Nucleic Acids Research

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Oxford University Press
 
 
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  • 2024 Journal Article
    ​ ​Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain​
    Kumar, N. H.; Kluever, V.; Barth, E.; Krautwurst, S.; Furlan, M.; Pelizzola, M. & Marz, M. et al.​ (2024) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gkae172 
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  • 2024 Journal Article
    ​ ​SeqCAT: Sequence Conversion and Analysis Toolbox​
    Kornrumpf, K.; Kurz, N.; Drofenik, K.; Krauß, L.; Schneider, C.; Koch, R. & Beißbarth, T. et al.​ (2024) 
    Nucleic Acids Research, art. gkae422​.​ DOI: https://doi.org/10.1093/nar/gkae422 
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  • 2024 Journal Article
    ​ ​Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment​
    Tarău, D.; Grünberger, F.; Pilsl, M.; Reichelt, R.; Heiß, F.; König, S. & Urlaub, H. et al.​ (2024) 
    Nucleic Acids Research, art. gkae282​.​ DOI: https://doi.org/10.1093/nar/gkae282 
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  • 2024 Journal Article
    ​ ​Kinetics of programmed and spontaneous ribosome sliding along the mRNA​
    Senyushkina, T.; Samatova, E.; Klimova, M. & Rodnina, M.​ (2024) 
    Nucleic Acids Research, art. gkae396​.​ DOI: https://doi.org/10.1093/nar/gkae396 
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  • 2023 Journal Article
    ​ ​Helical coiling of metaphase chromatids​
    Kubalová, I.; Câmara, A. S.; Cápal, P.; Beseda, T.; Rouillard, J.-M.; Krause, G. & Holušová, K. et al.​ (2023) 
    Nucleic Acids Research, art. gkad028​.​ DOI: https://doi.org/10.1093/nar/gkad028 
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  • 2023 Journal Article
    ​ ​Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex​
    Breindl, M.; Spitzer, D.; Gerasimaitė, R.; Kairys, V.; Schubert, T.; Henfling, R. & Schwartz, U. et al.​ (2023) 
    Nucleic Acids Research, art. gkad1096​.​ DOI: https://doi.org/10.1093/nar/gkad1096 
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  • 2023 Journal Article
    ​ ​Conformational dynamics of the RNA binding channel regulates loading and translocation of the DEAH-box helicase Prp43​
    Enders, M.; Ficner, R. & Adio, S.​ (2023) 
    Nucleic Acids Research, art. gkad362​.​ DOI: https://doi.org/10.1093/nar/gkad362 
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  • 2023 Journal Article
    ​ ​PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks​
    Elfmann, C. & Stülke, J. ​ (2023) 
    Nucleic Acids Research, art. gkad350​.​ DOI: https://doi.org/10.1093/nar/gkad350 
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  • 2023 Journal Article
    ​ ​GPATCH4 regulates rRNA and snRNA 2′- O -methylation in both DHX15-dependent and DHX15-independent manners​
    Kanwal, N.; Krogh, N.; Memet, I.; Lemus-Diaz, N.; Thomé, C.; Welp, L. & Mizi, A. et al.​ (2023) 
    Nucleic Acids Research, art. gkad1202​.​ DOI: https://doi.org/10.1093/nar/gkad1202 
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  • 2023 Journal Article
    ​ ​DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options​
    Basu, S.; Zhao, B.; Biró, B.; Faraggi, E.; Gsponer, J.; Hu, G. & Kloczkowski, A. et al.​ (2023) 
    Nucleic Acids Research, art. gkad985​.​ DOI: https://doi.org/10.1093/nar/gkad985 
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  • 2023 Journal Article
    ​ ​The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome​
    Khreiss, A.; Capeyrou, R.; Lebaron, S.; Albert, B.; Bohnsack, K.; Bohnsack, M. & Henry, Y. et al.​ (2023) 
    Nucleic Acids Research51(2) pp. 744​-764​.​ DOI: https://doi.org/10.1093/nar/gkac1196 
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  • 2023 Journal Article
    ​ ​Surveillance of 3′ mRNA cleavage during transcription termination requires CF IB/Hrp1​
    Li, J.; Querl, L.; Coban, I.; Salinas, G. & Krebber, H.​ (2023) 
    Nucleic Acids Research, art. gkad530​.​ DOI: https://doi.org/10.1093/nar/gkad530 
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  • 2023 Journal Article
    ​ ​N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing​
    Wang, C.; Ulryck, N.; Herzel, L.; Pythoud, N.; Kleiber, N.; Guérineau, V. & Jactel, V. et al.​ (2023) 
    Nucleic Acids Research, art. gkad487​.​ DOI: https://doi.org/10.1093/nar/gkad487 
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  • 2023 Journal Article
    ​ ​The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro​
    Wicke, D.; Neumann, P.; Gößringer, M.; Chernev, A.; Davydov, S.; Poehlein, A. & Daniel, R. et al.​ (2023) 
    Nucleic Acids Research, art. gkad1171​.​ DOI: https://doi.org/10.1093/nar/gkad1171 
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  • 2022 Journal Article
    ​ ​Conformational rearrangements upon start codon recognition in human 48S translation initiation complex​
    Yi, S.-H.; Petrychenko, V.; Schliep, J. E.; Goyal, A.; Linden, A.; Chari, A. & Urlaub, H. et al.​ (2022) 
    Nucleic Acids Research50(9) pp. 5282​-5298​.​ DOI: https://doi.org/10.1093/nar/gkac283 
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  • 2022 Journal Article
    ​ ​Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome​
    Herzel, L.; Stanley, J. A; Yao, C.-C. & Li, G.-W.​ (2022) 
    Nucleic Acids Research50(9) pp. 5029​-5046​.​ DOI: https://doi.org/10.1093/nar/gkac295 
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  • 2022 Journal Article | 
    ​ ​Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA​
    Maciej, V. D; Mateva, N.; Schwarz, J.; Dittmers, T.; Mallick, M.; Urlaub, H.   & Chakrabarti, S.​ (2022) 
    Nucleic Acids Research, art. gkac797​.​ DOI: https://doi.org/10.1093/nar/gkac797 
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  • 2022 Journal Article
    ​ ​A guard protein mediated quality control mechanism monitors 5’-capping of pre-mRNAs​
    Klama, S.; Hirsch, A. G; Schneider, U. M; Zander, G.; Seel, A. & Krebber, H.​ (2022) 
    Nucleic Acids Research50(19) art. gkac952​.​ DOI: https://doi.org/10.1093/nar/gkac952 
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  • 2022 Journal Article | 
    ​ ​Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network​
    Bohnsack, K. E. ; Kanwal, N. & Bohnsack, M. T. ​ (2022) 
    Nucleic Acids Research, art. gkac687​.​ DOI: https://doi.org/10.1093/nar/gkac687 
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  • 2022 Journal Article
    ​ ​Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA​
    Keil, P.; Wulf, A.; Kachariya, N.; Reuscher, S.; Hühn, K.; Silbern, I. & Altmüller, J. et al.​ (2022) 
    Nucleic Acids Research, art. gkac1206​.​ DOI: https://doi.org/10.1093/nar/gkac1206 
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  • 2022 Journal Article
    ​ ​DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks​
    Shutta, K. H; Weighill, D.; Burkholz, R.; Guebila, M.; DeMeo, D. L; Zacharias, H. U & Quackenbush, J. et al.​ (2022) 
    Nucleic Acids Research, art. gkac1157​.​ DOI: https://doi.org/10.1093/nar/gkac1157 
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  • 2022 Journal Article
    ​ ​MirDIP 5.2: tissue context annotation and novel microRNA curation​
    Hauschild, A.-C.; Pastrello, C.; Ekaputeri, G.; Bethune-Waddell, D.; Abovsky, M.; Ahmed, Z. & Kotlyar, M. et al.​ (2022) 
    Nucleic Acids Research51(D1) pp. D217​-D225​.​ DOI: https://doi.org/10.1093/nar/gkac1070 
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  • 2022 Journal Article | Research Paper | 
    ​ ​Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel​
    Kolář, M. H.; Nagy, G.; Kunkel, J.; Vaiana, S. M.; Bock, L. V.   & Grubmüller, H. ​ (2022) 
    Nucleic Acids Research50(4) pp. 2258​-2269​.​ DOI: https://doi.org/10.1093/nar/gkac038 
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  • 2021 Journal Article
    ​ ​Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis​
    Benda, M.; Woelfel, S.; Faßhauer, P.; Gunka, K.; Klumpp, S.; Poehlein, A. & Kálalová, D. et al.​ (2021) 
    Nucleic Acids Research49(12) pp. 7088​-7102​.​ DOI: https://doi.org/10.1093/nar/gkab528 
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  • 2021 Journal Article
    ​ ​Fractal construction of constrained code words for DNA storage systems​
    Löchel, H. F; Welzel, M.; Hattab, G.; Hauschild, A.-C.   & Heider, D.​ (2021) 
    Nucleic Acids Research50(5) pp. e30​-e30​.​ DOI: https://doi.org/10.1093/nar/gkab1209 
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  • 2021 Journal Article
    ​ ​Choice of fluorophore affects dynamic DNA nanostructures​
    Jahnke, K.; Grubmüller, H. ; Igaev, M. & Göpfrich, K.​ (2021) 
    Nucleic Acids Research49(7) pp. 4186​-4195​.​ DOI: https://doi.org/10.1093/nar/gkab201 
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  • 2021 Journal Article | Research Paper | 
    ​ ​RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2′- O -methylation​
    Aquino, G.; Krogh, N.; Hackert, P.; Martin, R.; Gallesio, J.; van Nues, R. W. & Schneider, C. et al.​ (2021) 
    Nucleic Acids Research49(7) pp. 4066​-4084​.​ DOI: https://doi.org/10.1093/nar/gkab159 
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  • 2021 Journal Article | Research Paper | 
    ​ ​Structure of an inactive RNA polymerase II dimer​
    Aibara, S.; Dienemann, C. & Cramer, P. ​ (2021) 
    Nucleic Acids Research49(18) pp. 10747​-10755​.​ DOI: https://doi.org/10.1093/nar/gkab783 
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  • 2021 Journal Article
    ​ ​The current state of Subti Wiki, the database for the model organism Bacillus subtilis​
    Pedreira, T.; Elfmann, C. & Stülke, J.​ (2021) 
    Nucleic Acids Research50(D1) pp. D875​-D882​.​ DOI: https://doi.org/10.1093/nar/gkab943 
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  • 2021 Journal Article
    ​ ​SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes​
    Yildirim, A.; Mozaffari-Jovin, S.; Wallisch, A.-K.; Schäfer, J.; Ludwig, S. E J; Urlaub, H. & Lührmann, R. et al.​ (2021) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gkab386 
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  • 2021 Journal Article
    ​ ​Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor​
    Karki, P.; Carney, T. D; Maracci, C.; Yatsenko, A. S; Shcherbata, H. & Rodnina, M. V. ​ (2021) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gkab1189 
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  • 2021 Journal Article
    ​ ​Methylated HNRNPK acts on RPS19 to regulate ALOX15 synthesis in erythropoiesis​
    Naarmann-de Vries, I. S; Senatore, R.; Moritz, B.; Marx, G.; Urlaub, H.; Niessing, D. & Ostareck, D. H et al.​ (2021) 
    Nucleic Acids Research49(6) pp. 3507​-3523​.​ DOI: https://doi.org/10.1093/nar/gkab116 
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  • 2020 Journal Article
    ​ ​VarFish: comprehensive DNA variant analysis for diagnostics and research​
    Holtgrewe, M.; Stolpe, O.; Nieminen, M.; Mundlos, S.; Knaus, A.; Kornak, U.   & Seelow, D. et al.​ (2020) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gkaa241 
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  • 2020 Journal Article
    ​ ​DescribePROT: database of amino acid-level protein structure and function predictions​
    Zhao, B.; Katuwawala, A.; Oldfield, C. J; Dunker, A K.; Faraggi, E.; Gsponer, J. & Kloczkowski, A. et al.​ (2020) 
    Nucleic Acids Research49(D1) pp. D298​-D308​.​ DOI: https://doi.org/10.1093/nar/gkaa931 
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  • 2020 Journal Article
    ​ ​CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation​
    Tellier, M.; Zaborowska, J.; Caizzi, L.; Mohammad, E.; Velychko, T.; Schwalb, B. & Ferrer-Vicens, I. et al.​ (2020) 
    Nucleic Acids Research48(14) pp. 7712​-7727​.​ DOI: https://doi.org/10.1093/nar/gkaa514 
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  • 2020 Journal Article
    ​ ​DNA damage alters nuclear mechanics through chromatin reorganization​
    dos Santos, Á.; Cook, A. W; Gough, R. E; Schilling, M.; Olszok, N.; Brown, I. & Wang, L. et al.​ (2020) 
    Nucleic Acids Research49(1) pp. 340​-353​.​ DOI: https://doi.org/10.1093/nar/gkaa1202 
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  • 2020 Journal Article | Research Paper | 
    ​ ​The human box C/D snoRNA U3 is a miRNA source and miR-U3 regulates expression of sortin nexin 27​
    Lemus-Diaz, N.; Ferreira, R. R.; Bohnsack, K. E. ; Gruber, J. & Bohnsack, M. T. ​ (2020) 
    Nucleic Acids Research48(14) pp. 8074​-8089​.​ DOI: https://doi.org/10.1093/nar/gkaa549 
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  • 2020 Journal Article | Research Paper | 
    ​ ​Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes​
    Lavdovskaia, E.; Denks, K.; Nadler, F.; Steube, E.; Linden, A.; Urlaub, H.   & Rodnina, M. V  et al.​ (2020) 
    Nucleic Acids Research48(22) pp. 12929​-12942​.​ DOI: https://doi.org/10.1093/nar/gkaa1132 
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  • 2020 Journal Article
    ​ ​Egr2-guided histone H2B monoubiquitination is required for peripheral nervous system myelination​
    Wüst, H. M; Wegener, A.; Fröb, F.; Hartwig, A. C; Wegwitz, F. ; Kari, V.   & Schimmel, M. et al.​ (2020) 
    Nucleic Acids Research48(16) pp. 8959​-8976​.​ DOI: https://doi.org/10.1093/nar/gkaa606 
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  • 2019 Journal Article | 
    ​ ​Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance​
    Korniy, N.; Goyal, A. ; Hoffmann, M.; Samatova, E. ; Peske, F. ; Pöhlmann, S.   & Rodnina, M. V ​ (2019) 
    Nucleic Acids Research47(10) pp. 5210​-5222​.​ DOI: https://doi.org/10.1093/nar/gkz202 
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  • 2019 Journal Article
    ​ ​SEAweb: the small RNA Expression Atlas web application​
    Rahman, R.-U. ; Liebhoff, A.-M.; Bansal, V.; Fiosins, M.; Rajput, A. ; Sattar, A. & Magruder, D. S et al.​ (2019) 
    Nucleic Acids Research48(D1) pp. D204​-D219​.​ DOI: https://doi.org/10.1093/nar/gkz869 
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  • 2019 Journal Article | 
    ​ ​Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis​
    Reuß, D. R; Faßhauer, P.; Mroch, P. J.; Ul-Haq, I.; Koo, B.-M.; Pöhlein, A. & Gross, C. A et al.​ (2019) 
    Nucleic Acids Research47(10) pp. 5231​-5242​.​ DOI: https://doi.org/10.1093/nar/gkz260 
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  • 2019 Journal Article | 
    ​ ​The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112​
    van Tran, N.; Ernst, F. G.; Hawley, B. R; Zorbas, C.; Ulryck, N.; Hackert, P.   & Bohnsack, K. E et al.​ (2019) 
    Nucleic Acids Research47(15) pp. 7719​-7733​.​ DOI: https://doi.org/10.1093/nar/gkz619 
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  • 2019 Journal Article | 
    ​ ​Structural basis for RNA translocation by DEAH-box ATPases​
    Hamann, F.; Enders, M. & Ficner, R. ​ (2019) 
    Nucleic Acids Research47(8) pp. 4349​-4362​.​ DOI: https://doi.org/10.1093/nar/gkz150 
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  • 2019 Journal Article
    ​ ​SMCHD1 is involved in de novo methylation of the DUX4 -encoding D4Z4 macrosatellite​
    Dion, C.; Roche, S.; Laberthonnière, C.; Broucqsault, N.; Mariot, V.; Xue, S. & Gurzau, A. D et al.​ (2019) 
    Nucleic Acids Research47(6) pp. 2822​-2839​.​ DOI: https://doi.org/10.1093/nar/gkz005 
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  • 2019 Journal Article
    ​ ​Translational recoding: canonical translation mechanisms reinterpreted​
    Rodnina, M. V. ; Korniy, N.; Klimova, M.; Karki, P.; Peng, B.-Z.; Senyushkina, T. & Belardinelli, R. et al.​ (2019) 
    Nucleic Acids Research48(3) pp. 1056​-1067​.​ DOI: https://doi.org/10.1093/nar/gkz783 
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  • 2019 Journal Article
    ​ ​Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit​
    Braun, C. M; Hackert, P. ; Schmid, C. E; Bohnsack, M. T ; Bohnsack, K. E & Perez-Fernandez, J.​ (2019) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gkz1079 
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  • 2019 Journal Article | Research Paper | 
    ​ ​YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries​
    Dubreuil, B.; Sass, E.; Nadav, Y.; Heidenreich, M.; Georgeson, J. M.; Weill, U. & Duan, Y. et al.​ (2019) 
    Nucleic Acids Research47(D1) pp. D1245​-D1249​.​ DOI: https://doi.org/10.1093/nar/gky941 
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  • 2019 Journal Article | 
    ​ ​Broad range of missense error frequencies in cellular proteins​
    Garofalo, R.; Wohlgemuth, I.; Pearson, M.; Lenz, C.; Urlaub, H. & Rodnina, M. V. ​ (2019) 
    Nucleic Acids Research47(6) pp. 2932​-2945​.​ DOI: https://doi.org/10.1093/nar/gky1319 
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  • 2019 Journal Article | 
    ​ ​The hRPC62 subunit of human RNA polymerase III displays helicase activity​
    Ayoubi, L. E.; Dumay-Odelot, H.; Chernev, A.; Boissier, F.; Minvielle-Sébastia, L.; Urlaub, H. & Fribourg, S. et al.​ (2019) 
    Nucleic Acids Research47(19) pp. 10313​-10326​.​ DOI: https://doi.org/10.1093/nar/gkz788 
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  • 2019 Journal Article
    ​ ​Reconstructing complex lineage trees from scRNA-seq data using MERLoT​
    Parra, R G.; Papadopoulos, N.; Ahumada-Arranz, L.; Kholtei, J. E.; Mottelson, N.; Horokhovsky, Y. & Treutlein, B. et al.​ (2019) 
    Nucleic Acids Research47(17) pp. 8961​-8974​.​ DOI: https://doi.org/10.1093/nar/gkz706 
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  • 2019 Journal Article | 
    ​ ​Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3​
    Beissel, C. ; Neumann, B. ; Uhse, S. ; Hampe, I. ; Karki, P.   & Krebber, H. ​ (2019) 
    Nucleic Acids Research47(9) pp. 4798​-4813​.​ DOI: https://doi.org/10.1093/nar/gkz177 
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  • 2018 Journal Article
    ​ ​Shaping epigenetic memory via genomic bookmarking​
    Michieletto, D.; Chiang, M.; Colì, D.; Papantonis, A. ; Orlandini, E.; Cook, P. R. & Marenduzzo, D.​ (2018) 
    Nucleic Acids Research46(1) pp. 83​-93​.​ DOI: https://doi.org/10.1093/nar/gkx1200 
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  • 2018 Journal Article
    ​ ​The APT complex is involved in non-coding RNA transcription and is distinct from CPF​
    Lidschreiber, M.; Easter, A. D; Battaglia, S.; Rodríguez-Molina, J. B; Casañal, A.; Carminati, M. & Baejen, C. et al.​ (2018) 
    Nucleic Acids Research,.​ DOI: https://doi.org/10.1093/nar/gky845 
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  • 2018 Journal Article
    ​ ​The BaMM web server for de-novo motif discovery and regulatory sequence analysis​
    Kiesel, A.; Roth, C.; Ge, W.; Wess, M.; Meier, M. & Söding, J. ​ (2018) 
    Nucleic Acids Research46(W1) pp. W215​-W220​.​ DOI: https://doi.org/10.1093/nar/gky431 
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  • 2018 Journal Article
    ​ ​Small synthetic molecule-stabilized RNA pseudoknot as an activator for –1 ribosomal frameshifting​
    Matsumoto, S.; Caliskan, N.; Rodnina, M. V. ; Murata, A. & Nakatani, K.​ (2018) 
    Nucleic Acids Research46(16) pp. 8079​-8089​.​ DOI: https://doi.org/10.1093/nar/gky689 
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  • 2018 Journal Article
    ​ ​Identification of new high affinity targets for Roquin based on structural conservation​
    Braun, J.; Fischer, S.; Xu, Z. Z; Sun, H.; Ghoneim, D. H; Gimbel, A. T & Plessmann, U. et al.​ (2018) 
    Nucleic Acids Research46(22) pp. 12109​-12125​.​ DOI: https://doi.org/10.1093/nar/gky908 
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  • 2018 Journal Article
    ​ ​EndoDB: a database of endothelial cell transcriptomics data​
    Khan, S.; Taverna, F.; Rohlenova, K.; Treps, L.; Geldhof, V.; de Rooij, L. & Sokol, L. et al.​ (2018) 
    Nucleic Acids Research47(D1) pp. D736​-D744​.​ DOI: https://doi.org/10.1093/nar/gky997 
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  • 2018 Journal Article | Research Paper
    ​ ​mirDIP 4.1-integrative database of human microRNA target predictions​
    Tokar, T.; Pastrello, C.; Rossos, A. E. M.; Abovsky, M.; Hauschild, A.-C. ; Tsay, M. & Lu, R. et al.​ (2018) 
    Nucleic Acids Research46(D1) pp. D360​-D370​.​ DOI: https://doi.org/10.1093/nar/gkx1144 
    Details  DOI  PMID  PMC 
  • 2018 Journal Article | 
    ​ ​TFClass: expanding the classification of human transcription factors to their mammalian orthologs​
    Wingender, E.; Schoeps, T.; Haubrock, M. ; Krull, M. & Dönitz, J.​ (2018) 
    Nucleic Acids Research46(D1) pp. D343​-D347​.​ DOI: https://doi.org/10.1093/nar/gkx987 
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  • 2018 Journal Article | Research Paper | 
    ​ ​A context-specific cardiac β-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart​
    Iyer, L. M ; Nagarajan, S. ; Woelfer, M.; Schoger, E.; Khadjeh, S. ; Zafiriou, M. P.   & Kari, V.  et al.​ (2018) 
    Nucleic Acids Research46(6) pp. 2850​-2867​.​ DOI: https://doi.org/10.1093/nar/gky049 
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  • 2018 Journal Article | Research Paper | 
    ​ ​The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis​
    Lavdovskaia, E.; Kolander, E.; Steube, E.; Mai, M. M. Mai, Mandy Mong-Quyen; Urlaub, H.   & Richter-Dennerlein, R. ​ (2018) 
    Nucleic Acids Research46(16) pp. 8471​-8482​.​ DOI: https://doi.org/10.1093/nar/gky701 
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  • 2018 Journal Article
    ​ ​Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis​
    Haase, N.; Holtkamp, W.; Lipowsky, R.; Rodnina, M.   & Rudorf, S.​ (2018) 
    Nucleic Acids Research46(22) pp. e130​-e130​.​ DOI: https://doi.org/10.1093/nar/gky740 
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  • 2018 Journal Article
    ​ ​Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis​
    Haase, N.; Holtkamp, W.; Lipowsky, R.; Rodnina, M.   & Rudorf, S.​ (2018) 
    Nucleic Acids Research46(22) pp. 12186​-12187​.​ DOI: https://doi.org/10.1093/nar/gky1101 
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  • 2017 Journal Article | Research Paper | 
    ​ ​Signal recognition particle binds to translating ribosomes before emergence of a signal anchor sequence​
    Mercier, E.; Holtkamp, W. ; Rodnina, M. V.   & Wintermeyer, W. ​ (2017) 
    Nucleic acids research45(20) pp. 11858​-11866​.​ DOI: https://doi.org/10.1093/nar/gkx888 
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  • 2017 Journal Article | 
    ​ ​Expanded and updated data and a query pipeline for iBeetle-Base.​
    Dönitz, J. ; Gerischer, L.; Hahnke, S.; Pfeiffer, S. & Bucher, G. ​ (2017) 
    Nucleic acids research,.​ DOI: https://doi.org/10.1093/nar/gkx984 
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  • 2017 Journal Article | 
    ​ ​Histone deacetylase class-I inhibition promotes epithelial gene expression in pancreatic cancer cells in a BRD4-and MYC-dependent manner​
    Mishra, V. K.; Wegwitz, F.; Kosinsky, R. L.; Sen, M. ; Baumgartner, R.; Wulff, T. & Siveke, J. T. et al.​ (2017) 
    Nucleic Acids Research45(11) pp. 6334​-6349​.​ DOI: https://doi.org/10.1093/nar/gkx212 
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  • 2017 Journal Article
    ​ ​mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines​
    Hua, X.; Tang, R.; Xu, X.; Wang, Z.; Xu, Q.; Chen, L. & Wingender, E.  et al.​ (2017) 
    Nucleic Acids Research46(D1) pp. D168​-D174​.​ DOI: https://doi.org/10.1093/nar/gkx996 
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  • 2017 Journal Article
    ​ ​A new role for FBP21 as regulator of Brr2 helicase activity​
    Henning, L. M.; Santos, K. F.; Sticht, J.; Jehle, S.; Lee, C.-T. ; Wittwer, M. & Urlaub, H.  et al.​ (2017) 
    Nucleic Acids Research45(13) pp. 7922​-7937​.​ DOI: https://doi.org/10.1093/nar/gkx535 
    Details  DOI 
  • 2017 Journal Article
    ​ ​SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis​
    Zhu, B. & Stülke, J. ​ (2017) 
    Nucleic Acids Research46(D1) pp. D743​-D748​.​ DOI: https://doi.org/10.1093/nar/gkx908 
    Details  DOI 
  • 2017 Journal Article | 
    ​ ​Regulation of Prp43-mediated disassembly of spliceosomes by its cofactors Ntr1 and Ntr2​
    Fourmann, J.-B.; Tauchert, M. J. ; Ficner, R. ; Fabrizio, P. & Lührmann, R. ​ (2017) 
    Nucleic Acids Research45(7) pp. 4068​-4080​.​ DOI: https://doi.org/10.1093/nar/gkw1225 
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  • 2017 Journal Article | 
    ​ ​Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism​
    Gonzalez, G. M.; Durica-Mitic, S.; Hardwick, S. W.; Moncrieffe, M. C.; Resch, M.; Neumann, P.   & Ficner, R.  et al.​ (2017) 
    Nucleic Acids Research45(18) pp. 10845​-10860​.​ DOI: https://doi.org/10.1093/nar/gkx732 
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  • 2017 Journal Article | 
    ​ ​SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing​
    Pozzi, B.; Bragado, L.; Will, C. L.; Mammi, P.; Risso, G.; Urlaub, H. & Luehrmann, R. et al.​ (2017) 
    Nucleic Acids Research45(11) pp. 6729​-6745​.​ DOI: https://doi.org/10.1093/nar/gkx213 
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  • 2017 Journal Article
    ​ ​Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa​
    Sonnleitner, E.; Wulf, A.; Campagne, S.; Pei, X.-Y.; Wolfinger, M. T; Forlani, G. & Prindl, K. et al.​ (2017) 
    Nucleic Acids Research46(3) pp. 1470​-1485​.​ DOI: https://doi.org/10.1093/nar/gkx1245 
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  • 2017 Journal Article
    ​ ​Mechanistic insight into the assembly of the HerA–NurA helicase–nuclease DNA end resection complex​
    Ahdash, Z.; Lau, A. M.; Byrne, R. T.; Lammens, K.; Stüetzer, A.; Urlaub, H.   & Booth, P. J. et al.​ (2017) 
    Nucleic Acids Research45(20) pp. 12025​-12038​.​ DOI: https://doi.org/10.1093/nar/gkx890 
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  • 2017 Journal Article
    ​ ​CHD1 regulates cell fate determination by activation of differentiation-induced genes​
    Baumgart, S. J. ; Najafova, Z. ; Hossan, T. ; Xie, W. ; Nagarajan, S. ; Kari, V.   & Ditzel, N. et al.​ (2017) 
    Nucleic Acids Research45(13) pp. 7722​-7735​.​ DOI: https://doi.org/10.1093/nar/gkx377 
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  • 2017 Journal Article | 
    ​ ​The SmAP2 RNA binding motif in the 3′UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus​
    Martens, B.; Sharma, K.; Urlaub, H.   & Bläsi, U.​ (2017) 
    Nucleic Acids Research45(15) pp. 8957​-8967​.​ DOI: https://doi.org/10.1093/nar/gkx581 
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  • 2017 Journal Article | 
    ​ ​BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire​
    Najafova, Z.; Tirado-Magallanes, R.; Subramaniam, M.; Hossan, T.; Schmidt, G.; Nagarajan, S. & Baumgart, S. J. et al.​ (2017) 
    Nucleic Acids Research45(1) pp. 127​-141​.​ DOI: https://doi.org/10.1093/nar/gkw826 
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  • 2017 Journal Article | 
    ​ ​Self-cytoplasmic DNA upregulates the mutator enzyme APOBEC3A leading to chromosomal DNA damage​
    Suspène, R.; Mussil, B.; Laude, H.; Caval, V.; Berry, N.; Bouzidi, M. S. & Thiers, V. et al.​ (2017) 
    Nucleic Acids Research45(6) pp. 3231​-3241​.​ DOI: https://doi.org/10.1093/nar/gkx001 
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  • 2017 Journal Article | 
    ​ ​BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells​
    Nagarajan, S.; Bedi, U.; Budida, A. ; Hamdan, F. H. ; Mishra, V. K.; Najafova, Z. & Xie, W. et al.​ (2017) 
    Nucleic Acids Research45(6) pp. 3130​-3145​.​ DOI: https://doi.org/10.1093/nar/gkw1276 
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  • 2017 Journal Article | 
    ​ ​The ribosome biogenesis factor yUtp23/hUTP23 coordinates key interactions in the yeast and human pre-40S particle and hUTP23 contains an essential PIN domain​
    Wells, G. R.; Weichmann, F.; Sloan, K. E.; Colvin, D.; Watkins, N. J. & Schneider, C.​ (2017) 
    Nucleic Acids Research45(8) pp. 4796​-4809​.​ DOI: https://doi.org/10.1093/nar/gkw1344 
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  • 2017 Journal Article
    ​ ​Disentangling polydispersity in the PCNA-p15(PAF) complex, a disordered, transient and multivalent macromolecular assembly​
    Cordeiro, T. N.; Chen, P.-c.; De Biasio, A.; Sibille, N.; Blanco, F. J.; Hub, J. S. & Crehuet, R. et al.​ (2017) 
    Nucleic Acids Research45(3) pp. 1501​-1515​.​ DOI: https://doi.org/10.1093/nar/gkw1183 
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  • 2017 Journal Article | 
    ​ ​The G-patch protein NF-kappa B-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis​
    Memet, I.; Doebele, C.; Sloan, K. E. & Bohnsack, M. T. ​ (2017) 
    Nucleic Acids Research45(9) pp. 5359​-5374​.​ DOI: https://doi.org/10.1093/nar/gkx013 
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  • 2016 Journal Article
    ​ ​Uniclust databases of clustered and deeply annotated protein sequences and alignments​
    Mirdita, M.; von den Driesch, L.; Galiez, C.; Martin, M. J.; Söding, J.   & Steinegger, M.​ (2016) 
    Nucleic Acids Research45(D1) pp. D170​-D176​.​ DOI: https://doi.org/10.1093/nar/gkw1081 
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  • 2016 Journal Article
    ​ ​The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans (vol 44, pg 5399, 2016)​
    Wells, G. R.; Weichmann, F.; Colvin, D.; Sloan, K. E.; Kudla, G.; Tollervey, D. & Watkins, N. J. et al.​ (2016) 
    Nucleic Acids Research44(18).​ DOI: https://doi.org/10.1093/nar/gkw645 
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  • 2016 Journal Article
    ​ ​The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis​
    Alva, V.; Nam, S.-Z.; Söding, J.   & Lupas, A. N.​ (2016) 
    Nucleic Acids Research44(W1) pp. W410​-W415​.​ DOI: https://doi.org/10.1093/nar/gkw348 
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  • 2016 Journal Article
    ​ ​Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences​
    Siebert, M. & Söding, J. ​ (2016) 
    Nucleic Acids Research44(13) pp. 6055​-6069​.​ DOI: https://doi.org/10.1093/nar/gkw521 
    Details  DOI 
  • 2016 Journal Article | 
    ​ ​SubtiWiki 2.0-an integrated database for the model organism Bacillus subtilis​
    Michna, R. H.; Zhu, B.; Maeder, U. & Stuelke, J.​ (2016) 
    Nucleic Acids Research44(D1) pp. D654​-D662​.​ DOI: https://doi.org/10.1093/nar/gkv1006 
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  • 2016 Journal Article
    ​ ​The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans​
    Wells, G. R.; Weichmann, F.; Colvin, D.; Sloan, K. E.; Kudla, G.; Tollervey, D. & Watkins, N. J. et al.​ (2016) 
    Nucleic Acids Research44(11) pp. 5399​-5409​.​ DOI: https://doi.org/10.1093/nar/gkw213 
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  • 2016 Journal Article | 
    ​ ​Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system​
    Gleditzsch, D.; Mueller-Esparza, H.; Pausch, P.; Sharma, K.; Dwarakanath, S.; Urlaub, H. & Bange, G. et al.​ (2016) 
    Nucleic Acids Research44(12) pp. 5872​-5882​.​ DOI: https://doi.org/10.1093/nar/gkw469 
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  • 2015 Journal Article
    ​ ​Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories​
    Caudron-Herger, M.; Cook, P. R.; Rippe, K. & Papantonis, A. ​ (2015) 
    Nucleic Acids Research43(14) pp. e95​-e95​.​ DOI: https://doi.org/10.1093/nar/gkv390 
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  • 2015 Journal Article
    ​ ​Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation​
    Bock, L. V. ; Blau, C. ; Vaiana, A. C.   & Grubmüller, H. ​ (2015) 
    Nucleic Acids Research43(14) pp. 6747​-6760​.​ DOI: https://doi.org/10.1093/nar/gkv649 
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  • 2015 Journal Article
    ​ ​Splicing of many human genes involves sites embedded within introns​
    Kelly, S.; Georgomanolis, T.; Zirkel, A.; Diermeier, S.; O'Reilly, D.; Murphy, S. & Längst, G. et al.​ (2015) 
    Nucleic Acids Research43(9) pp. 4721​-4732​.​ DOI: https://doi.org/10.1093/nar/gkv386 
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  • 2015 Journal Article | Research Paper
    ​ ​Directional transition from initiation to elongation in bacterial translation​
    Goyal, A. ; Belardinelli, R. ; Maracci, C. ; Milón, P.   & Rodnina, M. ​ (2015) 
    Nucleic Acids Research43(22) pp. 10700​-10712​.​ DOI: https://doi.org/10.1093/nar/gkv869 
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  • 2015 Journal Article | 
    ​ ​The complex portal--an encyclopaedia of macromolecular complexes.​
    Meldal, B. H. M.; Forner-Martinez, O.; Costanzo, M. C.; Dana, J.; Demeter, J.; Dumousseau, M. & Dwight, S. S. et al.​ (2015) 
    Nucleic acids research43(Database issue) pp. D479​-D484​.​ DOI: https://doi.org/10.1093/nar/gku975 
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  • 2015 Journal Article | Research Paper | 
    ​ ​Architecture of the eIF2B regulatory subcomplex and its implications for the regulation of guanine nucleotide exchange on eIF2​
    Kuhle, B.; Eulig, N. K. & Ficner, R. ​ (2015) 
    Nucleic Acids Research43(20) pp. 9994​-10014​.​ DOI: https://doi.org/10.1093/nar/gkv930 
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  • 2015 Journal Article | Research Paper
    ​ ​A model for transcription initiation in human mitochondria​
    Morozov, Y. I.; Parshin, A. V.; Agaronyan, K.; Cheung, A. C. M.; Anikin, M.; Cramer, P.   & Temiakov, D.​ (2015) 
    Nucleic Acids Research43(7) pp. 3726​-3735​.​ DOI: https://doi.org/10.1093/nar/gkv235 
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  • 2015 Journal Article | 
    ​ ​Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins​
    Crisci, A.; Raleff, F.; Bagdiul, I.; Raabe, M.; Urlaub, H.; Rain, J.-C. & Kraemer, A.​ (2015) 
    Nucleic Acids Research43(21) pp. 10456​-10473​.​ DOI: https://doi.org/10.1093/nar/gkv952 
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  • 2015 Journal Article | 
    ​ ​TFClass: a classification of human transcription factors and their rodent orthologs​
    Wingender, E.; Schoeps, T.; Haubrock, M.   & Doenitz, J.​ (2015) 
    Nucleic Acids Research43(D1) pp. D97​-D102​.​ DOI: https://doi.org/10.1093/nar/gku1064 
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  • 2015 Journal Article | 
    ​ ​iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum​
    Doenitz, J.; Schmitt-Engel, C.; Grossmann, D.; Gerischer, L.; Tech, M. ; Schoppmeier, M. & Klingler, M. et al.​ (2015) 
    Nucleic Acids Research43(D1) pp. D720​-D725​.​ DOI: https://doi.org/10.1093/nar/gku1054 
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  • 2015 Journal Article | Research Paper
    ​ ​Partitioning between recoding and termination at a stop codon-selenocysteine insertion sequence​
    Kotini, S. B. ; Peske, F.   & Rodnina, M. V. ​ (2015) 
    Nucleic Acids Research43(13) pp. 6426​-6438​.​ DOI: https://doi.org/10.1093/nar/gkv558 
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  • 2015 Journal Article | 
    ​ ​Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence​
    Turriani, E.; Hoebartner, C. & Jovin, T. M.​ (2015) 
    Nucleic Acids Research43(1) pp. 40​-50​.​ DOI: https://doi.org/10.1093/nar/gku1268 
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  • 2015 Journal Article | 
    ​ ​WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics​
    Knight, C. J. & Hub, J. S.​ (2015) 
    Nucleic Acids Research43(W1) pp. W225​-W230​.​ DOI: https://doi.org/10.1093/nar/gkv309 
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  • 2015 Journal Article | 
    ​ ​The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21​
    Sloan, K. E.; Leisegang, M. S.; Doebele, C.; Ramirez, A. S.; Simm, S.; Safferthal, C. & Kretschmer, J. et al.​ (2015) 
    Nucleic Acids Research43(1) pp. 553​-564​.​ DOI: https://doi.org/10.1093/nar/gku1291 
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  • 2014 Journal Article | Research Paper
    ​ ​Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast​
    Hirschmann, W. D.; Westendorf, H.; Mayer, A.; Cannarozzi, G.; Cramer, P.   & Jansen, R.-P.​ (2014) 
    Nucleic Acids Research42(6) pp. 4043​-4055​.​ DOI: https://doi.org/10.1093/nar/gkt1392 
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  • 2014 Journal Article | Research Paper | 
    ​ ​Insights into the activation of the helicase Prp43 by biochemical studies and structural mass spectrometry​
    Christian, H.; Hofele, R. V.; Urlaub, H.   & Ficner, R. ​ (2014) 
    Nucleic Acids Research42(2) pp. 1162​-1179​.​ DOI: https://doi.org/10.1093/nar/gkt985 
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  • 2014 Journal Article | 
    ​ ​Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches​
    Horwege, S.; Lindner, S.; Boden, M.; Hatje, K.; Kollmar, M.; Leimeister, C.-A. & Morgenstern, B. ​ (2014) 
    Nucleic Acids Research42(W1) pp. W7​-W11​.​ DOI: https://doi.org/10.1093/nar/gku398 
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  • 2014 Journal Article | 
    ​ ​SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information​
    Michna, R. H.; Commichau, F. M.; Toedter, D.; Zschiedrich, C. P. & Stuelke, J.​ (2014) 
    Nucleic Acids Research42(D1) pp. D692​-D698​.​ DOI: https://doi.org/10.1093/nar/gkt1002 
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  • 2014 Journal Article | Research Paper | 
    ​ ​Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes​
    Khoshnevis, S.; Gunisova, S.; Vlckova, V.; Kouba, T.; Neumann, P. ; Beznoskova, P. & Ficner, R.  et al.​ (2014) 
    Nucleic Acids Research42(6) pp. 4123​-4139​.​ DOI: https://doi.org/10.1093/nar/gkt1369 
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  • 2014 Journal Article | 
    ​ ​The evolution of the ribosome biogenesis pathway from a yeast perspective​
    Ebersberger, I.; Simm, S.; Leisegang, M. S.; Schmitzberger, P.; Mirus, O.; von Haeseler, A. & Bohnsack, M. T.  et al.​ (2014) 
    Nucleic Acids Research42(3) pp. 1509​-1523​.​ DOI: https://doi.org/10.1093/nar/gkt1137 
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  • 2014 Journal Article | Research Paper | 
    ​ ​Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification​
    Neumann, P. ; Lakomek, K.; Naumann, P.-T.; Erwin, W. M.; Lauhon, C. T. & Ficner, R. ​ (2014) 
    Nucleic Acids Research42(10) pp. 6673​-6685​.​ DOI: https://doi.org/10.1093/nar/gku249 
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  • 2014 Journal Article | 
    ​ ​Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break​
    Vlasic, I.; Mertens, R.; Seco, E. M.; Carrasco, B.; Ayora, S.; Reitz, G. & Commichau, F. M. et al.​ (2014) 
    Nucleic Acids Research42(4) pp. 2295​-2307​.​ DOI: https://doi.org/10.1093/nar/gkt1194 
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  • 2014 Journal Article | Research Paper
    ​ ​A novel intermediate in transcription initiation by human mitochondrial RNA polymerase​
    Morozov, Y. I.; Agaronyan, K.; Cheung, A. C. M.; Anikin, M.; Cramer, P.   & Temiakov, D.​ (2014) 
    Nucleic Acids Research42(6) pp. 3884​-3893​.​ DOI: https://doi.org/10.1093/nar/gkt1356 
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  • 2014 Journal Article
    ​ ​Timing of GTP binding and hydrolysis by translation termination factor RF3​
    Peske, F. ; Kuhlenkoetter, S. ; Rodnina, M. V.   & Wintermeyer, W. ​ (2014) 
    Nucleic acids research42(3) pp. 1812​-1820​.​ DOI: https://doi.org/10.1093/nar/gkt1095 
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  • 2013 Journal Article
    ​ ​Space exploration by the promoter of a long human gene during one transcription cycle​
    Larkin, J. D.; Papantonis, A. ; Cook, P. R. & Marenduzzo, D.​ (2013) 
    Nucleic Acids Research41(4) pp. 2216​-2227​.​ DOI: https://doi.org/10.1093/nar/gks1441 
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  • 2013 Journal Article | 
    ​ ​DIALIGN at GOBICS-multiple sequence alignment using various sources of external information​
    Al Ait, L.; Yamak, Z. & Morgenstern, B. ​ (2013) 
    Nucleic Acids Research41(W1) pp. W3​-W7​.​ DOI: https://doi.org/10.1093/nar/gkt283 
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  • 2013 Journal Article | 
    ​ ​Post-transcriptional regulation of CD83 expression by AUF1 proteins​
    Ehlers, C.; Schirmer, S.; Kehlenbach, R. H.; Hauber, J. & Chemnitz, J.​ (2013) 
    Nucleic Acids Research41(1) pp. 206​-219​.​ DOI: https://doi.org/10.1093/nar/gks1069 
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  • 2013 Journal Article | Research Paper
    ​ ​The RNA polymerase trigger loop functions in all three phases of the transcription cycle​
    Fouqueau, T.; Zeller, M. E.; Cheung, A. C.; Cramer, P.   & Thomm, M.​ (2013) 
    Nucleic Acids Research41(14) pp. 7048​-7059​.​ DOI: https://doi.org/10.1093/nar/gkt433 
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  • 2013 Journal Article | 
    ​ ​TFClass: an expandable hierarchical classification of human transcription factors​
    Wingender, E.; Schoeps, T. & Doenitz, J.​ (2013) 
    Nucleic Acids Research41(D1) pp. D165​-D170​.​ DOI: https://doi.org/10.1093/nar/gks1123 
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  • 2013 Journal Article | Research Paper
    ​ ​Model of the Mediator middle module based on protein cross-linking​
    Lariviere, L.; Plaschka, C.; Seizl, M.; Petrotchenko, E. V.; Wenzeck, L.; Borchers, C. H. & Cramer, P. ​ (2013) 
    Nucleic Acids Research41(20) pp. 9266​-9273​.​ DOI: https://doi.org/10.1093/nar/gkt704 
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  • 2012 Journal Article
    ​ ​The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences​
    Luehr, S.; Hartmann, H. & Söding, J. ​ (2012) 
    Nucleic Acids Research40(W1) pp. W104​-W109​.​ DOI: https://doi.org/10.1093/nar/gks602 
    Details  DOI 
  • 2012 Journal Article | 
    ​ ​jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus​
    Schultz, A.-K.; Bulla, I.; Abdou-Chekaraou, M.; Gordien, E.; Morgenstern, B. ; Zoulim, F. & Deny, P. et al.​ (2012) 
    Nucleic Acids Research40(W1) pp. W193​-W198​.​ DOI: https://doi.org/10.1093/nar/gks414 
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  • 2012 Journal Article | Research Paper
    ​ ​One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data​
    Duemcke, S.; Seizl, M.; Etzold, S.; Pirkl, N.; Martin, D. E.; Cramer, P.   & Tresch, A.​ (2012) 
    Nucleic Acids Research40(18) pp. 8883​-8892​.​ DOI: https://doi.org/10.1093/nar/gks695 
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  • 2012 Journal Article
    ​ ​Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation​
    Burakovsky, D. E. ; Prokhorova, I. V.; Sergiev, P. V.; Milón, P. ; Sergeeva, O. V.; Bogdanov, A. A. & Rodnina, M. V.  et al.​ (2012) 
    Nucleic Acids Research40(16) pp. 7885​-7895​.​ DOI: https://doi.org/10.1093/nar/gks508 
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  • 2012 Journal Article | Research Paper | 
    ​ ​Structure and activity of the only human RNase T2​
    Thorn, A.; Steinfeld, R. ; Ziegenbein, M.; Grapp, M.; Hsiao, H.-H.; Urlaub, H.   & Sheldrick, G. M.  et al.​ (2012) 
    Nucleic Acids Research40(17) pp. 8733​-8742​.​ DOI: https://doi.org/10.1093/nar/gks614 
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  • 2012 Journal Article | Research Paper
    ​ ​Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage​
    Jennebach, S.; Herzog, F.; Aebersold, R. & Cramer, P. ​ (2012) 
    Nucleic Acids Research40(12) pp. 5591​-5601​.​ DOI: https://doi.org/10.1093/nar/gks220 
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  • 2012 Journal Article
    ​ ​SubtiWiki-a comprehensive community resource for the model organism Bacillus subtilis​
    Maeder, U.; Schmeisky, A. G.; Florez, L. A. & Stuelke, J.​ (2012) 
    Nucleic Acids Research40(D1) pp. D1278​-D1287​.​ DOI: https://doi.org/10.1093/nar/gkr923 
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  • 2011 Journal Article
    ​ ​Structural and functional analysis of the archaeal endonuclease Nob1​
    Veith, T.; Martin, R.; Wurm, J. P.; Weis, B. L.; Duchardt-Ferner, E.; Safferthal, C. & Hennig, R. et al.​ (2011) 
    Nucleic Acids Research40(7) pp. 3259​-3274​.​ DOI: https://doi.org/10.1093/nar/gkr1186 
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  • 2011 Journal Article
    ​ ​The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset​
    Feller, C.; Prestel, M.; Hartmann, H.; Straub, T.; Söding, J.   & Becker, P. B.​ (2011) 
    Nucleic Acids Research40(4) pp. 1509​-1522​.​ DOI: https://doi.org/10.1093/nar/gkr869 
    Details  DOI 
  • 2011 Journal Article | 
    ​ ​CoMet-a web server for comparative functional profiling of metagenomes​
    Lingner, T.; Asshauer, K. P.; Schreiber, F. & Meinicke, P. ​ (2011) 
    Nucleic Acids Research39 pp. W518​-W523​.​ DOI: https://doi.org/10.1093/nar/gkr388 
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  • 2011 Journal Article | 
    ​ ​Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae​
    Goepel, Y.; Luettmann, D.; Heroven, A. K.; Reichenbach, B.; Dersch, P. & Goerke, B.​ (2011) 
    Nucleic Acids Research39(4) pp. 1294​-1309​.​ DOI: https://doi.org/10.1093/nar/gkq986 
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  • 2011 Journal Article | Research Paper
    ​ ​Towards computional specificity screening of DNA-binding proteins​
    Seeliger, D.; Buelens, F. P.; Goette, M.; Groot, B. L. de   & Grubmüller, H. ​ (2011) 
    Nucleic Acids Research39(19) pp. 8281​-8290​.​ DOI: https://doi.org/10.1093/nar/gkr531 
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  • 2011 Journal Article | Research Paper
    ​ ​Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization​
    Seizl, M.; Lariviere, L.; Pfaffeneder, T.; Wenzeck, L. & Cramer, P. ​ (2011) 
    Nucleic Acids Research39(14) pp. 6291​-6304​.​ DOI: https://doi.org/10.1093/nar/gkr229 
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  • 2011 Journal Article | 
    ​ ​Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family​
    Huebner, S.; Declerck, N.; Diethmaier, C.; Le Coq, D.; Aymerich, S. & Stuelke, J.​ (2011) 
    Nucleic Acids Research39(10) pp. 4360​-4372​.​ DOI: https://doi.org/10.1093/nar/gkr021 
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  • 2010 Journal Article
    ​ ​jpHMM: improving the reliability of recombination prediction in HIV-1​
    Schultz, A.-K.; Zhang, M.; Bulla, I.; Leitner, T.; Korber, B.; Morgenstern, B.   & Stanke, M.​ (2010) 
    Nucleic Acids Research38(3) pp. 1059​-1059​.​ DOI: https://doi.org/10.1093/nar/gkq015 
    Details  DOI 
  • 2010 Journal Article
    ​ ​The Bowen–Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA​
    Meyer, B.; Wurm, J. P.; Kötter, P.; Leisegang, M. S.; Schilling, V.; Buchhaupt, M. & Held, M. et al.​ (2010) 
    Nucleic Acids Research39(4) pp. 1526​-1537​.​ DOI: https://doi.org/10.1093/nar/gkq931 
    Details  DOI 
  • 2010 Journal Article | 
    ​ ​DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS​
    Subramanian, A. R.; Hiran, S.; Steinkamp, R.; Meinicke, P. ; Corel, E. & Morgenstern, B. ​ (2010) 
    Nucleic Acids Research38 pp. W19​-W22​.​ DOI: https://doi.org/10.1093/nar/gkq442 
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  • 2010 Journal Article | Research Paper
    ​ ​Preparation and topology of the Mediator middle module​
    Koschubs, T.; Lorenzen, K.; Baumli, S.; Sandstroem, S.; Heck, A. J. R. & Cramer, P. ​ (2010) 
    Nucleic Acids Research38(10) pp. 3186​-3195​.​ DOI: https://doi.org/10.1093/nar/gkq029 
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  • 2010 Journal Article | Research Paper
    ​ ​The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis​
    Beck, K.; Vannini, A.; Cramer, P.   & Lipps, G.​ (2010) 
    Nucleic Acids Research38(19) pp. 6707​-6718​.​ DOI: https://doi.org/10.1093/nar/gkq447 
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  • 2010 Journal Article
    ​ ​Helix-hairpin-helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues​
    Schomacher, L.; Smolorz, S.; Ciirdaeva, E.; Ber, S.; Kramer, W. & Fritz, H.-J.​ (2010) 
    Nucleic Acids Research38(15) pp. 5119​-5129​.​ DOI: https://doi.org/10.1093/nar/gkq270 
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  • 2010 Journal Article | Research Paper
    ​ ​Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif​
    Hirtreiter, A.; Damsma, G. E.; Cheung, A. C. M.; Klose, D.; Grohmann, D.; Vojnic, E. & Martin, A. C. R. et al.​ (2010) 
    Nucleic Acids Research38(12) pp. 4040​-4051​.​ DOI: https://doi.org/10.1093/nar/gkq135 
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  • 2010 Journal Article
    ​ ​Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs​
    Brameier, M.; Herwig, A.; Reinhardt, R.; Walter, L. & Gruber, J.​ (2010) 
    Nucleic Acids Research39(2) pp. 675​-686​.​ DOI: https://doi.org/10.1093/nar/gkq776 
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  • 2010 Journal Article | Research Paper
    ​ ​The crystal structure of unmodified tRNA(Phe) from Escherichia coli​
    Byrne, R. T.; Konevega, A. L. ; Rodnina, M. V.   & Antson, A. A.​ (2010) 
    Nucleic Acids Research38(12) pp. 4154​-4162​.​ DOI: https://doi.org/10.1093/nar/gkq133 
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  • 2010 Journal Article | Research Paper | 
    ​ ​Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry​
    Kuehn-Hoelsken, E.; Lenz, C. ; Dickmanns, A. ; Hsiao, H.-H.; Richter, F. M.; Kastner, B. & Ficner, R.  et al.​ (2010) 
    Nucleic Acids Research38(16) pp. 5581​-5593​.​ DOI: https://doi.org/10.1093/nar/gkq272 
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  • 2009 Journal Article
    ​ ​HHomp—prediction and classification of outer membrane proteins​
    Remmert, M.; Linke, D.; Lupas, A. N. & Söding, J. ​ (2009) 
    Nucleic Acids Research37(suppl_2) pp. W446​-W451​.​ DOI: https://doi.org/10.1093/nar/gkp325 
    Details  DOI 
  • 2009 Review | 
    ​ ​Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins​
    Orthaus, S.; Klement, K.; Happel, N.; Hoischen, C.& Diekmann, S.​ (2009)
    Nucleic Acids Research, 37​(10) pp. 3391​-3406​.​
    Oxford Univ Press. DOI: https://doi.org/10.1093/nar/gkp199 
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  • 2009 Journal Article
    ​ ​OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences​
    Schreiber, F.; Woerheide, G. & Morgenstern, B. ​ (2009) 
    Nucleic Acids Research37 pp. W185​-W188​.​ DOI: https://doi.org/10.1093/nar/gkp434 
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  • 2009 Journal Article
    ​ ​jpHMM: Improving the reliability of recombination prediction in HIV-1​
    Schultz, A.-K.; Zhang, M.; Bulla, I.; Leitner, T.; Korber, B.; Morgenstern, B.   & Stanke, M.​ (2009) 
    Nucleic Acids Research37 pp. W647​-W651​.​ DOI: https://doi.org/10.1093/nar/gkp371 
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  • 2009 Journal Article
    ​ ​A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility​
    Klostermeier, D. & Rudolph, M. G.​ (2009) 
    Nucleic Acids Research37(2) pp. 421​-430​.​ DOI: https://doi.org/10.1093/nar/gkn947 
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  • 2009 Journal Article
    ​ ​DNA translocation activity of the multifunctional replication protein ORF904 from the archaeal plasmid pRN1​
    Sanchez, M.; Drechsler, M.; Stark, H.   & Lipps, G.​ (2009) 
    Nucleic Acids Research37(20) pp. 6831​-6848​.​ DOI: https://doi.org/10.1093/nar/gkp742 
    Details  DOI 
  • 2009 Journal Article | 
    ​ ​Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies​
    Gordon, P. M. K.; Schuetz, E.; Beck, J.; Urnovitz, H. B.; Graham, C.; Clark, R. & Dudas, S. et al.​ (2009) 
    Nucleic Acids Research37(2) pp. 550​-556​.​ DOI: https://doi.org/10.1093/nar/gkn963 
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  • 2009 Journal Article | Research Paper
    ​ ​Structural basis for m(7)G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1​
    Monecke, T. ; Dickmanns, A.   & Ficner, R. ​ (2009) 
    Nucleic Acids Research37(12) pp. 3865​-3877​.​ DOI: https://doi.org/10.1093/nar/gkp249 
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  • 2009 Journal Article | 
    ​ ​Orphelia: predicting genes in metagenomic sequencing reads​
    Hoff, K. J.; Lingner, T.; Meinicke, P.   & Tech, M. ​ (2009) 
    Nucleic Acids Research37 pp. W101​-W105​.​ DOI: https://doi.org/10.1093/nar/gkp327 
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  • 2009 Journal Article
    ​ ​DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision​
    Schomacher, L.; Chong, J. P. J.; McDermott, P.; Kramer, W. & Fritz, H.-J.​ (2009) 
    Nucleic Acids Research37(7) pp. 2283​-2293​.​ DOI: https://doi.org/10.1093/nar/gkp102 
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  • 2009 Journal Article | Research Paper
    ​ ​Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex​
    Andrecka, J.; Treutlein, B.; Izquierdo Arcusa, M. A.; Muschielok, A.; Lewis, R.; Cheung, A. C. M. & Cramer, P.  et al.​ (2009) 
    Nucleic Acids Research37(17) pp. 5803​-5809​.​ DOI: https://doi.org/10.1093/nar/gkp601 
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  • 2008 Journal Article
    ​ ​The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3′ processing pathway​
    Ciais, D.; Bohnsack, M. T.   & Tollervey, D.​ (2008) 
    Nucleic Acids Research36(9) pp. 3075​-3084​.​ DOI: https://doi.org/10.1093/nar/gkn160 
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  • 2008 Journal Article | 
    ​ ​The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli​
    Reichenbach, B.; Maes, A.; Kalamorz, F.; Hajnsdorf, E. & Goerke, B.​ (2008) 
    Nucleic Acids Research36(8) pp. 2570​-2580​.​ DOI: https://doi.org/10.1093/nar/gkn091 
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  • 2008 Journal Article
    ​ ​Superimpose: a 3D structural superposition server​
    Bauer, R. A.; Bourne, P. E.; Formella, A.; Froemmel, C.; Gille, C.; Goede, A. & Guerler, A. et al.​ (2008) 
    Nucleic Acids Research36 pp. W47​-W54​.​ DOI: https://doi.org/10.1093/nar/gkn285 
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  • 2008 Journal Article
    ​ ​Crystal structure of trioxacarcin A covalently bound to DNA​
    Pfoh, R.; Laatsch, H. & Sheldrick, G. M.​ (2008) 
    Nucleic Acids Research36(10) pp. 3508​-3514​.​ DOI: https://doi.org/10.1093/nar/gkn245 
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  • 2008 Journal Article | Research Paper
    ​ ​Site specific phosphorylation of yeast RNA polymerase I​
    Gerber, J.; Reiter, A.; Steinbauer, R.; Jakob, S.; Kuhn, C.-D.; Cramer, P.   & Griesenbeck, J. et al.​ (2008) 
    Nucleic Acids Research36(3) pp. 793​-802​.​ DOI: https://doi.org/10.1093/nar/gkm1093 
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  • 2008 Journal Article | Research Paper
    ​ ​Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement​
    Naji, S.; Bertero, M. G.; Spitalny, P.; Cramer, P.   & Thomm, M.​ (2008) 
    Nucleic Acids Research36(2) pp. 676​-687​.​ DOI: https://doi.org/10.1093/nar/gkm1086 
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  • 2008 Journal Article | 
    ​ ​EndoNet: an information resource about regulatory networks of cell-to-cell communication​
    Doenitz, J.; Goemann, B.; Lize, M.; Michael, H.; Sasse, N.; Wingender, E. & Potapov, A. P.​ (2008) 
    Nucleic Acids Research36 pp. D689​-D694​.​ DOI: https://doi.org/10.1093/nar/gkm940 
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  • 2008 Journal Article | Research Paper
    ​ ​p160/SRC/NCoA coactivators form complexes via specific interaction of their PAS-B domain with the CID/AD1 domain​
    Lodrini, M.; Muenz, T.; Coudevylle, N.; Griesinger, C. ; Becker, S.   & Pfitzner, E.​ (2008) 
    Nucleic Acids Research36(6) pp. 1847​-1860​.​ DOI: https://doi.org/10.1093/nar/gkn029 
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  • 2007 Journal Article
    ​ ​The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases​
    Leulliot, N.; Bohnsack, M. T. ; Graille, M.; Tollervey, D. & Van Tilbeurgh, H.​ (2007) 
    Nucleic Acids Research36(2) pp. 629​-639​.​ DOI: https://doi.org/10.1093/nar/gkm1074 
    Details  DOI 
  • 2007 Journal Article | 
    ​ ​DEEP - A tool for differential expression effector prediction​
    Degenhardt, J.; Haubrock, M. ; Doenitz, J.; Wingender, E. & Crass, T.​ (2007) 
    Nucleic Acids Research35 pp. W619​-W624​.​ DOI: https://doi.org/10.1093/nar/gkm469 
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  • 2007 Journal Article | 
    ​ ​Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs​
    Xie, J.; Zhang, M.; Zhou, T.; Hua, X.; Tang, L. & Wu, W.​ (2007) 
    Nucleic Acids Research35 pp. D183​-D187​.​ DOI: https://doi.org/10.1093/nar/gkl873 
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  • 2006 Journal Article
    ​ ​HHsenser: exhaustive transitive profile search using HMM-HMM comparison​
    Söding, J. ; Remmert, M.; Biegert, A. & Lupas, A. N.​ (2006) 
    Nucleic Acids Research34(Web Server) pp. W374​-W378​.​ DOI: https://doi.org/10.1093/nar/gkl195 
    Details  DOI 
  • 2006 Journal Article
    ​ ​HHrep: de novo protein repeat detection and the origin of TIM barrels​
    Söding, J. ; Remmert, M. & Biegert, A.​ (2006) 
    Nucleic Acids Research34(Web Server) pp. W137​-W142​.​ DOI: https://doi.org/10.1093/nar/gkl130 
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  • 2006 Journal Article
    ​ ​The MPI Bioinformatics Toolkit for protein sequence analysis​
    Biegert, A.; Mayer, C.; Remmert, M.; Söding, J.   & Lupas, A. N.​ (2006) 
    Nucleic Acids Research34(Web Server) pp. W335​-W339​.​ DOI: https://doi.org/10.1093/nar/gkl217 
    Details  DOI 
  • 2006 Journal Article | 
    ​ ​jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1​
    Zhang, M.; Schultz, A.-K.; Calef, C.; Kuiken, C.; Leitner, T.; Korber, B. & Morgenstern, B.  et al.​ (2006) 
    NUCLEIC ACIDS RESEARCH34 pp. W463​-W465​.​ DOI: https://doi.org/10.1093/nar/gkl255 
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  • 2006 Journal Article | 
    ​ ​Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination.​
    Wiese, C.; Hinz, J. M.; Tebbs, R. S.; Nham, P. B.; Urbin, S. S.; Collins, D. W. & Thompson, L. H. et al.​ (2006) 
    Nucleic Acids Research34(9) pp. 2833​-2843​.​ DOI: https://doi.org/10.1093/nar/gkl366 
    Details  DOI 
  • 2006 Journal Article | 
    ​ ​AUGUSTUS: ab initio prediction of alternative transcripts​
    Stanke, M.; Keller, O.; Gunduz, I.; Hayes, A.; Waack, S. & Morgenstern, B. ​ (2006) 
    NUCLEIC ACIDS RESEARCH34 pp. W435​-W439​.​ DOI: https://doi.org/10.1093/nar/gkl200 
    Details  DOI 
  • 2006 Journal Article
    ​ ​EndoNet: an information resource about endocrine networks​
    Potapov, A. P.; Liebich, I.; Doenitz, J.; Schwarzer, K.; Sasse, N.; Schoeps, T. & Crass, T. et al.​ (2006) 
    Nucleic Acids Research34 pp. D540​-D545​.​ DOI: https://doi.org/10.1093/nar/gkj121 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article
    ​ ​TiProD: the Tissue-specific Promoter Database​
    Chen, X.; Wu, J.; Hornischer, K.; Kel, A. E. & Wingender, E.​ (2006) 
    Nucleic Acids Research34 pp. D104​-D107​.​ DOI: https://doi.org/10.1093/nar/gkj113 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article | 
    ​ ​Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples​
    Schilling, O.; Herzberg, C.; Hertrich, T.; Voersmann, H.; Jessen, D.; Huebner, S. & Titgemeyer, F. et al.​ (2006) 
    Nucleic Acids Research34(21) pp. 6102​-6115​.​ DOI: https://doi.org/10.1093/nar/gkl733 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article | 
    ​ ​TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites​
    Tech, M. ; Morgenstern, B.   & Meinicke, P. ​ (2006) 
    Nucleic Acids Research34 pp. W588​-W590​.​ DOI: https://doi.org/10.1093/nar/gkl313 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article | 
    ​ ​Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm​
    Waleev, T.; Shtokalo, D.; Konovalova, T.; Voss, N.; Cheremushkin, E.; Stegmaier, P. & Kel-Margoulis, O. V. et al.​ (2006) 
    Nucleic Acids Research34 pp. W541​-W545​.​ DOI: https://doi.org/10.1093/nar/gkl342 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article | 
    ​ ​The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease​
    Georg, J.; Schomacher, L.; Chong, J. P. J.; Majernik, A. I.; Raabe, M.; Urlaub, H. & Mueller, S. et al.​ (2006) 
    Nucleic Acids Research34(18) pp. 5325​-5336​.​ DOI: https://doi.org/10.1093/nar/gkl604 
    Details  DOI  PMID  PMC  WoS 
  • 2006 Journal Article
    ​ ​TRANSPATH (R): an information resource for storing and visualizing signaling pathways and their pathological aberrations​
    Krull, M.; Pistor, S.; Voss, N.; Kel, A. E.; Reuter, I.; Kronenberg, D. & Michael, H. et al.​ (2006) 
    Nucleic Acids Research34 pp. D546​-D551​.​ DOI: https://doi.org/10.1093/nar/gkj107 
    Details  DOI  PMID  PMC  WoS 
  • 2005 Journal Article
    ​ ​REPPER--repeats and their periodicities in fibrous proteins​
    Gruber, M.; Söding, J.   & Lupas, A. N.​ (2005) 
    Nucleic Acids Research33(Web Server) pp. W239​-W243​.​ DOI: https://doi.org/10.1093/nar/gki405 
    Details  DOI 
  • 2005 Journal Article
    ​ ​The HHpred interactive server for protein homology detection and structure prediction​
    Söding, J. ; Biegert, A. & Lupas, A. N.​ (2005) 
    Nucleic Acids Research33(Web Server) pp. W244​-W248​.​ DOI: https://doi.org/10.1093/nar/gki408 
    Details  DOI 
  • 2005 Journal Article | 
    ​ ​AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints​
    Stanke, M. & Morgenstern, B. ​ (2005) 
    Nucleic Acids Research33 pp. W465​-W467​.​ DOI: https://doi.org/10.1093/nar/gki458 
    Details  DOI  PMID  PMC  WoS 
  • 2005 Journal Article | 
    ​ ​Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC​
    Pohler, D.; Werner, N.; Steinkamp, R. & Morgenstern, B. ​ (2005) 
    Nucleic Acids Research33 pp. W532​-W534​.​ DOI: https://doi.org/10.1093/nar/gki386 
    Details  DOI  PMID  PMC  WoS 
  • 2005 Journal Article | 
    ​ ​CYGD: the comprehensive Yeast Genome Database​
    Guldener, U.; Munsterkotter, M.; Kastenmuller, G.; Strack, N.; van Helden, J.; Lemer, C. & Richelles, J. et al.​ (2005) 
    Nucleic Acids Research33 pp. D364​-D368​.​ DOI: https://doi.org/10.1093/nar/gki053 
    Details  DOI  PMID  PMC  WoS 
  • 2005 Journal Article | 
    ​ ​Activity of Lac repressor anchored to the Escherichia coli inner membrane​
    Gorke, B.; Reinhardt, J. & Rak, B.​ (2005) 
    Nucleic Acids Research33(8) pp. 2504​-2511​.​ DOI: https://doi.org/10.1093/nar/gki549 
    Details  DOI  PMID  PMC  WoS 
  • 2004 Journal Article | 
    ​ ​A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity.​
    Schilling, O.; Langbein, I.; Müller, M.; Schmalisch, M. H. & Stülke, J.​ (2004) 
    NUCLEIC ACIDS RESEARCH32(9) pp. 2853​-2864​.​
    Details 
  • 2004 Journal Article | 
    ​ ​AUGUSTUS: a web server for gene finding in eukaryotes​
    Stanke, M.; Steinkamp, R.; Waack, S. & Morgenstern, B. ​ (2004) 
    Nucleic Acids Research32 pp. W309​-W312​.​ DOI: https://doi.org/10.1093/nar/gkh379 
    Details  DOI  PMID  PMC  WoS 
  • 2004 Journal Article | 
    ​ ​The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences​
    Brudno, M.; Steinkamp, R. & Morgenstern, B. ​ (2004) 
    Nucleic Acids Research32 pp. W41​-W44​.​ DOI: https://doi.org/10.1093/nar/gkh361 
    Details  DOI  PMID  PMC  WoS 
  • 2004 Journal Article | Research Paper
    ​ ​Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes​
    Hesslein, A. E.; Katunin, V. I.; Beringer, M.; Kosek, A. B.; Rodnina, M.   & Strobel, S. A.​ (2004) 
    Nucleic Acids Research32(12) pp. 3760​-3770​.​ DOI: https://doi.org/10.1093/nar/gkh672 
    Details  DOI  PMID  PMC  WoS 
  • 2004 Journal Article | 
    ​ ​AGenDA: gene prediction by cross-species sequence comparison​
    Taher, L.; Rinner, O.; Garg, S.; Sczyrba, A. & Morgenstern, B. ​ (2004) 
    Nucleic Acids Research32 pp. W305​-W308​.​ DOI: https://doi.org/10.1093/nar/gkh386 
    Details  DOI  PMID  PMC  WoS 
  • 2004 Journal Article | 
    ​ ​DIALIGN: multiple DNA and protein sequence alignment at BiBiServ​
    Morgenstern, B. ​ (2004) 
    Nucleic Acids Research32 pp. W33​-W36​.​ DOI: https://doi.org/10.1093/nar/gkh373 
    Details  DOI  PMID  PMC  WoS 
  • 2003 Journal Article | 
    ​ ​PRODORIC: prokaryotic database of gene regulation.​
    Munch, R.; Hiller, K.; Barg, H.; Heldt, D.; Linz, S.; Wingender, E. & Jahn, D.​ (2003) 
    Nucleic Acids Research31(1) pp. 266​-269​.​
    Details 
  • 2003 Journal Article | 
    ​ ​TRANSFAC(R): transcriptional regulation, from patterns to profiles​
    Matys, V.; Haubrock, M.   & Wingender, E.​ (2003) 
    Nucleic Acids Research31(1) pp. 374​-378​.​ DOI: https://doi.org/10.1093/nar/gkg108 
    Details  DOI 
  • 2003 Journal Article | 
    ​ ​Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.​
    Laging, M.; Lindner, E.; Fritz, H.-J. & Kramer, W.​ (2003) 
    NUCLEIC ACIDS RESEARCH31(7) pp. 1913​-1920​.​
    Details 
  • 2003 Journal Article | 
    ​ ​MATCH (TM): a tool for searching transcription factor binding sites in DNA sequences​
    Kel, A. E.; Gossling, E.; Reuter, I.; Cheremushkin, E.; Kel-Margoulis, O. V. & Wingender, E.​ (2003) 
    Nucleic Acids Research31(13) pp. 3576​-3579​.​
    Details 
  • 2003 Journal Article | 
    ​ ​TRANSPATH (R): an integrated database on signal transduction and a tool for array analysis​
    Krull, M.; Voss, N.; Choi, C.; Pistor, S.; Potapov, A. & Wingender, E.​ (2003) 
    Nucleic Acids Research31(1) pp. 97​-100​.​
    Details 
  • 2003 Journal Article
    ​ ​Cloning and characterization of tRNA (m(1)A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures​
    Droogmans, L.; Roovers, M.; Bujnicki, J. M.; Tricot, C.; Hartsch, T.; Stalon, V. & Grosjean, H.​ (2003) 
    Nucleic Acids Research31(8) pp. 2148​-2156​.​ DOI: https://doi.org/10.1093/nar/gkg314 
    Details  DOI  PMID  PMC  WoS 
  • 2003 Journal Article
    ​ ​High mobility group A2 protein and its derivatives bind a specific region of the promoter of DNA repair gene ERCC1 and modulate its activity​
    Borrmann, L.; Schwanbeck, R.; Heyduk, T.; Seebeck, B.; Rogalla, P.; Bullerdiek, J. & Wisniewski, J. R.​ (2003) 
    Nucleic Acids Research31(23) pp. 6841​-6851​.​ DOI: https://doi.org/10.1093/nar/gkg884 
    Details  DOI  PMID  PMC  WoS 
  • 2003 Journal Article | Research Paper
    ​ ​Two protein-protein interaction sites on the spliceosome-associated human cyclophilin CypH​
    Ingelfinger, D.; Gothel, S.; Marahiel, M.; Reidt, U.; Ficner, R. ; Luhrmann, R. & Achsel, T.​ (2003) 
    Nucleic Acids Research31(16) pp. 4791​-4796​.​ DOI: https://doi.org/10.1093/nar/gkg660 
    Details  DOI  PMID  PMC  WoS 
  • 2002 Journal Article | 
    ​ ​MIPS: a database for genomes and protein sequences.​
    Mewes, H. W.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Mayer, K.; Mokrejs, M. & Morgenstern, B.  et al.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(1) pp. 31​-34​.​
    Details 
  • 2002 Journal Article | 
    ​ ​Two amino acid replacements change the substrate preference of DNA mismatch glycosylase Mig.MthI from T/G to A/G.​
    Fondufe-Mittendorf, Y. N.; Härer, C.; Kramer, W. & Fritz, H.-J.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(2) pp. 614​-621​.​
    Details 
  • 2002 Journal Article | 
    ​ ​S/MARt DB: a database on scaffold/matrix attached regions.​
    Liebich, I.; Bode, J.; Frisch, M. & Wingender, E.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(1) pp. 372​-374​.​
    Details 
  • 2002 Journal Article | 
    ​ ​TRANSCompel: a database on composite regulatory elements in eukaryotic genes.​
    Kel-Margoulis, O. V.; Kel, A. E.; Reuter, I.; Deineko, I. V. & Wingender, E.​ (2002) 
    Nucleic Acids Research30(1) pp. 332​-334​.​
    Details 
  • 2002 Journal Article | 
    ​ ​A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus.​
    Starkuviene, V. & Fritz, H.-J.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(10) pp. 2097​-2102​.​
    Details 
  • 2002 Journal Article | 
    ​ ​Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential.​
    Krawczyk, S.; Thurow, C.; Niggeweg, R. & Gatz, C.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(3) pp. 775​-781​.​
    Details 
  • 2002 Journal Article | 
    ​ ​Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs).​
    Liebich, I.; Bode, J.; Reuter, I. & Wingender, E.​ (2002) 
    NUCLEIC ACIDS RESEARCH30(15) pp. 3433​-3442​.​
    Details 
  • 2001 Journal Article | 
    ​ ​The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms​
    Emmert, S.; Schneider, T. D.; Kraemer, K. H. & Khan, S. G.​ (2001) 
    Nucleic Acids Research29(7) pp. 1443​-1452​.​ DOI: https://doi.org/10.1093/nar/29.7.1443 
    Details  DOI  PMID  PMC  WoS 
  • 2001 Journal Article
    ​ ​Conditional cell ablation by stringent tetracycline-dependent regulation of barnase in mammalian cells​
    Leuchtenberger, S.; Perz, A.; Gatz, C. & Bartsch, J. W.​ (2001) 
    Nucleic Acids Research29(16) pp. art. no.​-e76​.​ DOI: https://doi.org/10.1093/nar/29.16.e76 
    Details  DOI  PMID  PMC  WoS 
  • 2000 Journal Article
    ​ ​Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes​
    Amarzguioui, M.; Brede, G.; Babaie, E.; Grotli, M.; Sproat, B. & Prydz, H.​ (2000) 
    Nucleic Acids Research28(21) pp. 4113​-4124​.​ DOI: https://doi.org/10.1093/nar/28.21.4113 
    Details  DOI  PMID  PMC  WoS 
  • 1999 Journal Article
    ​ ​Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues​
    Schmitt, A. O. ; Specht, T.; Beckmann, G.; Dahl, E.; Pilarsky, C. P.; Hinzmann, B. & Rosenthal, A.​ (1999) 
    Nucleic Acids Research27(21) pp. 4251​-4260​.​ DOI: https://doi.org/10.1093/nar/27.21.4251 
    Details  DOI 
  • 1998 Journal Article | 
    ​ ​Highly sensitive detection of gene expression of an intronless gene: amplification of mRNA, but not genomic DNA by nucleic acid sequence based amplification (NASBA).​
    Heim, A.; Grumbach, I. M.; Zeuke, S. & Top, B.​ (1998) 
    Nucleic Acids Research26(9) pp. 2250​-2251​.​
    Details 
  • 1998 Journal Article | 
    ​ ​Single-tube nested competitive PCR with homologous competitor forquantitation of DNA target sequences: theoretical description ofheteroduplex formation, evaluation of sensitivity, precision and linearrange of the method.​
    Serth, J.; Panitz, F.; Herrmann, H. & Alves, J.​ (1998) 
    Nucleic Acids Research26(19) pp. 4401​-4408​.​
    Details 
  • 1998 Journal Article
    ​ ​Comparative gene expression profiling by oligonucleotide fingerprinting​
    Meier-Ewert, S.​ (1998) 
    Nucleic Acids Research26(9) pp. 2216​-2223​.​ DOI: https://doi.org/10.1093/nar/26.9.2216 
    Details  DOI 
  • 1995 Journal Article | 
    ​ ​Nuclear degradation of nonsense mutated beta-globin mRNA: a post-transcriptional mechanism to protect heterozygotes from severe clinical manifestations of beta-thalassemia?​
    Kugler, W.; Enssle, J.; Hentze, M. W. & Kulozik, A. E.​ (1995) 
    Nucleic Acids Research23(3) pp. 413​-418​.​
    Details 
  • 1991 Journal Article | 
    ​ ​Direct cloning of sequence tagged microsatellite sites by DNA affinity chromatography.​
    Brenig, B. & Brem, G.​ (1991) 
    Nucleic Acids Research19(19) pp. 5441​.​
    Details 
  • 1990 Journal Article | 
    ​ ​The porcine PHIcDNA linked to the halothane gene detects a HindIII and XbaI RFLP in normal and malignant hyperthermia susceptible pigs.​
    Brenig, B.; Jürs, S. & Brem, G.​ (1990) 
    Nucleic Acids Research18(2) pp. 388​.​
    Details 
  • 1990 Journal Article | 
    ​ ​BAP, a rat liver protein that activates transcription through a promoter element with similarity to the USF/MLTF binding site.​
    Kugler, W.; Kaling, M.; Wagner, U.; Ryffel, G. U. & Ross, K.​ (1990) 
    NUCLEIC ACIDS RESEARCH18(23) pp. 6943​-6951​.​
    Details 
  • 1990 Journal Article | 
    ​ ​The porcine PHIcDNA linked to the halothane gene detects a NotI RFLP in normal and malignant hyperthermia susceptible pigs.​
    Brenig, B.; Jürs, S. & Brem, G.​ (1990) 
    Nucleic Acids Research18(2) pp. 388​.​
    Details 
  • 1990 Journal Article
    ​ ​Improvement of PCR amplified DNA sequencing with the aid of detergents​
    Bachmann, B.; Lüke, W. & Hunsmann, G.​ (1990) 
    Nucleic Acids Research18(5) pp. 1309​-1309​.​ DOI: https://doi.org/10.1093/nar/18.5.1309 
    Details  DOI 
  • 1989 Journal Article | 
    ​ ​A fast detection protocol for screening large numbers of transgenic animals.​
    Brenig, B.; Müller, M. & Brem, G.​ (1989) 
    Nucleic Acids Research17(15) pp. 6422​.​
    Details 
  • 1988 Journal Article | 
    ​ ​Tissue-specificity of liver gene expression: a common liver-specific promoter element.​
    Kugler, W.; Wagner, U. & Ryffel, G. U.​ (1988) 
    NUCLEIC ACIDS RESEARCH16(8) pp. 3165​-3174​.​
    Details 
  • 1987 Journal Article
    ​ ​Screening of pUC plasmid clones for inserts based on growth rate​
    Karlovsky, P.   & Prell, H. H.​ (1987) 
    Nucleic Acids Research15 pp. 6753​.​
    Details 

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