajewsky N.
Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals
Cell Reports 10 (2): 170-177 (2015-01-13)



2014

Ost A.; Lempradl A.; Casas E.; Weigert M.; Tiko T.; Deniz M.; Pantano L.; Boenisch U.; Itskov P.M.; Stoeckius M.; Ruf M.; Rajewsky N.; Reuter G.; Iovino N.; Ribeiro C.; Alenius M.; Heyne S.; Vavouri T.; Pospisilik J.A.
Paternal diet defines offspring chromatin state and intergenerational obesity
Cell 159 (6): 1352-1364 (2014-12-04)



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



Maaskola J.; Rajewsky N.
Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models
Nucleic Acids Research 42 (21): 12995-13011 (2014-12-01)



Rybak-Wolf A.; Jens M.; Murakawa Y.; Herzog M.; Landthaler M.; Rajewsky N.
A variety of dicer substrates in human and C. elegans
Cell 159 (5): 1153-1167 (2014-11-20)



Glazar P.; Papavasileiou P.; Rajewsky N.
circBase: a database for circular RNAs
RNA 20 (11): 1666-1670 (2014-11)



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



Ashwal-Fluss R.; Meyer M.; Pamudurti N.R.; Ivanov A.; Bartok O.; Hanan M.; Evantal N.; Memczak S.; Rajewsky N.; Kadener S.
circRNA biogenesis competes with pre-mRNA splicing
Molecular Cell 56 (1): 55-66 (2014-10-02)



Stoeckius M.; Gruen D.; Rajewsky N.
Paternal RNA contributions in the Caenorhabditis elegans zygote
EMBO Journal 33 (16): 1740-1750 (2014-08-18)



Stoeckius M.; Gruen D.; Kirchner M.; Ayoub S.; Torti F.; Piano F.; Herzog M.; Selbach M.; Rajewsky N.
Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism
EMBO Journal 33 (16): 1751-1766 (2014-08-18)



Maatz H.; Jens M.; Liss M.; Schafer S.; Heinig M.; Kirchner M.; Adami E.; Rintisch C.; Dauksaite V.; Radke M.H.; Selbach M.; Barton P.J.R.; Cook S.A.; Rajewsky N.; Gotthardt M.; Landthaler M.; Hubner N.
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing
Journal of Clinical Investigation 124 (8): 3419-3430 (2014-08-01)



Grosswendt S.; Filipchyk A.; Manzano M.; Klironomos F.; Schilling M.; Herzog M.; Gottwein E.; Rajewsky N.
Unambiguous identification of miRNA:target site interactions by different types of ligation reactions
Molecular Cell 54 (6): 1042-1054 (2014-06-19)



Bazzini A.A.; Johnstone T.G.; Christiano R.; Mackowiak S.D.; Obermayer B.; Fleming E.S.; Vejnar C.E.; Lee M.T.; Rajewsky N.; Walther T.C.; Giraldez A.J.
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
EMBO Journal 33 (9): 981-993 (2014-05-02)



Gruen D.; Kirchner M.; Thierfelder N.; Stoeckius M.; Selbach M.; Rajewsky N.
Conservation of mRNA and protein expression during development of C. elegans
Cell Reports 6 (3): 565-577 (2014-02-13)



2013

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



Hao B.; Zhang C.; Li Y.; Li H.; Wei L.; Kanehisa M.; Lai L.; Chen R.; Rajewsky N.; Zhang M.Q.; Han J.; Jiang R.; Zhang X.; Li Y.
Advanced topics in bioinformatics and computational biology
Basics of Bioinformatics : 369-395 (2013-07-01)



Graf R.; Munschauer M.; Mastrobuoni G.; Mayr F.; Heinemann U.; Kempa S.; Rajewsky N.; Landthaler M.
Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation
RNA Biology 10 (7): 1146-1159 (2013-07-01)



Memczak S.; Jens M.; Elefsinioti A.; Torti F.; Krueger J.; Rybak A.; Maier L.; Mackowiak S.D.; Gregersen L.H.; Munschauer M.; Loewer A.; Ziebold U.; Landthaler M.; Kocks C.; le Noble F.; Rajewsky N.
Circular RNAs are a large class of animal RNAs with regulatory potency
Nature 495 (7441): 333-338 (2013-03-21)



2012

Onal P.; Gruen D.; Adamidi C.; Rybak A.; Solana J.; Mastrobuoni G.; Wang Y.; Rahn H.P.; Chen W.; Kempa S.; Ziebold U.; Rajewsky N.
Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells
EMBO Journal 31 (12): 2755-2769 (2012-04-27)



von Eyss B.; Maaskola J.; Memczak S.; Moellmann K.; Schuetz A.; Loddenkemper C.; Tanh M.D.; Otto A.; Muegge K.; Heinemann U.; Rajewsky N.; Ziebold U.
The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation
EMBO Journal 31 (4): 972-985 (2012-02-15)



Song J.L.; Stoeckius M.; Maaskola J.; Friedlaender M.; Stepicheva N.; Juliano C.; Lebedeva S.; Thompson W.; Rajewsky N.; Wessel G.M.
Select microRNAs are essential for early development in the sea urchin
Developmental Biology 362 (1): 104-113 (2012-02-01)



Anders G.; Mackowiak S.D.; Jens M.; Maaskola J.; Kuntzagk A.; Rajewsky N.; Landthaler M.; Dieterich C.
doRiNA: a database of RNA interactions in post-transcriptional regulation
Nucleic Acids Research 40 (1): D180-D186 (2012-01)



Friedlaender M.R.; Mackowiak S.D.; Li N.; Chen W.; Rajewsky N.
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Nucleic Acids Research 40 (1): 37-52 (2012-01-01)



2011

Jungkamp A.C.; Stoeckius M.; Mecenas D.; Gruen D.; Mastrobuoni G.; Kempa S.; Rajewsky N.
In vivo and transcriptome-wide identification of RNA binding protein target sites
Molecular Cell 44 (5): 828-840 (2011-12-09)



Lebedeva S.; Jens M.; Theil K.; Schwanhaeusser B.; Selbach M.; Landthaler M.; Rajewsky N.
Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR
Molecular Cell 43 (3): 340-352 (2011-08-05)



Adamidi C.; Wang Y.; Gruen D.; Mastrobuoni G.; You X.; Tolle D.; Dodt M.; Mackowiak S.D.; Gogol-Doering A.; Oenal P.; Rybak A.; Ross E.; Alvarado A.S.; Kempa S.; Dieterich C.; Rajewsky N.; Chen W.
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
Genome Research 21 (7): 1193-1200 (2011-07)



Rajewsky N.
microRNAs and the Operon paper
Journal of Molecular Biology 409 (1): 70-75 (2011-05-27)



Fang Z.; Rajewsky N.
The impact of miRNA target sites in coding sequences and in 3'UTRs
PLoS ONE 6 (3): e18067 (2011-03-22)



2010

Gerstein M.B.; Lu Z.J.; Van Nostrand E.L.; Cheng C.; Arshinoff B.I.; Liu T.; Yip K.Y.; Robilotto R.; Rechtsteiner A.; Ikegami K.; Alves P.; Chateigner A.; Perry M.; Morris M.; Auerbach R.K.; Feng X.; Leng J.; Vielle A.; Niu W.; Rhrissorrakrai K.; Agarwal A.; Alexander R.P.; Barber G.; Brdlik C.M.; Brennan J.; Brouillet J.J.; Carr A.; Cheung M.S.; Clawson H.; Contrino S.; Dannenberg L.O.; Dernburg A.F.; Desai A.; Dick L.; Dose A.C.; Du J.; Egelhofer T.; Ercan S.; Euskirchen G.; Ewing B.; Feingold E.A.; Gassmann R.; Good P.J.; Green P.; Gullier F.; Gutwein M.; Guyer M.S.; Habegger L.; Han T.; Henikoff J.G.; Henz S.R.; Hinrichs A.; Holster H.; Hyman T.; Iniguez A.L.; Janette J.; Jensen M.; Kato M.; Kent W.J.; Kephart E.; Khivansara V.; Khurana E.; Kim J.K.; Kolasinska-Zwierz P.; Lai E.C.; Latorre I.; Leahey A.; Lewis S.; Lloyd P.; Lochovsky L.; Lowdon R.F.; Lubling Y.; Lyne R.; Maccoss M.; Mackowiak S.D.; Mangone M.; McKay S.; Mecenas D.; Merrihew G.; Miller D.M.; Muroyama A.; Murray J.I.; Ooi S.L.; Pham H.; Phippen T.; Preston E.A.; Rajewsky N.; Raetsch G.; Rosenbaum H.; Rozowsky J.; Rutherford K.; Ruzanov P.; Sarov M.; Sasidharan R.; Sboner A.; Scheid P.; Segal E.; Shin H.; Shou C.; Slack F.J.; Slightam C.; Smith R.; Spencer W.C.; Stinson E.O.; Taing S.; Takasaki T.; Vafeados D.; Voronina K.; Wang G.; Washington N.L.; Whittle C.M.; Wu B.; Yan K.K.; Zeller G.; Zha Z.; Zhong M.; Zhou X.; Ahringer J.; Strome S.; Gunsalus K.C.; Micklem G.; Liu X.S.; Reinke V.; Kim S.K.; Hillier L.W.; Henikoff S.; Piano F.; Snyder M.; Stein L.; Lieb J.D.; Waterston R.H.
Integrative analysis of the caenorhabditis elegans genome by the modENCODE project
Science 330 (6012): 1775-1787 (2010-12-24)



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



Mangone M.; Manoharan A.P.; Thierry-Mieg D.; Thierry-Mieg J.; Han T.; Mackowiak S.; Mis E.; Zegar C.; Gutwein M.R.; Khivansara V.; Attie O.; Chen K.; Salehi-Ashtiani K.; Vidal M.; Harkins T.T.; Bouffard P.; Suzuki Y.; Sugano S.; Kohara Y.; Rajewsky N.; Piano F.; Gunsalus K.C.; Kim J.K.
The Landscape of C. elegans 3'UTRs
Science 329 (5990): 432-435 (2010-07-23)



Sharbati S.; Friedlaender M.R.; Sharbati J.; Hoeke L.; Chen W.; Keller A.; Stahler P.F.; Rajewsky N.; Einspanier R.
Deciphering the porcine intestinal microRNA transcriptome
BMC Genomics 11 (1): 275 (2010-04-30)



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



2009

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



Friedlaender M.R.; Adamidi C.; Han T.; Lebedeva S.; Isenbarger T.A.; Hirst M.; Marra M.; Nusbaum C.; Lee W.L.; Jenkin J.C.; Alvarado A.S.; Kim J.K.; Rajewsky N.
High-resolution profiling and discovery of planarian small RNAs
Proceedings of the National Academy of Sciences of the United States of America 106 (28): 11546-11551 (2009-07-14)



Chen K.; Maaskola J.; Siegal M.L.; Rajewsky N.
Reexamining microRNA site accessibility in Drosophila: a population genomics study
PLoS ONE 4 (5): e5681 (2009-05-25)



2008

Ender C.; Krek A.; Friedlaender M.R.; Beitzinger M.; Weinmann L.; Chen W.; Pfeffer S.; Rajewsky N.; Meister G.
A human snoRNA with microRNA-like functions
Molecular Cell 32 (4): 519-528 (2008-11-21)



Selbach M.; Schwanhaeusser B.; Thierfelder N.; Fang Z.; Khanin R.; Rajewsky N.
Widespread changes in protein synthesis induced by microRNAs
Nature 455 (7209): 58-63 (2008-09-04)



Friedlaender M.R.; Chen W.; Adamidi C.; Maaskola J.; Einspanier R.; Knespel S.; Rajewsky N.
Discovering microRNAs from deep sequencing data using miRDeep
Nature Biotechnology 26 (4): 407-415 (2008-04)



Koralov S.B.; Muljo S.A.; Galler G.R.; Krek A.; Chakraborty T.; Kanellopoulou C.; Jensen K.; Cobb B.S.; Merkenschlager M.; Rajewsky N.; Rajewsky K.
Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage
Cell 132 (5): 860-874 (2008-03-07)



2007

Xiao C.; Calado D.P.; Galler G.; Thai T.H.; Patterson H.C.; Wang J.; Rajewsky N.; Bender T.P.; Rajewsky K.
MiR-150 Controls B Cell Differentiation by Targeting the Transcription Factor c-Myb
Cell 131 (1): 146-159 (2007-10-05)



Thai T.H.; Calado D.P.; Casola S.; Ansel K.M.; Xiao C.; Xue Y.; Murphy A.; Frendewey D.; Valenzuela D.; Kutok J.L.; Schmidt-Supprian M.; Rajewsky N.; Yancopoulos G.; Rao A.; Rajewsky K.
Regulation of the germinal center response by microRNA-155
Science 316 (5824): 604-608 (2007-04-27)



Chen K.; Rajewsky N.
The evolution of gene regulation by transcription factors and microRNAs
Nature Reviews Genetics 8 (2): 93-103 (2007-02)



Gruen D.; Rajewsky N.
Computational prediction of microRNA targets in vertebrates, fruitflies and nematodes
MicroRNAs: From Basic Science to Disease Biology : 172-186 (2007)



2006

Chen K.; Rajewsky N.
Natural selection on human microRNA binding sites inferred from SNP data
Nature Genetics 38 (12): 1452-1456 (2006-12-01)



Rajewsky N.
L(ou)sy miRNA targets?
Nature Structural & Molecular Biology 13 (9): 754-755 (2006-09)



Rajewsky N.
microRNA target predictions in animals
Nature Genetics 38 (Suppl.): S8-S13 (2006-06)



Lall S.; Grun D.; Krek A.; Chen K.; Wang Y.L.; Dewey C.N.; Sood P.; Colombo T.; Bray N.; Macmenamin P.; Kao H.L.; Gunsalus K.C.; Pachter L.; Piano F.; Rajewsky N.
A genome-wide map of conserved microRNA targets in C. elegans
Current Biology 16 (5): 460-471 (2006-03-07)



Sood P.; Krek A.; Zavolan M.; Macino G.; Rajewsky N.
Cell type specific signatures of microRNAs on target mRNA expression
Proceedings of the National Academy of Sciences of the United States of America 103 (8): 2746-2751 (2006-02-21)



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



2005

Krutzfeldt J.; Rajewsky N.; Braich R.; Rajeev K.G.; Tuschl T.; Manoharan M.; Stoffel M.
Silencing of microRNAs in vivo with 'antagomirs'
Nature 438 (7068): 685-689 (2005-12-01)



Gruen D.; Wang Y.L.; Langenberger D.; Gunsalus K.C.; Rajewsky N.
microRNA target predictions across seven Drosophila species and comparison to mammalian targets
PLoS Computational Biology 1 (1): e13 (2005-06)



Krek A.; Gruen D.; Poy M.N.; Wolf R.; Rosenberg L.; Epstein E.J.; MacMenamin P.; da Piedade I.; Gunsalus K.C.; Stoffel M.; Rajewsky N.
Combinatorial microRNA target predictions
Nature Genetics 37 (5): 495-500 (2005-05)



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



2004

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



Schroeder M.D.; Pearce M.; Fak J.; Fan H.; Unnerstall U.; Emberly E.; Rajewsky N.; Siggia E.D.; Gaul U.
Transcriptional control in the segmentation gene network of Drosophila
PLoS Biology 2 (9): E271 (2004-09)



Kraus M.; Alimzhanov M.B.; Rajewsky N.; Rajewsky K.
Survival of resting mature B lymphocytes depends on BCR signaling via the Igalpha/beta heterodimer
Cell 117 (6): 787-800 (2004-06-11)



Yannoutsos N.; Barreto V.; Misulovin Z.; Gazumyan A.; Yu W.; Rajewsky N.; Peixoto B.R.; Eisenreich T.; Nussenzweig M.C.
A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer
Nature Immunology 5 (4): 443-450 (2004-04)



Rajewsky N.; Socci N.D.
Computational identification of microRNA targets
Developmental Biology 267 (2): 529-535 (2004-03-15)



2003

Emberly E.; Rajewsky N.; Siggia E.D.
Conservation of regulatory elements between two species of Drosophila
BMC Bioinformatics 4: 57 (2003-11-20)



Yang E.; van Nimwegen E.; Zavolan M.; Rajewsky N.; Schroeder M.; Magnasco M.; Darnell J.E.
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes
Genome Research 13 (8): 1863-1872 (2003-08)



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



2002

Rajewsky N.; Vergassola M.; Gaul U.; Siggia E.D.
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
BMC Bioinformatics 3: 30 (2002-10-24)



van Nimwegen E.; Zavolan M.; Rajewsky N.; Siggia E.D.
Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics
Proceedings of the National Academy of Sciences of the United States of America 99 (11): 7323-7328 (2002-05-28)



Rajewsky N.; Socci N.D.; Zapotocky M.; Siggia E.D.
The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
Genome Research 12 (2): 298-308 (2002-02)



2001

Claridge-Chang A.; Wijnen H.; Naef F.; Boothroyd C.; Rajewsky N.; Young M.W.
Circadian regulation of gene expression systems in the Drosophila head
Neuron 32 (4): 657-671 (2001-11-20)



2000

Rajewsky N.; Sasamoto T.; Speer E.R.
Spatial particle condensation for an exclusion process on a ring
Physica A: Statistical Mechanics and its Applications 279 (1-4): 123-142 (2000-05-01)



Luebeck S.; Rajewsky N.; Wolf D.E.
A deterministic sandpile automaton revisited
European Physical Journal B 13 (4): 715-721 (2000-02)



1999

Mallick K.; Mallick S.; Rajewsky N.
Exact solution of an exclusion process with three classes of particles and vacancies
Journal of Physics A 32 (48): 8399-8410 (1999-12-03)



Evans M.R.; Rajewsky N.; Speer E.R.
Exact solution of a cellular automaton for traffic
Journal of Statistical Physics 95 (1-2): 45-96 (1999-04)



1998

Rajewsky N.
The asymmetric exclusion model with different types of update
Traffic and Granular Flow '97 : 399-418 (1998-12)



Rajewsky N.; Santen L.; Schadschneider A.; Schreckenberg M.
The asymmetric exclusion process: Comparison of update procedures
Journal of Statistical Physics 92 (1-2): 151-194 (1998-07)



1997

Rajewsky N.; Schreckenberg M.
Exact results for one-dimensional cellular automata with different types of updates
Physica A: Statistical Mechanics and its Applications 245 (1-2): 139-144 (1997-10-15)



1996

Rajewsky N.; Schadschneider A.; Schreckenberg M.
The asymmetric exclusion model with sequential update
Journal of Physics A 29 (12): L305-L309 (1996-06-21)



Rajewsky N.; Santen L.; Schadschneider A.; Schreckenberg M.
The asymmetric exclusion model with time continous and time non-continous update
: (1996)



1995

Rajewsky N.; Schreckenberg M.
A probabilistic cellular-automaton for evolution
Journal de Physique I 5 (9): 1129-1134 (1995-09)



1990

Lehner C.; Rajewsky N.; Wolf D.E.; Kertesz J.
Anomalous roughening in 3-dimensional polynucleation growth
Physica A: Statistical Mechanics and its Applications 164 (1): 81-90 (1990-03-15)



1987

Allen D.; Cumano A.; Dildrop R.; Kocks C.; Rajewsky K.; Rajewsky N.; Roes J.; Sablitzky F.; Siekevitz M.
Timing, genetic requirements and functional consequences of somatic hypermutation during B-cell development
Immunological Reviews 96: 5-22 (1987-04)