Browse by Research Team

Advanced Materials

Curvature in biological systems: its quantification, emergence and implications across the scales.
Schamberger, B., Roschger, A., Ziege, R., Anselme, K., Amar, M.B., Bykowski, M., Castro, A.P.G., Cipitria, A., Coles, R., Dimova, R., Eder, M., Ehrig, S., Escudero, L.M., Evans, M.E., Fernandes, P.R., Fratzl, P., Geris, L., Gierlinger, N., Hannezo, E., Iglič, A., Kirkensgaard, J.J.K., Kollmannsberger, P., Kowalewska, Ł., Kurniawan, N.A., Papantoniou, I., Pieuchot, L., Pires, T.H.V., Renner, L., Sageman-Furnas, A., Schröder-Turk, G.E., Sengupta, A., Sharma, V.R., Tagua, A., Tomba, C., Trepat, X., Waters, S.L., Yeo, E., Bidan, C.M. and Dunlop, J.W.C.
Advanced Materials 35 (13): e2206110. 15 March 2023

Annual Review of Pathology : Mechanisms of Disease

Challenges and opportunities in the clinical translation of high-resolution spatial transcriptomics.
Pentimalli, T.M., Karaiskos, N. and Rajewsky, N.
Annual Review of Pathology : Mechanisms of Disease 30 October 2024 (In Press)

BMC Bioinformatics

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

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

BMC Biology

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Cell fixation and preservation for droplet-based single-cell transcriptomics.
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. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

BMC Genomics

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

Basics of Bioinformatics: Lecture Notes of the Graduate Summer School on Bioinformatics of China

Advanced topics in bioinformatics and computational biology.
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. and Li, Y.
In: Basics of Bioinformatics. Springer, Heidelberg, 369-395. ISBN 978-3-642-38950-4 1 July 2013

Biology of Sex Differences

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.
Al-Diab, O., Sünkel, C., Blanc, E., Catar, R.A., Ashraf, M.I., Zhao, H., Wang, P., Rinschen, M.M., Fritsche-Guenther, R., Grahammer, F., Bachmann, S., Beule, D., Kirwan, J.A., Rajewsky, N., Huber, T.B., Gürgen, D. and Kusch, A.
Biology of Sex Differences 15 (1): 72. 15 September 2024

Biosystems

SetQuence & SetOmic: deep set transformers for whole genome and exome tumour analysis.
Jurenaite, N., León-Periñán, D., Donath, V., Torge, S. and Jäkel, R.
Biosystems 235 : 105095. January 2024

Cancers

Gene expression signatures of a preclinical mouse model during colorectal cancer progression under low-dose metronomic chemotherapy.
Ho-Xuan, H., Lehmann, G., Glazar, P., Gypas, F., Eichner, N., Heizler, K., Schlitt, H.J., Zavolan, M., Rajewsky, N., Meister, G. and Hackl, C.
Cancers 13 (1): 49. 2021

Cell

Open-ST: high-resolution spatial transcriptomics in 3D.
Schott, M., León-Periñán, D., Splendiani, E., Strenger, L., Licha, J.R., Pentimalli, T.M., Schallenberg, S., Alles, J., Samut Tagliaferro, S., Boltengagen, A., Ehrig, S., Abbiati, S., Dommerich, S., Pagani, M., Ferretti, E., Macino, G., Karaiskos, N. and Rajewsky, N.
Cell 187 (15): 3953-3972.e26. 25 July 2024

Sites of transcription initiation drive mRNA isoform selection.
Alfonso-Gonzalez, C., Legnini, I., Holec, S., Arrigoni, L., Ozbulut, H.C., Mateos, F., Koppstein, D., Rybak-Wolf, A., Bönisch, U., Rajewsky, N. and Hilgers, V.
Cell 186 (11): 2438-2455. 25 May 2023

The translational landscape of the human heart.
van Heesch, S., Witte, F., Schneider-Lunitz, V., Schulz, J.F., Adami, E., Faber, A., Kirchner, M., Maatz, H., Blachut, S., Sandmann, C.L., Kanda, M., Worth, C.L., Schafer, S., Calviello, L., Merriott, R., Patone, G., Hummel, O., Wyler, E., Obermayer, B., Mücke, M., Lindberg, E.L., Trnka, F., Memczak, S., Schilling, M., Felkin, L.E., Barton, P.J.R., Quaife, N.M., Vanezis, K., Diecke, S., Mukai, M., Mah, N., Oh, S.J., Kurtz, A., Schramm, C., Schwinge, D., Sebode, M., Harakalova, M., Asselbergs, F.W., Vink, A., de Weger, R.A., Viswanathan, S., Widjaja, A.A., Gärtner-Rommel, A., Milting, H., Dos Remedios, C., Knosalla, C., Mertins, P., Landthaler, M., Vingron, M., Linke, W.A., Seidman, J.G., Seidman, C.E., Rajewsky, N., Ohler, U., Cook, S.A. and Hubner, N.
Cell 178 (1): 242-260. 27 June 2019

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

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, P.M., Stoeckius, M., Ruf, M., Rajewsky, N., Reuter, G., Iovino, N., Ribeiro, C., Alenius, M., Heyne, S., Vavouri, T. and Pospisilik, J.A.
Cell 159 (6): 1352-1364. 4 December 2014

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

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

MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb.
Xiao, C., Calado, D.P., Galler, G., Thai, T.H., Patterson, H.C., Wang, J., Rajewsky, N., Bender, T.P. and Rajewsky, K.
Cell 131 (1): 146-159. 5 October 2007

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

Cell Reports

ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling.
Scoyni, F., Sitnikova, V., Giudice, L., Korhonen, P., Trevisan, D.M., Hernandez de Sande, A., Gomez-Budia, M., Giniatullina, R., Ugidos, I.F., Dhungana, H., Pistono, C., Korvenlaita, N., Välimäki, N.N., Kangas, S.M., Hiltunen, A.E., Gribchenko, E., Kaikkonen-Määttä, M.U., Koistinaho, J., Ylä-Herttuala, S., Hinttala, R., Venø, M.T., Su, J., Stoffel, M., Schaefer, A., Rajewsky, N., Kjems, J., LaPierre, M.P., Piwecka, M., Jolkkonen, J., Giniatullin, R., Hansen, T.B. and Malm, T.
Cell Reports 43 (3): 113862. 26 March 2024

Mechanisms of IRF2BPL-related disorders and identification of a potential therapeutic strategy.
Sinha Ray, S., Dutta, D., Dennys, C., Powers, S., Roussel, F., Lisowski, P., Glažar, P., Zhang, X., Biswas, P., Caporale, J.R., Rajewsky, N., Bickle, M., Wein, N., Bellen, H.J., Likhite, S., Marcogliese, P.C. and Meyer, K.C.
Cell Reports 41 (10): 111751. 6 December 2022

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J., Uyar, B., Herzog, M., Theil, K., Glažar, P., Akalin, A. and Rajewsky, N.
Cell Reports 35 (2): 108988. 13 April 2021

A highly conserved circular RNA is required to keep neural cells in a progenitor state in the mammalian brain.
Suenkel, C., Cavalli, D., Massalini, S., Calegari, F. and Rajewsky, N.
Cell Reports 30 (7): 2170-2179. 18 February 2020

Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis.
Zywitza, V., Misios, A., Bunatyan, L., Willnow, T.E. and Rajewsky, N.
Cell Reports 25 (9): 2457-2469. 27 November 2018

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

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

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

Cell Research

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

Clinical Infectious Diseases

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M.P., Thielen, A., Kolbe-Busch, S., Göbels, K., Zotz, R., Pfeffer, K., Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

Cold Spring Harbor Perspectives in Biology

Roles of long noncoding RNAs and circular RNAs in translation.
Chekulaeva, M. and Rajewsky, N.
Cold Spring Harbor Perspectives in Biology 11 (6): a032680. 3 June 2019

Cold Spring Harbor Symposia on Quantitative Biology

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

Current Biology

A genome-wide map of conserved microRNA targets in C. elegans.
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. and Rajewsky, N.
Current Biology 16 (5): 460-471. 7 March 2006

Current Protocols in Bioinformatics

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

Developmental Biology

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

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

Developmental Cell

Spatiotemporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline.
Diag, A., Schilling, M., Klironomos, F., Ayoub, S. and Rajewsky, N.
Developmental Cell 47 (6): 785-800. 17 December 2018

EMBO Journal

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, M.N., Rajewsky, N. and Birchmeier, C.
EMBO Journal 34 (10): 1417-1433. 12 May 2015

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. and Rajewsky, N.
EMBO Journal 33 (16): 1751-1766. 18 August 2014

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

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.
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. and Giraldez, A.J.
EMBO Journal 33 (9): 981-993. 2 May 2014

Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells.
Onal, P., Gruen, D., Adamidi, C., Rybak, A., Solana, J., Mastrobuoni, G., Wang, Y., Rahn, H.P., Chen, W., Kempa, S., 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., Maaskola, J., Memczak, S., Möllmann, K., Schuetz, A., Loddenkemper, C., Tanh, M.D., Otto, A., Muegge, K., Heinemann, U., Rajewsky, N. and Ziebold, U.
EMBO Journal 31 (4): 972-985. 15 February 2012

EMBO Reports

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A., Kim, S.J., Thomas, G., Farsi, Z., Zolotarov, G., Dube, G., Deter, A., Bahry, E., Georgii, E., Woehler, A., Piwecka, M. and Rajewsky, N.
EMBO Reports 25 (7): 3039. July 2024

Epigenetics

Epigenetic targeting of transposon relics: beating the dead horses of the genome?
Sammarco, I., Pieters, J., Salony, S., Toman, I., Zolotarov, G. and Lafon Placette, C.
Epigenetics 17 (11): 1331-1344. November 2022

Epigenetics & Chromatin

Epigenetic dynamics of monocyte-to-macrophage differentiation.
Wallner, S., Schroeder, C., Leitão, E., Berulava, T., Haak, C., Beißer, D., Rahmann, S., Richter, A.S., 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. and Horsthemke, B.
Epigenetics & Chromatin 9 : 33. 29 July 2016

European Journal of Immunology

miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim.
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., Häupl, T., Sieper, J., Backhaus, M., Neumann, C., Hoffmann, U., Porstner, M., Chen, W., Grün, J.R., Baumgrass, R., Matz, M., Löhning, M., Scheffold, A., Wittmann, J., Chang, H.D., Rajewsky, N., Jäck, H.M., Radbruch, A. and Mashreghi, M.F.
European Journal of Immunology 45 (4): 1192-1205. April 2015

European Physical Journal B

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

Eurosurveillance

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart, Torsten, Belhaj, S., Tawalbeh, E., Nagels, D., Fröhlich, Y., Finzer, P., Ciruela, P., Sabrià, A., Herrero, M., Andrés, C., Antón, A., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., Nicolai, J., Stiller, M., Blum, J., Lange, C., Adelmann, C., Schroer, B., Osmers, U., Grice, C., Kirfel, P.P., Jomaa, H., Strelow, D., Hülse, L., Pigulla, M., Kreuzer, P., Tyshaieva, A., Weber, J., Wienemann, T., Kohns Vasconcelos, M., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Scholz, C.J., Jazmati, N., Göbels, K., Zotz, R., Pfeffer, K., Timm, J., Ehlkes, L., Walker, A. and Dilthey, A.T.
Eurosurveillance 27 (43): 2101089. 27 October 2022

EvoDevo

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

Frontiers in Cell and Developmental Biology

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

Frontiers in Human Neuroscience

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

Frontiers in Immunology

Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.
Pulvirenti, F., Giufrè, M., Pentimalli, T.M., Camilli, R., Milito, C., Villa, A., Sculco, E., Cerquetti, M., Pantosti, A. and Quinti, I.
Frontiers in Immunology 15 : 1371118. 30 May 2024

Frontiers in Molecular Neuroscience

Expression of circ_Satb1 is decreased in mesial temporal lobe epilepsy and regulates dendritic spine morphology.
Gomes-Duarte, A., Venø, M.T., de Wit, M., Senthilkumar, K., Broekhoven, M.H., van den Herik, J., Heeres, F.R., van Rossum, D., Rybiczka-Tesulov, M., Legnini, I., van Rijen, P.C., van Eijsden, P., Gosselaar, P.H., Rajewsky, N., Kjems, J., Vangoor, V.R. and Pasterkamp, R.J.
Frontiers in Molecular Neuroscience 15 : 832133. 3 March 2022

Genes

Viral infection identifies micropeptides differentially regulated in smORF-containing lncRNAs.
Razooky, B.S., Obermayer, B., O'May, J.B. and Tarakhovsky, A.
Genes 8 (8): 206. 21 August 2017

Genes & Development

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat.
Labi, V., Peng, S., Klironomos, F., Munschauer, M., Kastelic, N., Chakraborty, T., Schoeler, K., Derudder, E., Martella, M., Mastrobuoni, G., Hernandez-Miranda, L.R., Lahmann, I., Kocks, C., Birchmeier, C., Kempa, S., Quintanilla-Martinez de Fend, L., Landthaler, M., Rajewsky, N. and Rajewsky, K.
Genes & Development 33 : 23-24. 7 November 2019

Genome Biology

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A., Hamey, F.K., Plass, M., Solana, J., Dahlin, J.S., Göttgens, B., Rajewsky, N., Simon, L. and Theis, F.J.
Genome Biology 20 (1): 59. 19 March 2019

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. and Blandino, G.
Genome Biology 18 (1): 237. 20 December 2017

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. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

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

MicroRNA profiling of the murine hematopoietic system.
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. and Kosik, K.S.
Genome Biology 6 (8): R71. 2005

Genome Biology and Evolution

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

Genome Medicine

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C., Kocks, C., Leiz, J., Karaiskos, N., Boltengagen, A., Cao, S., Skopnik, C.M., Klocke, J., Hardenberg, J.H., Stockmann, H., Gotthardt, I., Obermayer, B., Haghverdi, L., Wyler, E., Landthaler, M., Bachmann, S., Hocke, A.C., Corman, V., Busch, J., Schneider, W., Himmerkus, N., Bleich, M., Eckardt, K.U., Enghard, P., Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

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

Genome Research

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
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. and Chen, W.
Genome Research 21 (7): 1193-1200. July 2011

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

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

GigaScience

Spacemake: processing and analysis of large-scale spatial transcriptomics data.
Sztanka-Toth, T.R., Jens, M., Karaiskos, N. and Rajewsky, N.
GigaScience 11 : giac064. 19 July 2022

Heliyon

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh, Y., Trautwein, C., Fendel, R., Krickeberg, N., Berezhnoy, G., Bissinger, R., Ossowski, S., Salker, M.S., Casadei, N. and Riess, O.
Heliyon 7 (6): e07147. June 2021

Immunity

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer, B., Knoll, R., Bonaguro, L., ToVinh, M., Raabe, J., Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K.M., Rieke, G.J., Bischoff, J., Monin, M.B., Hoffmeister, C., Schlabe, S., De Domenico, E., Reusch, N., Händler, K., Reynolds, G., Blüthgen, N., Hack, G., Finnemann, C., Nischalke, H.D., Strassburg, C.P., Stephenson, E., Su, Y., Gardner, L., Yuan, D., Chen, D., Goldman, J., Rosenstiel, P., Schmidt, S.V., Latz, E., Hrusovsky, K., Ball, A.J., Johnson, J.M., Koenig, P.A., Schmidt, F.I., Haniffa, M., Heath, J.R., Kümmerer, B.M., Keitel, V., Jensen, B., Stubbemann, P., Kurth, F., Sander, L.E., Sawitzki, B., Aschenbrenner, A.C., Schultze, J.L. and Nattermann, J.
Immunity 54 (11): 2650-2669. 9 November 2021

Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells, and plasmablasts as hallmarks of severe COVID-19.
Bernardes, J.P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J.I., Bordoni, D., Franzenburg, J., Geisen, U., Josephs-Spaulding, J., Köhler, P., Künstner, A., Rosati, E., Aschenbrenner, A.C., Bacher, P., Baran, N., Boysen, T., Brandt, B., Bruse, N., Dörr, J., Dräger, A., Elke, G., Ellinghaus, D., Fischer, J., Forster, M., Franke, A., Franzenburg, S., Frey, N., Friedrichs, A., Fuß, J., Glück, A., Hamm, J., Hinrichsen, F., Hoeppner, M.P., Imm, S., Junker, R., Kaiser, S., Kan, Y.H., Knoll, R., Lange, C., Laue, G., Lier, C., Lindner, M., Marinos, G., Markewitz, R., Nattermann, J., Noth, R., Pickkers, P., Rabe, K.F., Renz, A., Röcken, C., Rupp, J., Schaffarzyk, A., Scheffold, A., Schulte-Schrepping, J., Schunk, D., Skowasch, D., Ulas, T., Wandinger, K.P., Wittig, M., Zimmermann, J., Busch, H., Hoyer, B.F., Kaleta, C., Heyckendorf, J., Kox, M., Rybniker, J., Schreiber, S., Schultze, J.L. and Rosenstiel, P.
Immunity 53 (6): 1296-1314. 15 December 2020

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, A.., Ardakani, F.B., Feuerbach, L., Gorka, O., Ebert, P., Müller, F., Li, N., Frischbutter, S., Schlickeiser, S., Cendon, C., Fröhler, 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. and Polansky, J.K.
Immunity 45 (5): 1148-1161. 15 November 2016

Immunological Reviews

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

International Journal of Genomics

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. and Fulci, V.
International Journal of Genomics 2018 : 1243858. 26 April 2018

Journal de Physique I

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

Journal of Autoimmunity

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, 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. and Mashreghi, M.F.
Journal of Autoimmunity 89 : 41-52. May 2018

Journal of Biotechnology

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. and Stadler, P.F.
Journal of Biotechnology 261 : 76-84. 10 November 2017

Journal of Clinical Investigation

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, M.H., Selbach, M., Barton, P.J.R., Cook, S.A., Rajewsky, N., Gotthardt, M., Landthaler, M. and Hubner, N.
Journal of Clinical Investigation 124 (8): 3419-3430. 1 August 2014

Journal of Immunology

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

Journal of Medical Investigation

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

Journal of Molecular Biology

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

Journal of Molecular Medicine

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

Journal of Neuroscience

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

Journal of Physics A

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

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

Journal of Statistical Physics

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

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

Journal of Visualized Experiments

Generation and downstream analysis of single-cell and single-nuclei transcriptomes in brain organoids.
Wandres, M., Aigner, D., Kastelic, N., Boltengagen, A., Rybak-Wolf, A. and Rajewsky, N.
Journal of Visualized Experiments (205): e66225. 29 March 2024

Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing.
Leiz, J., Hinze, C., Boltengagen, A., Braeuning, C., Kocks, C., Rajewsky, N. and Schmidt-Ott, K.M.
Journal of Visualized Experiments (175): e62901. September 2021

Generation of human brain organoids for mitochondrial disease modeling.
Le, S., Petersilie, L., Inak, G., Menacho-Pando, C., Kafitz, K.W., Rybak-Wolf, A., Rajewsky, N., Rose, C.R. and Prigione, A.
Journal of Visualized Experiments (172): e62756. 21 June 2021

Journal of the American Society of Nephrology

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients.
Hinze, C., Karaiskos, N., Boltengagen, A., Walentin, K., Redo, K., Himmerkus, N., Bleich, M., Potter, S.S., Potter, A.S., Eckardt, K.U., Kocks, C., Rajewsky, N. and Schmidt-Ott, K.M.
Journal of the American Society of Nephrology 32 (2): 291-306. February 2021

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. and Müller, R.U.
Journal of the American Society of Nephrology 29 (8): 2060-2068. August 2018

Kidney International

Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury.
Klocke, J., Kim, S.J., Skopnik, C.M., Hinze, C., Boltengagen, A., Metzke, D., Grothgar, E., Prskalo, L., Wagner, L., Freund, P., Görlich, N., Muench, F., Schmidt-Ott, K.M., Mashreghi, M.F., Kocks, C., Eckardt, K.U., Rajewsky, N. and Enghard, P.
Kidney International 102 (6): 1359-1370. December 2022

Life Science Alliance

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
Tanevski, J., Nguyen, T., Truong, B., Karaiskos, N., Ahsen, M.E., Zhang, X., Shu, C., Xu, K., Liang, X., Hu, Y., Pham, H.V.V., Xiaomei, L., Le, T.D., Tarca, A.L., Bhatti, G., Romero, R., Karathanasis, N., Loher, P., Chen, Y., Ouyang, Z., Mao, D., Zhang, Y., Zand, M., Ruan, J., Hafemeister, C., Qiu, P., Tran, D., Nguyen, T., Gabor, A., Yu, T., Guinney, J., Glaab, E., Krause, R., Banda, P., Stolovitzky, G., Rajewsky, N., Saez-Rodriguez, J. and Meyer, P.
Life Science Alliance 3 (11): e202000867. November 2020

Living machines: a handbook of research in biomimetic and biohybrid systems

Toward living nanomachines.
Mast, C., Möller, F., Kreysing, M., Schink, S., Obermayer, B., Gerland, U. and Braun, D.
In: Living machines: a handbook of research in biomimetics and biohybrid systems. Oxford University Press, Oxford, 380-389. ISBN 9780199674923 2018

Methods in Molecular Biology

Identifying chromosome movement patterns during meiosis using ChroMo.
Pinto-Cruz, J., Correas, M., Mendoza-Madrigal, R., León-Periñán, D. and Fernández-Álvarez, A.
Methods in Molecular Biology 2818 : 271-288. 2024

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

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

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

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

Molecular & Cellular Proteomics

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

Molecular Cell

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. and Bozzoni, I.
Molecular Cell 66 (1): 22-37.e9. 6 April 2017

Translation of circRNAs.
Pamudurti, N.R., 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. and Kadener, S.
Molecular Cell 66 (1): 9-21. 6 April 2017

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, F.A., Rajewsky, N., Landthaler, M. and Meister, G.
Molecular Cell 63 (1): 110-124. 7 July 2016

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. and Rajewsky, N.
Molecular Cell 58 (5): 870-885. 4 June 2015

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

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. and Rajewsky, N.
Molecular Cell 54 (6): 1042-1054. 19 June 2014

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

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

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

Molecular Neurobiology

A circular RNA expressed from the FAT3 locus regulates neural development.
Seeler, S., Andersen, M.S., Sztanka-Toth, T., Rybiczka-Tešulov, M., van den Munkhof, M.H., Chang, C.C., Maimaitili, M., Venø, M.T., Hansen, T.B., Pasterkamp, R.J., Rybak-Wolf, A., Denham, M., Rajewsky, N., Kristensen, L.S. and Kjems, J.
Molecular Neurobiology 60 (6): 3239–3260. June 2023

Molecular Systems Biology

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Liu, H., Arsiè, R., Schwabe, D., Schilling, M., Minia, I., Alles, J., Boltengagen, A., Kocks, C., Falcke, M., Friedman, N., Landthaler, M. and Rajewsky, N.
Molecular Systems Biology 19 (10): e11427. 12 October 2023

The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D., Formichetti, S., Junker, J.P., Falcke, M. and Rajewsky, N.
Molecular Systems Biology 16 (11): e9946. 1 November 2020

NAR Genomics and Bioinformatics

Optocoder: computational decoding of spatially indexed bead arrays.
Senel, E., Rajewsky, N. and Karaiskos, N.
NAR Genomics and Bioinformatics 4 (2): lqac042. June 2022

Nature

Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal, S., Schultze, H., Shastry, K.L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N.A., Ktena, S., Tran, F., Bitzer, M., Ossowski, S., Casadei, N., Herr, C., Petersheim, D., Behrends, U., Kern, F., Fehlmann, T., Schommers, P., Lehmann, C., Augustin, M., Rybniker, J., Altmüller, J., Mishra, N., Bernardes, J.P., Krämer, B., Bonaguro, L., Schulte-Schrepping, J., De Domenico, E., Siever, C., Kraut, M., Desai, M., Monnet, B., Saridaki, M., Siegel, C.M., Drews, A., Nuesch-Germano, M., Theis, H., Heyckendorf, J., Schreiber, S., Kim-Hellmuth, S., Nattermann, J., Skowasch, D., Kurth, I., Keller, A., Bals, R., Nürnberg, P., Rieß, O., Rosenstiel, P., Netea, M.G., Theis, F., Mukherjee, S., Backes, M., Aschenbrenner, A.C., Ulas, T., Breteler, M.M.B., Giamarellos-Bourboulis, E.J., Kox, M., Becker, M., Cheran, S., Woodacre, M.S., Goh, E.L. and Schultze, J.L.
Nature 594 (7862): 265-270. 10 June 2021

LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, N., Almouzni, G., Gorski, S.A., Aerts, S., Amit, I., Bertero, M.G., Bock, C., Bredenoord, A.L., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fernández, X.M., Figlerowicz, M., Gasser, S.M., Hubner, N., Kjems, J., Knoblich, J.A., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J.C., Marioni, J., Marti-Renom, M.A., Netea, M.G., Nickel, D., Nollmann, M., Novak, H.R., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J.L., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F.J., Torres-Padilla, M.E., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M. and Voet, T.
Nature 587 (7834): 377-386. 19 November 2020

Gene expression cartography.
Nitzan, M., Karaiskos, N., Friedman, N. and Rajewsky, N.
Nature 576 (7785): 132-137. 5 December 2019

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, S.D., Gregersen, L.H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F. and Rajewsky, N.
Nature 495 (7441): 333-338. 21 March 2013

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

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

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

Nature Biotechnology

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

Nature Cell Biology

A guide to naming eukaryotic circular RNAs.
Chen, L.L., Bindereif, A., Bozzoni, I., Chang, H.Y., Matera, A.G., Gorospe, M., Hansen, T.B., Kjems, J., Ma, X.K., Pek, J.W., Rajewsky, N., Salzman, J., Wilusz, J.E., Yang, L. and Zhao, F.
Nature Cell Biology 25 (1): 1-5. January 2023

Nature Communications

Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.
Lisowski, P., Lickfett, S., Rybak-Wolf, A., Menacho, C., Le, S., Pentimalli, T.M., Notopoulou, S., Dykstra, W., Oehler, D., López-Calcerrada, S., Mlody, B., Otto, M., Wu, H., Richter, Y., Roth, P., Anand, R., Kulka, L.A.M., Meierhofer, D., Glazar, P., Legnini, I., Telugu, N.S., Hahn, T., Neuendorf, N., Miller, D.C., Böddrich, A., Polzin, A., Mayatepek, E., Diecke, S., Olzscha, H., Kirstein, J., Ugalde, C., Petrakis, S., Cambridge, S., Rajewsky, N., Kühn, R., Wanker, E.E., Priller, J., Metzger, J.J. and Prigione, A.
Nature Communications 15 (1): 7027. 22 August 2024

Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
Fuchs, S., Danßmann, C., Klironomos, F., Winkler, A., Fallmann, J., Kruetzfeldt, L.M., Szymansky, A., Naderi, J., Bernhart, S.H., Grunewald, L., Helmsauer, K., Rodriguez-Fos, E., Kirchner, M., Mertins, P., Astrahantseff, K., Suenkel, C., Toedling, J., Meggetto, F., Remke, M., Stadler, P.F., Hundsdoerfer, P., Deubzer, H.E., Künkele, A., Lang, P., Fuchs, J., Henssen, A.G., Eggert, A., Rajewsky, N., Hertwig, F. and Schulte, J.H.
Nature Communications 14 (1): 3936. 4 July 2023

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
Lin, M., Hartl, K., Heuberger, J., Beccaceci, G., Berger, H., Li, H., Liu, L., Müllerke, S., Conrad, T., Heymann, F., Woehler, A., Tacke, F., Rajewsky, N. and Sigal, M.
Nature Communications 14 (1): 3025. 25 May 2023

Cell type diversity in a developing octopus brain.
Styfhals, R., Zolotarov, G., Hulselmans, G., Spanier, K.I., Poovathingal, S., Elagoz, A.M., De Winter, S., Deryckere, A., Rajewsky, N., Ponte, G., Fiorito, G., Aerts, S. and Seuntjens, E.
Nature Communications 13 (1): 7392. 30 November 2022

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
Inak, G., Rybak-Wolf, A., Lisowski, P., Pentimalli, T.M., Jüttner, R., Glažar, P., Uppal, K., Bottani, E., Brunetti, D., Secker, C., Zink, A., Meierhofer, D., Henke, M.T., Dey, M., Ciptasari, U., Mlody, B., Hahn, T., Berruezo-Llacuna, M., Karaiskos, N., Di Virgilio, M., Mayr, J.A., Wortmann, S.B., Priller, J., Gotthardt, M., Jones, D.P., Mayatepek, E., Stenzel, W., Diecke, S., Kühn, R., Wanker, E.E., Rajewsky, N., Schuelke, M. and Prigione, A.
Nature Communications 12 (1): 1929. 26 March 2021

Tracing tumorigenesis in a solid tumor model at single-cell resolution.
Praktiknjo, S.D., Obermayer, B., Zhu, Q., Fang, L., Liu, H., Quinn, H., Stoeckius, M., Kocks, C., Birchmeier, W. and Rajewsky, N.
Nature Communications 11 (1): 991. 20 February 2020

Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7.
Marg, A., Escobar Fernandez, H., Karaiskos, N., Grunwald, S.A., Metzler, E., Kieshauer, J., Sauer, S., Pasemann, D., Malfatti, E., Mompoint, D., Quijano-Roy, S., Boltengagen, A., Schneider, J., Schülke, M., Kunz, S., Carlier, R., Birchmeier, C., Amthor, H., Spuler, A., Kocks, C., Rajewsky, N. and Spuler, S.
Nature Communications 10 (1): 5776. 18 December 2019

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program.
Wyler, E., Franke, V., Menegatti, J., Kocks, C., Boltengagen, A., Praktiknjo, S., Walch-Rückheim, B., Bosse, J., Rajewsky, N., Grässer, F., Akalin, A. and Landthaler, M.
Nature Communications 10 (1): 4878. 25 October 2019

Identification of proteins and miRNAs that specifically bind an mRNA in vivo.
Theil, K., Imami, K. and Rajewsky, N.
Nature Communications 10 (1): 4205. 16 September 2019

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, E.O., Selbach, M., Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

Translational regulation shapes the molecular landscape of complex disease phenotypes.
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. and Hubner, N.
Nature Communications 6 : 7200. 26 May 2015

Nature Genetics

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

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

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

Nature Immunology

The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes.
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. and Mashreghi, M.F.
Nature Immunology 11 (11): 1057-1062. November 2010

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

Nature Methods

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Rybak-Wolf, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Kempa, S., Zinzen, R., Woehler, A. and Rajewsky, N.
Nature Methods 20 (10): 1544-1552. October 2023

Best practice standards for circular RNA research.
Nielsen, A.F., Bindereif, A., Bozzoni, I., Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S., Legnini, I., Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J., Preibisch, S., Rajewsky, N., Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Legnini, I., Alles, J., Karaiskos, N., Ayoub, S. and Rajewsky, N.
Nature Methods 16 (9): 879-886. September 2019

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

Nature Microbiology

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A., Wyler, E., Pentimalli, T.M., Legnini, I., Oliveras Martinez, A., Glažar, P., Loewa, A., Kim, S.J., Kaufer, B.B., Woehler, A., Landthaler, M. and Rajewsky, N.
Nature Microbiology 8 (7): 1252-1266. July 2023

Nature Protocols

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N., Senel, E., Friedman, N., Rajewsky, N., Karaiskos, N. and Nitzan, M.
Nature Protocols 16 (9): 4177-4200. September 2021

Nature Reviews Genetics

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

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

Nature Reviews Neurology

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.
Piwecka, M., Rajewsky, N. and Rybak-Wolf, A.
Nature Reviews Neurology 19 (6): 346–362. June 2023

Nature Structural & Molecular Biology

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

Neuron

Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein, E.D., Ruffault, P.L., Misios, A., Osman, K.L., Li, H., Greenberg, R.S., Thompson, R., Song, K., Dietrich, S., Li, X., Vladimirov, N., Woehler, A., Brunet, J.F., Zampieri, N., Kühn, R., Liberles, S.D., Jia, S., Lewin, G.R., Rajewsky, N., Lever, T.E. and Birchmeier, C.
Neuron 111 (14): 2184-2200.e7. 19 July 2023

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

Nucleic Acids Research

Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts.
Ho-Xuan, H., Glažar, P., Latini, C., Heizler, K., Haase, J., Hett, R., Anders, M., Weichmann, F., Bruckmann, A., Van den Berg, D., Hüttelmaier, S., Rajewsky, N., Hackl, C. and Meister, G.
Nucleic Acids Research 48 (18): 10368-10382. 9 October 2020

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

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

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

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

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Friedlaender, M.R., Mackowiak, S.D., Li, N., 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., Mackowiak, S.D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

PLoS Biology

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

PLoS Computational Biology

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

PLoS Genetics

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea.
Schmidt, D., Reuter, H., Hüttner, K., Ruhe, L., Rabert, F., Seebeck, F., Irimia, M., Solana, J. and Bartscherer, K.
PLoS Genetics 14 (12): e1007828. 17 December 2018

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, C.Z., Fisher, A.G. and Merkenschlager, M.
PLoS Genetics 11 (2): e1005020. 25 February 2015

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. and Aboobaker, A.A.
PLoS Genetics 9 (12): e1004003. December 2013

PLoS ONE

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

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

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

PNAS Nexus

Twisted-plywood-like tissue formation in vitro. Does curvature do the twist?
Schamberger, B., Ehrig, S., Dechat, T., Spitzer, S., Bidan, C.M., Fratzl, P., Dunlop, J.W.C. and Roschger, A.
PNAS Nexus 3 (4): pgae121. April 2024

Pacific Symposium on Biocomputing 2008, PSB 2008

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

Physica A: Statistical Mechanics and its Applications

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

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

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

Proceedings of the IEEE Computer Society Bioinformatics Conference

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

Proceedings of the National Academy of Sciences of the United States of America

High-resolution profiling and discovery of planarian small RNAs.
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. and Rajewsky, N.
Proceedings of the National Academy of Sciences of the United States of America 106 (28): 11546-11551. 14 July 2009

Cell type specific signatures of microRNAs on target mRNA expression.
Sood, P., Krek, A., Zavolan, M., 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

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.
van Nimwegen, E., Zavolan, M., 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

RNA

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

RNA Biology

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. and Landthaler, M.
RNA Biology 10 (7): 1146-1159. 1 July 2013

Science

BCR-dependent lineage plasticity in mature B cells.
Graf, R., Seagal, J., Otipoby, K.L., Lam, K.P., Ayoub, S., Zhang, B., Sander, S., Chu, V.T. and Rajewsky, K.
Science 363 (6428): 748-753. 15 February 2019

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

The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N., Wahle, P., Alles, J., Boltengagen, A., Ayoub, S., Kipar, C., Kocks, C., 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., Glažar, 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., Kühn, R., Rosenmund, C., Birchmeier, C. and Rajewsky, N.
Science 357 (6357): eaam8526. 22 September 2017

Integrative analysis of the caenorhabditis elegans genome by the modENCODE project.
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. and Waterston, R.H.
Science 330 (6012): 1775-1787. 24 December 2010

The landscape of C. elegans 3'UTRs.
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. and Kim, J.K.
Science 329 (5990): 432-435. 23 July 2010

Regulation of the germinal center response by microRNA-155.
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. and Rajewsky, K.
Science 316 (5824): 604-608. 27 April 2007

Science Advances

MicroRNAs are deeply linked to the emergence of the complex octopus brain.
Zolotarov, G., Fromm, B., Legnini, I., Ayoub, S., Polese, G., Maselli, V., Chabot, P.J., Vinther, J., Styfhals, R., Seuntjens, E., Di Cosmo, A., Peterson, K.J. and Rajewsky, N.
Science Advances 8 (47): eadd9938. 25 November 2022

Science of the Total Environment

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F., de Castro Cuadrat, R.R., Wyler, E., Wurmus, R., Deter, A., Quedenau, C., Dohmen, J., Faxel, M., Borodina, T., Blume, A., Freimuth, J., Meixner, M., Grau, J.H., Liere, K., Hackenbeck, T., Zietzschmann, F., Gnirss, R., Böckelmann, U., Uyar, B., Franke, V., Barke, N., Altmüller, J., Rajewsky, N., Landthaler, M. and Akalin, A.
Science of the Total Environment 853 : 158931. 20 December 2022

Scientific Reports

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

bioRxiv

Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Rybak-Wolf, A., Kempa, S., Zinzen, R.P., Woehler, A. and Rajewsky, N.
bioRxiv : 2021.09.26.461850v3. 9 February 2022

The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S., Kim, S.J., Eede, P., Boltengagen, A., Braeuning, C., Andreadou, M., Becher, B., Karaiskos, N., Kocks, C., Rajewsky, N. and Heppner, F.L.
bioRxiv : 2021.04.25.441313. 27 April 2021

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1.
Rybak-Wolf, A., Wyler, E., Legnini, I., Loewa, A., Glažar, P., Kim, S.J., Pentimalli, T.M., Oliveras Martinez, A., Beyersdorf, B., Woehler, A., Landthaler, M. and Rajewsky, N.
bioRxiv : 2021.03.05.434122. 7 March 2021

eLife

Conserved functional antagonism of CELF 1 and MBNL proteins controls stem cell-specific alternative splicing in planarians.
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. and Rajewsky, N.
eLife 5 : e16797. 9 August 2016

iScience

Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J., Legnini, I., Pacelli, M. and Rajewsky, N.
iScience 26 (1): 105878. 20 January 2023

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

microPublication Biology

C. elegans gene regulatory alleles and reporter bashing studies.
Froehlich, J.J. and Rajewsky, N.
microPublication Biology 2023 20 January 2023

Estimation of C. elegans cell- and tissue volumes.
Froehlich, J.J., Rajewsky, N. and Ewald, C.Y.
microPublication Biology : 000345. 4 January 2021