Publications

Nucleic Acids Research PMID: 41626690

Epitranscriptomic control of stress adaptations in Escherichia coli

Riquelme-Barrios S, Cusack SA, Rivera-Montero L, Vásquez-Camus L, Burdack K, Brameyer S, Berg M, Yeşiltaç-Tosun GN, Kaiser S, Giehr P, Jung K.

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ChemBioChem PMID: 41869979

Detection of an Antagonist Bound to the Neurokinin a Receptor in Styrene-Maleic Acid Lipid Particles by 19F Ultrafast Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy

Seidl S, Patra AP, Li C, Becker-Baldus J, Kaiser S, Reinhart C, Glaubitz C.

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PlosOne PMID: 41941523

ALKBH1 activity in vitro and human cell lines by isotope dilution mass spectrometry

Henzeler B, Hofmeister O, Kögel K, Qi Y, Hagelskamp F, Heiß M, Schelter F, Xu F, Daumann LJ, Carell T, Kaiser S, Schneider S.

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Nucleic Acids Research PMID: 42258540

Long-term stability of RNA nucleoside standards for accurate LC-MS quantification

Kerkhoff K, Wesseling H, Qi Y, Obersteiner S, Liu K, Berg M, Rusling L, Zipse H, Kaiser S.

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ASM Journal of Bacteriology PMID: tbd

Short-chain fatty acids activate the glutamate-dependent acid resistance system via the tRNA-modifying Mnm pathway in Escherichia coli

tbd

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Nucleic Acids Research PMID: tbd

A Nanogram-Sensitive Workflow for Oligonucleotide Mass Spectrometry Using Ion-Pair–Free Nanoflow HILIC and RNase Benchmarking

tbd

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Nucleic Acids Research PMID: 39997220

NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment

Maximilian Berg, Chengkang Li & Stefanie Kaiser

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Cell Reports PMID: 39786990

Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs

Kejia Zhang, Aidan C. Manning, Jenna M. Lentini, Jonathan Howard, Felix Dalwigk, Reza Maroofian, Stephanie Efthymiou, Patricia Chan, Sergei I. Eliseev, Zi Yang, Hayley Chang, Ehsan Ghayoor Karimiani, Behnoosh Bakhshoodeh, Henry Houlden, Stefanie M. Kaiser, Todd M. Lowe, Dragony Fu

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Communications Chemistry PMID: 39953096

Chemical reactivity of RNA and its modifications with hydrazine.

Nur Yeşiltaç-Tosun, Yuyang Qi, Chengkang Li, Helena Stafflinger, Katja Hollnagel, Leona Rusling, Jens Wöhnert, Steffen Kaiser & Stefanie Kaiser

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Plos One PMID: 39992973

Chemical nucleases are a robust alternative for RNase H cleavage of human ribosomal RNA

Hagen Wesseling, Dennis Krug, Marvin Wehrheim, Michael W Göbel & Stefanie Kaiser

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Nucleic Acids Research PMID: 40114376

Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress

Sebastián Riquelme-Barrios, Leonardo Vásquez-Camus, Siobhan A Cusack, Korinna Burdack, Dimitar Plamenov Petrov, G Nur Yeşiltaç-Tosun, Stefanie Kaiser, Pascal Giehr & Kirsten Jung

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Vaccine PMID: 40120438

Quantification of objective concentrations of DNA impurities in mRNA vaccines

Stefanie Kaiser, Steffen Kaiser, Jenny Reis and Rolf Marschalek

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Microbiome PMID: 40128848

Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome

Byrne SR, DeMott MS, Yuan Y, Ghanegolmohammadi F, Kaiser S, Fox JG, Alm EJ and Dedon PC

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RNA PMID: 40796272

Temporal and spatial profiling of ALKBH5 activity through NAIL-MS and compartmentalized RNA Isolation

Hagen Wesseling and Stefanie Kaiser

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Journal of Molecular Biology PMID: 40461385

NAIL-MS elucidates crucial tRNA U34 modifications in response to heat stress across Eukaryotes and Prokaryotes

Alexandre Magno Vicente; Katarzyna Hencel; Jannick Schicktanz; Christian Hammann; Alper Akay and Stefanie Kaiser

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Cell Reports PMID: 40849905

YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition

Ho-Xuan H, Bruckmann A, Natali L, Prieto-Garcia C, Stuke JFM, Brunello L, Vicente A, Pfab A, Wesseling H, Cano-Franco S, Khatri A, Larivera S, Sanz-Martinez P, de la Cruz-Thea B, Jacomin AC, Prochazka J, Feederle R, Dötsch V, Sedlacek R, Hummer G, Kaiser S, Dikic I, Musri MM, Meister G, Stolz A.

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Genome Biology PMID: 41137159

Unlocking the regulatory code of RNA: launching the Human RNome Project

The Human RNome Project Consortium

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Nature Structural & Molecular Biology PMID: 38918637

Structural basis of tRNA recognition by the m3C-RNA-methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase

Philipp Throll, Luciano G. Dolce, Palma Rico Lastres, Katharina Arnold, Laura Tengo, Shibom Basu, Stefanie Kaiser, Robert Schneider, Eva Kowalinski

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BioRxiv doi: 10.1101/2024.04.04.588121

T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme

Maik Wolfram-Schauerte, Anastassiya Moskalchuk, Nadiia Pozhydaieva, Adán Andrés Ramírez Rojas, Daniel Schindler, Stefanie Kaiser, Nicole Pazcia, Katharina Höfer

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Nucleic Acid Research PMID 39711467

tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus

Alexander Bruch, Valentina Lazarova, Maximilian Berg, Thomas Krüger, Sascha Schäuble, Abdulrahman A. Kelani, Birte Mertens, Pamela Lehenberger, Olaf Kniemeyer, Stefanie Kaiser, Gianni Panagiotou, Fabio Gsaller, Matthew G. Blango

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Nature Communications PMID: 36631525

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

Lisa-Marie Appel, Vedran Franke, Johannes Benedum , Irina Grishkovskaya , Xué Strobl, Anton Polyansky, Gregor Ammann, Sebastian Platzer, Andrea Neudolt, Anna Wunder, Lena Walch, Stefanie Kaiser, Bojan Zagrovic, Kristina Djinovic-Carugo, Altuna Akalin, Dea Slade

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RSC Chemical Biology PMID: 37181633

Temporal resolution of NAIL-MS of tRNA, rRNA and Poly-A RNA is overcome by actinomycin D

Felix Hagelskamp, Kayla Borland, Gregor Ammann and Stefanie M. Kaiser

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Plant Commun. PMID: 37287225

The plant cytosolic m6A RNA methylome stabilizes photosynthesis in the cold

Alexandre Magno Vicente , Nikolay Manavski, Paul Torben Rohn, Lisa-Marie Schmid, Antoni Garcia-Molina, Dario Leister, Charlotte Seydel, Leo Bellin, Torsten Möhlmann, Gregor Ammann, Stefanie Kaiser and Jörg Meurer

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Pharmakon

Das Mikrobiom im Wechselspiel mit Nukleinsäure-Modifikationen

Stefanie Kaiser

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Nucleic Acids Research PMID: 37650648

Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs

Marcel-Joseph Yared, Yasemin Yoluç, Marjorie Catala, Carine Tisné, Stefanie Kaiser, Pierre Barraud

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Biochim Biophys Acta Mol Basis Dis . PMID: 37640114

Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis

Marisa Pereira, Diana R Ribeiro, Maximilian Berg, Andy P Tsai, Chuanpeng Dong, Kwangsik Nho, Stefanie Kaiser, Miguel Moutinho, Ana R Soares

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Antiviral Res . PMID: 37690700

Sangivamycin is preferentially incorporated into viral RNA by the SARS-CoV-2 polymerase

Ryan P Bennett, Yasemin Yoluç, Jason D Salter, Alexander Ripp, Henning J Jessen, Stefanie M Kaiser, Harold C Smith

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Acc Chem Res. PMID: 37944919

Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry

Gregor Ammann, Maximilian Berg, Jan Felix Dalwigk, Stefanie M Kaiser

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ACS Chem Biol. PMID: 37962075

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications

Mark Helm, Markus T Bohnsack, Thomas Carell, Alexander Dalpke, Karl-Dieter Entian, Ann Ehrenhofer-Murray, Ralf Ficner, Christian Hammann, Claudia Höbartner, Andres Jäschke, Albert Jeltsch, Stefanie Kaiser, Roland Klassen, Sebastian A Leidel, Andreas Marx, Mario Mörl, Jochen C Meier, Gunter Meister, Andrea Rentmeister, Marina Rodnina, Jean-Yves Roignant, Raffael Schaffrath, Peter Stadler, Thorsten Stafforst

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Front Cell Dev Biol. PMCID: PMC9125315

Editorial: Viruses and Epitranscriptomes: Regulation of Infection and Antiviral Response.

Soares AR, Kikkert M, Kellner-Kaiser S, Ribeiro D.

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ChemBioChem https://doi.org/10.1002/cbic.202200270

Opportunities and challenges to profile mRNA modifications in Escherichia coli

Dimitar Plamenov Petrov, Steffen Kaiser, Stefanie Kaiser, Kirsten Jung

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Clin Epigenetics . PMID: 36089606

Comprehensive comparison between azacytidine and decitabine treatment in an acute myeloid leukemia cell line

Aumer, T., Gremmelmaier, C. B., Runtsch, L. S., Pforr, J. C., Yeşiltaç, G. N., Kaiser, S., & Traube, F. R.

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Nat Immunol . PMID: 35879451

The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells

Ito-Kureha, T., Leoni, C., Borland, K., Cantini, G., Bataclan, M., Metzger, R. N., Ammann, G., Krug, A. B., Marsico, A., Kaiser, S., Canzar, S., Feske, S., Monticelli, S., König, J., & Heissmeyer, V.

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Nature Communications PMID: 33452242

Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo.

Heiss, M., F. Hagelskamp, V. Marchand, Y. Motorin and S. Kellner

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Methods Mol Biol. PMID: 34085252

Quantification of Modified Nucleosides in the Context of NAIL-MS.

Heiss M, Borland K, Yoluç Y, Kellner S.

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Genes (Basel) PMID: 34573326

The Stress-Dependent Dynamics of S. cerevisiae tRNA and rRNA Modification Profiles.

Yoluç Y, van de Logt E., Kellner-Kaiser S.

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Angew Chem Int Ed Engl. PMID: 34339593

Strategies to avoid artifacts in mass spectrometry-based epitranscriptome analyses.

Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluc Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S.

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Methods Enzymol. PMID: 34517944

Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry.

Hagelskamp F, Kellner S.

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Int J Mol Sci. PMID: 33799331

m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs.

Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR.

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RNA Biology PMID: 32138588

Production and Purification of Endogenously Modified tRNA-Derived Small RNAs

Drino, A., Oberbauer, V., Troger, C., Janisiw, E., Anrather, D., Hartl, M., Kaiser, S., Kellner, S. and Schaefer, M.

Nucleic Acids Research PMID: 32083657

Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro

Hagelskamp, F., Borland, K., Ramos, J., Hendrick, A., Fu, D. and Kellner S.

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Genes Dev PMID: 32217665

The rRNA m(6)A methyltransferase METTL5 is involved in pluripotency and developmental programs

Ignatova, V. V., S. Kaiser, J. S. Y. Ho, X. Bing, P. Stolz, Y. X. Tan, C. L. Lee, F. P. H. Gay, P. R. Lastres, R. Gerlini, B. Rathkolb, A. Aguilar-Pimentel, A. Sanz-Moreno, T. Klein-Rodewald, J. Calzada-Wack, E. Ibragimov, M. Valenta, S. Lukauskas, A. Pavesi, S. Marschall, S. Leuchtenberger, H. Fuchs, V. Gailus-Durner, M. H. de Angelis, S. Bultmann, O. J. Rando, E. Guccione, S. M. Kellner and R. Schneider

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Angew Chem Int Ed Engl PMID: 32160400

Synthesis of Galactosyl-Queuosine and Distribution of Hypermodified Q-Nucleosides in Mouse Tissues

Thumbs, P., T. T. Ensfelder, M. Hillmeier, M. Wagner, M. Heiss, C. Scheel, A. Schon, M. Muller, S. Michalakis, S. Kellner and T. Carell

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ChemBioChem PMID: 32394608

Synthesis and Metabolic Fate of 4-Methylthiouridine in Bacterial tRNA

Borek, C., Reichle, V.F. & Kellner, S.

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Nucleic Acids Res (2020)

Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyosteliumdiscoideum

Schack, M.A. et al.

RNA doi:10.1261/rna.076380.120 PMID: 32763916

Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder

Ramos J, Proven M, Halvardson J, Hagelskamp F, Kuchinskaya E, Phelan B, Bell R, Kellner S, Feuk L, Thuresson AC, Fu D

RNA Biology (2020)

tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast

Tavares et al.

Angew Chem Int Ed Engl (2020)

Chemical amination/imination of carbonothiolated nucleosides during RNA hydrolysis

Jora, M., K. Borland, S. Abernathy, R. Zhao, M. Kelley, S. Kellner, B. Addepalli and P. A. Limbach

Science advances PMID: 32923617

METTL6 is a tRNA m(3)C methyltransferase that regulates pluripotency and tumor cell growth.

Ignatova, V. V., S. Kaiser, J. S. Y. Ho, X. Bing, P. Stolz, Y. X. Tan, C. L. Lee, F. P. H. Gay, P. R. Lastres, R. Gerlini, B. Rathkolb, A. Aguilar-Pimentel, A. Sanz-Moreno, T. Klein-Rodewald, J. Calzada-Wack, E. Ibragimov, M. Valenta, S. Lukauskas, A. Pavesi, S. Marschall, S. Leuchtenberger, H. Fuchs, V. Gailus-Durner, M. H. de Angelis, S. Bultmann, O. J. Rando, E. Guccione, S. M. Kellner and R. Schneider

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Nucleic Acids Research PMID: 33330931

Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6.

Selmi, T., S. Hussain, S. Dietmann, M. Heiss, K. Borland, S. Flad, J. M. Carter, R. Dennison, Y. L. Huang, S. Kellner, S. Bornelov and M. Frye

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Nature Protocols PMID: 30559375

Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides

Traube FR, Schiffers S, Iwan K, Kellner S, Spada F, Müller M, Carell T.

Genes (Basel) 10. PMID: 30621251

Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis.

Borland, K., Diesend, J., Ito-Kureha, T., Heissmeyer, V., Hammann, C., Buck, A.H., Michalakis, S. and Kellner, S.

Biol Chem. PMID: 30893050

Benefits of stable isotope labeling in RNA analysis

Asadi-Atoi, P., Barraud, P., Tisne, C. and Kellner, S.

PLoS Biol 17, e3000297. PMID: 31199786

Cytosine-5 RNA methylation links protein synthesis to cell metabolism

Gkatza, N.A., Castro, C., Harvey, R.F., Heiss, M., Popis, M.C., Blanco, S., Bornelov, S., Sajini, A.A., Gleeson, J.G., Griffin, J.L. et al.

Mol Cell Biol. PMID: 31263000

Formation of tRNA wobble inosine in humans is disrupted by a millennia-old mutation causing intellectual disability

Ramos, J., Han, L., Li, Y., Hagelskamp, F., Kellner, S.M., Alkuraya, F.S., Phizicky, E.M. and Fu, D.

Nat Commun 10, 3373. PMID: 31358763

Time-resolved NMR monitoring of tRNA maturation

Barraud, P., Gato, A., Heiss, M., Catala, M., Kellner, S. and Tisne, C.

Nucleic Acids Res. PMID: 31863583

Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs

Meyer, B., Immer, C., Kaiser, S., Sharma, S., Yang, J., Watzinger, P., Weiss, L., Kotter, A., Helm, M., Seitz, H.M. et al.

Nature Communications PMID: 31811240

NAIL-MS reveals the repair of 2-methylthiocytidine by AlkB in E. coli

Reichle, V.F., Petrov, D.P., Weber, V., Jung, K. and Kellner, S.

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Methods PMID: 30395967

Surpassing limits of static RNA modification analysis with dynamic NAIL-MS

Reichle VF, Kaiser S, Heiss M, Hagelskamp F, Borland K, Kellner S.

ChemBioChem PMID: 30328661

NAIL-MS in E. coli determines the source and fate of methylation in tRNA

Reichle V., Weber V. and Kellner S.

RNA Biol. 2017 May 10:0. doi: 10.1080/15476286.2017.1325063.

Observing the fate of tRNA and its modifications by nucleic acid isotope labeling mass spectrometry: NAIL-MS

Heiss, M., Reichle, V. & Kellner, S.

Mol Cell Biol. doi: 10.1128/MCB.00214-17. PubMed PMID: 28784718.

TRMT1-catalyzed tRNA modifications are required for redox homeostasis to ensure proper cellular proliferation and oxidative stress survival.

Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D.

Nature Chemical Biology PMID: 28604692

Oxidation of labile phosphorothioate DNA modifications leads to lethal genomic instability

Kellner S.*, Demott M.*, Chen C., Cao B. and Dedon P.

Proc Natl Acad Sci U S A 2016

Novel genomic island modifies DNA with 7-deazaguanine derivatives

Thiaville, J.J., et al.

RNA Biol 1-11. doi:10.1080/15476286.2016.1236170

The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA

Kaiser, S., Jurkowski, T. P., Kellner, S., Schneider, D., Jeltsch, A., & Helm, M.

RNA Biol 2016 Nov 30:1-9. doi: 10.1080/15476286.2016.1261788.

Detection of nucleic acid modifications by chemical reagents

Heiss, M., & Kellner, S.

PLoS One 2015. 10(7): p. e0133321.

Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120

Bourgeois, G., et al.

Methods Enzymol 2015. 560: p. 29-71.

A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications

Cai, W.M., et al.

RNA 2015. 21(12): p. 2103-18.

An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis

Lin, C.J., et al.

RNA Biol 2015. 12(10): p. 1152-8.

Variable presence of 5-methylcytosine in commercial RNA and DNA

Schmid, K., et al.

EMBO J 2014. 33(18): p. 2020-39.

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

Blanco, S., et al.

PLoS One 2014. 9(2): p. e89640.

Partial methylation at Am100 in 18S rRNA of baker’s yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification

Buchhaupt, M., et al.

Chem Commun (Camb) 2014. 50(26): p. 3516-8.

Profiling of RNA modifications by multiplexed stable isotope labelling

Kellner, S., et al.

Nucleic Acids Res 2014. 42(18): p. e142.

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

Kellner, S.

Nucleic Acids Res 2014. 42(20): p. 12735-45.

Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor

Spenkuch, F., et al.

PLoS One 2013. 8(7): p. e67945.

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

Kellner, S., et al.

Nucleic Acids Res 2012. 40(12): p. 5523-34.

Related haloarchaeal pleomorphic viruses contain different genome types

Sencilo, A., et al.,

Nat Struct Mol Biol 2012. 19(9): p. 900-5.

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

Tuorto, F., et al.

Nucleic Acids Res 2011. 39(16): p. 7348-60.

A multifunctional bioconjugate module for versatile photoaffinity labeling and click chemistry of RNA

Nucleic Acids Res

RNA Biol, 2010. 7(2): p. 237-47

Detection of RNA modifications

Kellner, S., J. Burhenne, and M. Helm