Works by Rajewsky, Nikolaus

Results: 67

Transcriptional Control in the Segmentation Gene Network of Drosophila.

Published in:

PLoS Biology, 2004, v. 2, n. 9, p. 1396, doi. 10.1371/journal.pbio.0020271

By:

Schroeder, Mark D.;
Pearce, Michael;
Fak, John;
Fan, Hongqing;
Unnerstall, Ulrich;
Emberly, Eldon;
Rajewsky, Nikolaus;
Siggia, Eric D.;
Gaul, Ulrike

Publication type:

Article

Transcriptional Control in the Segmentation Gene Network of Drosophila.

Published in:

PLoS Biology, 2004, v. 2, n. 8, p. 1, doi. 10.1371/journal.pbio.0020271

By:

Schroeder, Mark D;
Pearce, Michael;
Fak, John;
Fan, HongQing;
Unnerstall, Ulrich;
Emberly, Eldon;
Rajewsky, Nikolaus;
Siggia, Eric D;
Gaul, Ulrike

Publication type:

Article

A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer.

Published in:

Nature Immunology, 2004, v. 5, n. 4, p. 443, doi. 10.1038/ni1053

By:

Barreto, Vasco;
Misulovin, Ziva;
Gazumyan, Anna;
Wong Yu;
Rajewsky, Nikolaus;
Peixoto, Bernardo R.;
Eisenreich, Thomas;
Yannoutsos, Nikos;
Nussenzweig, Michel C.

Publication type:

Article

Spacemake: processing and analysis of large-scale spatial transcriptomics data.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac064

By:

Sztanka-Toth, Tamas Ryszard;
Jens, Marvin;
Karaiskos, Nikos;
Rajewsky, Nikolaus

Publication type:

Article

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1663-x

By:

Wolf, F. Alexander;
Hamey, Fiona K.;
Plass, Mireya;
Solana, Jordi;
Dahlin, Joakim S.;
Göttgens, Berthold;
Rajewsky, Nikolaus;
Simon, Lukas;
Theis, Fabian J.

Publication type:

Article

Epigenetic dynamics of monocyteto-macrophage differentiation.

Published in:

Epigenetics & Chromatin, 2016, v. 8, p. 1, doi. 10.1186/s13072-016-0079-z

By:

Wallner, Stefan;
Schröder, Christopher;
Leitão, Elsa;
Berulava, Tea;
Haak, Claudia;
Beiβer, Daniela;
Rahmann, Sven;
Richter, Andreas S.;
Manke, Thomas;
Bönisch, Ulrike;
Arrigoni, Laura;
Fröhler, Sebastian;
Klironomos, Filippos;
Wei Chen;
Rajewsky, Nikolaus;
Müller, Fabian;
Ebert, Peter;
Lengauer, Thomas;
Barann, Matthias;
Rosenstiel, Philip

Publication type:

Article

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

Published in:

BMC Biology, 2017, v. 15, p. 1, doi. 10.1186/s12915-017-0383-5

By:

Alles, Jonathan;
Karaiskos, Nikos;
Praktiknjo, Samantha D.;
Grosswendt, Stefanie;
Wahle, Philipp;
Ruffault, Pierre-Louis;
Ayoub, Salah;
Schreyer, Luisa;
Boltengagen, Anastasiya;
Birchmeier, Carmen;
Zinzen, Robert;
Kocks, Christine;
Rajewsky, Nikolaus

Publication type:

Article

SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle.

Published in:

Molecular Systems Biology, 2023, v. 19, n. 10, p. 1, doi. 10.15252/msb.202211427

By:

Liu, Haiyue;
Arsiè, Roberto;
Schwabe, Daniel;
Schilling, Marcel;
Minia, Igor;
Alles, Jonathan;
Boltengagen, Anastasiya;
Kocks, Christine;
Falcke, Martin;
Friedman, Nir;
Landthaler, Markus;
Rajewsky, Nikolaus

Publication type:

Article

Widespread changes in protein synthesis induced by microRNAs.

Published in:

Nature, 2008, v. 455, n. 7209, p. 58, doi. 10.1038/nature07228

By:

Selbach, Matthias;
Schwanhäusser, Björn;
Thierfelder, Nadine;
Zhuo Fang;
Khanin, Raya;
Rajewsky, Nikolaus

Publication type:

Article

Making the paper: David Bartel & Nikolaus Rajewsky.

Published in:

Nature, 2008, v. 455, n. 7209, p. x, doi. 10.1038/7209xa

By:

Bartel, David;
Rajewsky, Nikolaus

Publication type:

Article

Silencing of microRNAs in vivo with ‘antagomirs’.

Published in:

Nature, 2005, v. 438, n. 7068, p. 685, doi. 10.1038/nature04303

By:

Krützfeldt, Jan;
Rajewsky, Nikolaus;
Braich, Ravi;
Rajeev, Kallanthottathil G.;
Tuschl, Thomas;
Manoharan, Muthiah;
Stoffel, Markus

Publication type:

Article

A pancreatic islet-specific microRNA regulates insulin secretion.

Published in:

Nature, 2004, v. 432, n. 7014, p. 226, doi. 10.1038/nature03076

By:

Poy, Matthew N.;
Eliasson, Lena;
Krutzfeldt, Jan;
Kuwajima, Satoru;
Ma, Xiaosong;
MacDonald, Patrick E.;
Pfeffer, Sébastien;
Tuschl, Thomas;
Rajewsky, Nikolaus;
Rorsman, Patrik;
Stoffel, Markus

Publication type:

Article

doRiNA: a database of RNA interactions in post-transcriptional regulation.

Published in:

Nucleic Acids Research, 2012, p. D180, doi. 10.1093/nar/gkr1007

By:

Anders, Gerd;
Mackowiak, Sebastian D.;
Jens, Marvin;
Maaskola, Jonas;
Kuntzagk, Andreas;
Rajewsky, Nikolaus;
Landthaler, Markus;
Dieterich, Christoph

Publication type:

Article

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 1, p. 37, doi. 10.1093/nar/gkr688

By:

Friedländer, Marc R.;
Mackowiak, Sebastian D.;
Na Li;
Wei Chen;
Rajewsky, Nikolaus

Publication type:

Article

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

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1368-y

By:

Verduci, Lorena;
Ferraiuolo, Maria;
Sacconi, Andrea;
Ganci, Federica;
Vitale, Jlenia;
Colombo, Teresa;
Paci, Paola;
Strano, Sabrina;
Macino, Giuseppe;
Rajewsky, Nikolaus;
Blandino, Giovanni

Publication type:

Article

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

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1329-5

By:

Wyler, Emanuel;
Menegatti, Jennifer;
Franke, Vedran;
Kocks, Christine;
Boltengagen, Anastasiya;
Hennig, Thomas;
Theil, Kathrin;
Rutkowski, Andrzej;
Ferrai, Carmelo;
Baer, Laura;
Kermas, Lisa;
Friedel, Caroline;
Rajewsky, Nikolaus;
Akalin, Altuna;
Dölken, Lars;
Grässer, Friedrich;
Landthaler, Markus

Publication type:

Article

Natural selection on human microRNA binding sites inferred from SNP data.

Published in:

Nature Genetics, 2006, v. 38, n. 12, p. 1452, doi. 10.1038/ng1910

By:

Chen, Kevin;
Rajewsky, Nikolaus

Publication type:

Article

microRNA target predictions in animals.

Published in:

Nature Genetics, 2006, v. 38, p. S8, doi. 10.1038/ng1798

By:

Rajewsky, Nikolaus

Publication type:

Article

Combinatorial microRNA target predictions.

Published in:

Nature Genetics, 2005, v. 37, n. 5, p. 495, doi. 10.1038/ng1536

By:

Krek, Azra;
Grün, Dominic;
Poy, Matthew N;
Wolf, Rachel;
Rosenberg, Lauren;
Epstein, Eric J;
MacMenamin, Philip;
da Piedade, Isabelle;
Gunsalus, Kristin C;
Stoffel, Markus;
Rajewsky, Nikolaus

Publication type:

Article

microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes.

Published in:

PLoS Genetics, 2015, v. 11, n. 2, p. 1, doi. 10.1371/journal.pgen.1005020

By:

Blevins, Rory;
Bruno, Ludovica;
Carroll, Thomas;
Elliott, James;
Marcais, Antoine;
Loh, Christina;
Hertweck, Arnulf;
Krek, Azra;
Rajewsky, Nikolaus;
Chen, Chang-Zheng;
Fisher, Amanda G.;
Merkenschlager, Matthias

Publication type:

Article

The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation.

Published in:

PLoS Genetics, 2013, v. 9, n. 12, p. 1, doi. 10.1371/journal.pgen.1004003

By:

Solana, Jordi;
Gamberi, Chiara;
Mihaylova, Yuliana;
Grosswendt, Stefanie;
Chen, Chen;
Lasko, Paul;
Rajewsky, Nikolaus;
Aboobaker, A. Aziz

Publication type:

Article

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

Published in:

Journal of Clinical Investigation, 2014, v. 124, n. 8, p. 3419, doi. 10.1172/JCI74523

By:

Maatz, Henrike;
Jens, Marvin;
Liss, Martin;
Schafer, Sebastian;
Heinig, Matthias;
Kirchner, Marieluise;
Adami, Eleonora;
Rintisch, Carola;
Dauksaite, Vita;
Radke, Michael H.;
Selbach, Matthias;
Barton, Paul J. R.;
Cook, Stuart A.;
Rajewsky, Nikolaus;
Gotthardt, Michael;
Landthaler, Markus;
Hubner, Norbert

Publication type:

Article

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

Published in:

Nature Reviews Genetics, 2015, v. 16, n. 2, p. 113, doi. 10.1038/nrg3853

By:

Jens, Marvin;
Rajewsky, Nikolaus

Publication type:

Article

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38780-3

By:

Lin, Manqiang;
Hartl, Kimberly;
Heuberger, Julian;
Beccaceci, Giulia;
Berger, Hilmar;
Li, Hao;
Liu, Lichao;
Müllerke, Stefanie;
Conrad, Thomas;
Heymann, Felix;
Woehler, Andrew;
Tacke, Frank;
Rajewsky, Nikolaus;
Sigal, Michael

Publication type:

Article

Cell type diversity in a developing octopus brain.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-35198-1

By:

Styfhals, Ruth;
Zolotarov, Grygoriy;
Hulselmans, Gert;
Spanier, Katina I.;
Poovathingal, Suresh;
Elagoz, Ali M.;
De Winter, Seppe;
Deryckere, Astrid;
Rajewsky, Nikolaus;
Ponte, Giovanna;
Fiorito, Graziano;
Aerts, Stein;
Seuntjens, Eve

Publication type:

Article

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.

Published in:

Nature Protocols, 2021, v. 16, n. 9, p. 4177, doi. 10.1038/s41596-021-00573-7

By:

Moriel, Noa;
Senel, Enes;
Friedman, Nir;
Rajewsky, Nikolaus;
Karaiskos, Nikos;
Nitzan, Mor

Publication type:

Article

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

Published in:

EMBO Journal, 2015, v. 34, n. 10, p. 1417, doi. 10.15252/embj.201490819

By:

Jia, Shiqi;
Ivanov, Andranik;
Blasevic, Dinko;
Müller, Thomas;
Purfürst, Bettina;
Sun, Wei;
Chen, Wei;
Poy, Matthew N;
Rajewsky, Nikolaus;
Birchmeier, Carmen

Publication type:

Article

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

Published in:

EMBO Journal, 2014, v. 33, n. 16, p. 1751, doi. 10.15252/embj.201488769

By:

Stoeckius, Marlon;
Grün, Dominic;
Kirchner, Marieluise;
Ayoub, Salah;
Torti, Francesca;
Piano, Fabio;
Herzog, Margareta;
Selbach, Matthias;
Rajewsky, Nikolaus

Publication type:

Article

Paternal RNA contributions in the Caenorhabditis elegans zygote.

Published in:

EMBO Journal, 2014, v. 33, n. 16, p. 1740, doi. 10.15252/embj.201488117

By:

Stoeckius, Marlon;
Grün, Dominic;
Rajewsky, Nikolaus

Publication type:

Article

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

Published in:

EMBO Journal, 2014, v. 33, n. 9, p. 981, doi. 10.1002/embj.201488411

By:

Bazzini, Ariel A;
Johnstone, Timothy G;
Christiano, Romain;
Mackowiak, Sebastian D;
Obermayer, Benedikt;
Fleming, Elizabeth S;
Vejnar, Charles E;
Lee, Miler T;
Rajewsky, Nikolaus;
Walther, Tobias C;
Giraldez, Antonio J

Publication type:

Article

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.

Published in:

BMC Biology, 2022, v. 20, p. 1, doi. 10.1186/s12915-022-01471-4

By:

Preusser, Friedrich;
Neuschulz, Anika;
Junker, Jan Philipp;
Rajewsky, Nikolaus;
Preibisch, Stephan

Publication type:

Article

microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets.

Published in:

PLoS Computational Biology, 2005, v. 1, n. 1, p. 51, doi. 10.1371/journal.pcbi.0010013

By:

Grün, Dominic;
Yi-Lu Wang;
Langenberger, David;
Gunsalus, Kristin C.;
Rajewsky, Nikolaus;
Eisen, Michael

Publication type:

Article

The evolution of gene regulation by transcription factors and microRNAs.

Published in:

Nature Reviews Genetics, 2007, v. 8, n. 2, p. 93, doi. 10.1038/nrg1990

By:

Chen, Kevin;
Rajewsky, Nikolaus

Publication type:

Article

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

Published in:

International Journal of Genomics, 2018, p. 1, doi. 10.1155/2018/1243858

By:

Laudadio, Ilaria;
Formichetti, Sara;
Gioiosa, Silvia;
Klironomos, Filippos;
Rajewsky, Nikolaus;
Macino, Giuseppe;
Carissimi, Claudia;
Fulci, Valerio

Publication type:

Article

Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy.

Published in:

Cancers, 2021, v. 13, n. 1, p. 49, doi. 10.3390/cancers13010049

By:

Ho-Xuan, Hung;
Lehmann, Gerhard;
Glazar, Petar;
Gypas, Foivos;
Eichner, Norbert;
Heizler, Kevin;
Schlitt, Hans J.;
Zavolan, Mihaela;
Rajewsky, Nikolaus;
Meister, Gunter;
Hackl, Christina

Publication type:

Article

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

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00690-6

By:

Zappulo, Alessandra;
van den Bruck, David;
Mattioli, Camilla Ciolli;
Franke, Vedran;
Imami, Koshi;
McShane, Erik;
Moreno-Estelles, Mireia;
Calviello, Lorenzo;
Filipchyk, Andrei;
Peguero-Sanchez, Esteban;
Müller, Thomas;
Woehler, Andrew;
Birchmeie, Carmen;
Merino, Enrique;
Rajewsky, Nikolaus;
Ohler, Uwe;
Mazzoni, Esteban O.;
Selbach, Matthias;
Akalin, Altuna;
Chekulaeva, Marina

Publication type:

Article

Translational regulation shapes the molecular landscape of complex disease phenotypes.

Published in:

Nature Communications, 2015, v. 6, n. 5, p. 7200, doi. 10.1038/ncomms8200

By:

Schafer, Sebastian;
Adami, Eleonora;
Heinig, Matthias;
Rodrigues, Katharina E. Costa;
Kreuchwig, Franziska;
Silhavy, Jan;
van Heesch, Sebastiaan;
Simaite, Deimante;
Rajewsky, Nikolaus;
Cuppen, Edwin;
Pravenec, Michal;
Vingron, Martin;
Cook, Stuart A.;
Hubner, Norbert

Publication type:

Article

Expression of Circ_Satb1 Is Decreased in Mesial Temporal Lobe Epilepsy and Regulates Dendritic Spine Morphology.

Published in:

Frontiers in Molecular Neuroscience, 2022, v. 15, p. 1, doi. 10.3389/fnmol.2022.832133

By:

Gomes-Duarte, Andreia;
Venø, Morten T.;
de Wit, Marina;
Senthilkumar, Ketharini;
Broekhoven, Mark H.;
van den Herik, Joëlle;
Heeres, Fleur R.;
van Rossum, Daniëlle;
Rybiczka-Tesulov, Mateja;
Legnini, Ivano;
van Rijen, Peter C.;
van Eijsden, Pieter;
Gosselaar, Peter H.;
Rajewsky, Nikolaus;
Kjems, Jørgen;
Vangoor, Vamshidhar R.;
Pasterkamp, R. Jeroen

Publication type:

Article

Conservation of regulatory elements between two species of Drosophila.

Published in:

BMC Bioinformatics, 2003, v. 4, p. 57, doi. 10.1186/1471-2105-4-57

By:

Emberly, Eldon;
Rajewsky, Nikolaus;
Siggia, Eric D.

Publication type:

Article

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

Published in:

BMC Bioinformatics, 2002, v. 3, p. 1

By:

Rajewsky, Nikolaus;
Vergassola, Massimo;
Gaul, Ulrike;
Siggia, Eric D.

Publication type:

Article

A map of human circular RNAs in clinically relevant tissues.

Published in:

Journal of Molecular Medicine, 2017, v. 95, n. 11, p. 1179, doi. 10.1007/s00109-017-1582-9

By:

Maass, Philipp;
Glažar, Petar;
Memczak, Sebastian;
Dittmar, Gunnar;
Hollfinger, Irene;
Schreyer, Luisa;
Sauer, Aisha;
Toka, Okan;
Aiuti, Alessandro;
Luft, Friedrich;
Rajewsky, Nikolaus

Publication type:

Article

Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts.

Published in:

Nucleic Acids Research, 2020, v. 48, n. 18, p. 10368, doi. 10.1093/nar/gkaa704

By:

Ho-Xuan, Hung;
Glažar, Petar;
Latini, Claudia;
Heizler, Kevin;
Haase, Jacob;
Hett, Robert;
Anders, Marvin;
Weichmann, Franziska;
Bruckmann, Astrid;
Van den Berg, Debbie;
Hüttelmaier, Stefan;
Rajewsky, Nikolaus;
Hackl, Christina;
Meister, Gunter

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. 10, p. 1, doi. 10.1093/nar/gkx120

By:

Uyar, Bora;
Yusuf, Dilmurat;
Wurmus, Ricardo;
Rajewsky, Nikolaus;
Ohler, Uwe;
Akalin, Altuna

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D160, doi. 10.1093/nar/gku1180

By:

Blin, Kai;
Dieterich, Christoph;
Wurmus, Ricardo;
Rajewsky, Nikolaus;
Landthaler, Markus;
Akalin, Altuna

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2014, v. 42, n. 21, p. 12995, doi. 10.1093/nar/gku1083

By:

Maaskola, Jonas;
Rajewsky, Nikolaus

Publication type:

Article

Extensive identification and analysis of conserved small ORFs in animals.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0742-x

By:

Mackowiak, Sebastian D.;
Zauber, Henrik;
Bielow, Chris;
Thie, Denise;
Kutz, Kamila;
Calviello, Lorenzo;
Mastrobuoni, Guido;
Rajewsky, Nikolaus;
Kempa, Stefan;
Selbach, Matthias;
Obermayer, Benedikt

Publication type:

Article

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

Published in:

EMBO Journal, 2012, v. 31, n. 12, p. 2755, doi. 10.1038/emboj.2012.110

By:

Önal, Pinar;
Grün, Dominic;
Adamidi, Catherine;
Rybak, Agnieszka;
Solana, Jordi;
Mastrobuoni, Guido;
Wang, Yongbo;
Rahn, Hans-Peter;
Chen, Wei;
Kempa, Stefan;
Ziebold, Ulrike;
Rajewsky, Nikolaus

Publication type:

Article

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

Published in:

EMBO Journal, 2012, v. 31, n. 4, p. 972, doi. 10.1038/emboj.2011.451

By:

von Eyss, Björn;
Maaskola, Jonas;
Memczak, Sebastian;
Möllmann, Katharina;
Schuetz, Anja;
Loddenkemper, Christoph;
Tanh, Mai-Dinh;
Otto, Albrecht;
Muegge, Kathrin;
Heinemann, Udo;
Rajewsky, Nikolaus;
Ziebold, Ulrike

Publication type:

Article

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.

Published in:

Nature Methods, 2009, v. 6, n. 10, p. 745, doi. 10.1038/nmeth.1370

By:

Stoeckius, Marlon;
Maaskola, Jonas;
Colombo, Teresa;
Rahn, Hans-Peter;
Friedländer, Marc R.;
Na Li;
Wei Chen;
Piano, Fabio;
Rajewsky, Nikolaus

Publication type:

Article

The transcriptome dynamics of single cells during the cell cycle.

Published in:

Molecular Systems Biology, 2020, v. 16, n. 11, p. 1, doi. 10.15252/msb.20209946

By:

Schwabe, Daniel;
Formichetti, Sara;
Junker, Jan Philipp;
Falcke, Martin;
Rajewsky, Nikolaus

Publication type:

Article