Temperature-dependent sRNA transcriptome of the Lyme disease spirochete.
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Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa.
Pusic P, Tata M, Wolfinger MT, Sonnleitner E, Häussler S, Bläsi U. Sci Rep. 2016 Dec 21;6:39621. doi: 10.1038/srep39621

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Non-uniformity of the Expected Fragment Starting Point and Coverage Profile.
Prakash C and von Haeseler A. J Comput Biol. 2017 Mar;24(3):200-212. doi: 10.1089/cmb.2016.0096.

A to I editing in disease is not fake news.
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Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’.
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RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA.
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ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins.
Anantharaman A, Tripathi V, Khan A, Yoon JH, Singh DK, Gholamalamdari O, Guang S, Ohlson J, Wahlstedt H, Ohman M, Jantsch MF, Conrad NK, Ma J, Gorospe M, Prasanth SG, Prasanth KV. Nucleic Acids Res. 2017 Apr 20;45(7):4189-4201. doi: 10.1093/nar/gkw1304.

RNA in Disease and development.
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The Other Face of an Editor: ADAR1 Functions in Editing-Independent Ways. Licht K, Jantsch MFBioessays. 2017 Nov;39(11). doi: 10.1002/bies.201700129.


Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered RNA decay in Drosophila.
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The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.
Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC. Nucl. Acids Res. 44 (4): 1703-1717. doi: 10.1093/nar/gkv1473.

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium. Tata M, Wolfinger MT, Amma F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S and Bläsi U. PLoS One. 11 e0147811. doi: 10.1371/journal.pone.0147811.

Computational design of a circular RNA with prion-like behavior.
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AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
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Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution.
Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker IL, and Kovarik P. Mol Syst Biol, 12(5):868, 2016. doi:10.15252/msb.20156628.

RNAlien – Unsupervised RNA family model construction. 
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Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA Polymerase II.
Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I and Jantsch MF. Genome Biol. 2016 Oct 25;17(1):220.

The dynamic epitranscriptome: A to I editing modulates genetic information.
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Adenosine to Inosine editing frequency controlled by splicing efficiency.
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Nuclear Envelope Retention of LINC Complexes Is Promoted by SUN-1 Oligomerization in the Caenorhabditis elegans Germ Line.
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Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA.
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Nuclear Envelope Retention of LINC Complexes Is Promoted by SUN-1 Oligomerization in the Caenorhabditis elegans Germ Line.
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Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications.
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Insights into the stress response triggered by Kasugamycin in Escherichia coli.
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The MazF-regulon: A toolbox for the post-transcriptional stress response in Escherichia coli.
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The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli.
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sRNA-Mediated Control of Transcription Termination in E. coli.
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Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery.
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Lamarckian Illusions.  Weiss A. Trends Ecol Evol. 2015 Oct; 30:566-8. doi: 10.1016/j.tree.2015.08.003

forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Kerpedjiev P, Hammer S, and Hofacker IL. Bioinformatics, 31:3377–3379, 2015. doi:10.1093/bioinformatics/btv372.

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
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Uridylation of RNA-hairpins by Tailor confines the emergence of microRNAs in Drosophila.
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Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.
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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines. Wolfinger MT, Fallmann J, Eggenhofer F, Amman F. F1000Res. 2015 Feb 20 [revised 2015 Jul 20];4:50. doi: 10.12688/f1000research.6157.2.

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M.

AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW. New Phytol. 2015 Jun 25. doi: 10.1111/nph.13545.

Predicting RNA 3D structure using a coarse-grain helix-centered model.
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker ILRNA. 2015 Jun;21(6):1110-21. doi: 10.1261/rna.047522.114.

Thermodynamic and kinetic folding of riboswitches.
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The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets.
Märtens B, Bezerra GA, Kreuter MJ, Grishkovskaya I, Manica A, Arkhipova V, Djinovic-Carugo K, Bläsi ULife (Basel). 2015 Apr 21;5(2):1264-81. doi: 10.3390/life5021264. PMID: 25905548

Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified.
Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF. Dev Cell. 2015 Mar 23;32(6):765-71. doi: 10.1016/j.devcel.2015.01.013. PMID: 25805138

Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2. Fieber C, Janos M, Koestler T, Gratz N, Li XD, Castiglia V, Aberle M, Sauert M, Wegner M, Alexopoulou L, Kirschning CJ, Chen ZJ, von Haeseler A, Kovarik P

Thermodynamic and kinetic folding of Riboswitches.
Badelt S, Hammer S, Flamm C, Hofacker IL. Methods in Enzymology, Volume 554 (2015). doi:10.1016/bs.mie.2014.10.060

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation. Zabidi MA*, Arnold CD*, Schernhuber K, Pagani M, Rath M, Frank O, Stark A.  Nature, 2015. Feb 26;518(7540):556-9. 

A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms.
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Molecular insights into HSD10 disease: impact of SDR5C1 mutations on the human mitochondrial RNase P complex.
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Structural basis for the flexible interaction of protein S1 with the Escherichia coli ribosome.
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Development of giant bacteriophage ϕKZ is independent of the host transcription apparatus.
Ceyssens PJ, Minakhin L, Van den Bossche A, Yakunina M, Klimuk E, Blasdel B, De Smet J, Noben JP, Bläsi U, Severinov K, Lavigne R.
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Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.
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Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):591-600. doi: 10.1002/wrna.1243. PMID: 25045147

The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.
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ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
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Shedding light on the chloroplast as a remote control of nuclear gene expression.
Godoy Herz MA, Kornblihtt AR, Barta A, Kalyna M, Petrillo E.
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Let there be light: regulation of gene expression in plants.
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A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1.
Barraud P, Silpi B, Mohamed WI, Jantsch MF; Allain FHT (2014).  P NATL ACAD SCI USA;111(18):E1852-61. PMID: 24753571
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Göhring J, Fulcher N, Schilcher K, Barta A, Jacak J. Plant Methods. 2014 May 31;10:15. doi: 10.1186/1746-4811-10-15. eCollection 2014.

Drosha protein levels are translationally regulated during Xenopus oocyte maturation.
Muggenhumer D,  Vesely C, Nimpf S, Tian N, Yongfeng J. Jantsch MF (2014).  MOL BIOL CELL;25(13):2094-104. PMID: 24829383

A chloroplast retrograde signal regulates nuclear alternative splicing.
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Göhring, Janett; Fulcher, Nick; Schilcher, Kurt; Barta, Andrea; Jacak, Jaroslaw (2014). Suitable transfection methods for single particle tracing in plant suspension cells. Plant methods;10:15. PMID: 24991230

Göhring, Janett (Barta lab); Fulcher, Nick; Jacak, Jaroslaw; Riha, Karel (2014). TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction. NUCLEIC ACIDS RES;42(3):e21. PMID: 24366880

Sams, Michael; Silye, Rene; Göhring, Janett (Barta lab); Muresan, Leila; Schilcher, Kurt; Jacak, Jaroslaw (2014). Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue. Journal of biomedical optics.;19(1):011021. PMID: 24297043

Singh, Amarjeet; Kanwar, Poonam; Yadav, Akhilesh K; Mishra, Manali; Jha, Saroj K; Baranwal, Vinay; Pandey, Amita; Kapoor, Sanjay; Tyagi, Akhilesh K; Pandey, Girdhar K (2014). Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice. FEBS J;281(3):894-915. PMID: 24286292

Hämmerle, Hermann; Amman, Fabian; Vecerek, Branislav; Stülke, Jörg; Hofacker, Ivo; Bläsi, Udo (2014). Impact of Hfq on the Bacillus subtilis transcriptome. PLOS ONE;9(6):e98661. PMID: 24932523

Sonnleitner, Elisabeth; Bläsi, Udo (2014). Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression. PLOS GENET;10(6):e1004440. PMID: 24945892

Ceyssens, Pieter-Jan; Minakhin, Leonid; Van den Bossche, An; Yakunina, Maria; Klimuk, Evgeny; Blasdel, Bob; De Smet, Jeroen; Noben, Jean-Paul; Bläsi, Udo; Severinov, Konstantin; Lavigne, Rob (2014). Development of giant bacteriophage? KZ is independent of the host transcription apparatus. J VIROL. PMID: 24965474

Hayashi, R., Handler, D., Ish-Horowicz, D., Brennecke, J. (2014). The exon junction complex is required for definition and excision of neighboring introns in Drosophila. Genes Dev.

Mohn, F., Sienski, G., Handler, D., Brennecke, J. (2014). The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell. 157(6):1364-79

Lybecker, Meghan; Zimmermann, Bob; Bilusic, Ivana; Tukhtubaeva, Nadezda; Schroeder, Renée (2014). The double-stranded transcriptome of Escherichia coli. P NATL ACAD SCI USA. PMID: 24453212

Mann, Martin; Kucharík, Marcel; Flamm, Christoph; Wolfinger, Michael T (2014). Memory-efficient RNA energy landscape exploration. BIOINFORMATICS. PMID: 24833804

Arnold, CD., Gerlach, D., Spies, D., Matts, JA., Sytnikova, YA., Pagani, M., Lau, NC., Stark, A. (2014). Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet. 46(7):685-92 (abstract)

Kvon, EZ., Kazmar, T., Stampfel, G., Yáñez-Cuna, JO., Pagani, M., Schernhuber, K., Dickson, BJ., Stark, A. (2014). Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature. 512(7512):91-5 (abstract)

Meireles-Filho, AC., Bardet, AF., Yáñez-Cuna, JO., Stampfel, G., Stark, A. (2014). cis-regulatory requirements for tissue-specific programs of the circadian clock. Curr Biol. 24(1):1-10 (abstract)

Muerdter, F., Stark, A. (2014). Genomics: Hiding in plain sight. Nature. 512(7515):374-5 (abstract)

Rembold, M., Ciglar, L., Yáñez-Cuna, JO., Zinzen, RP., Girardot, C., Jain, A., Welte, MA., Stark, A., Leptin, M., Furlong, EE. (2014). A conserved role for Snail as a potentiator of active transcription. Genes Dev. 28(2):167-81 (abstract)

Shlyueva, D., Stampfel, G., Stark, A. (2014). Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 15(4):272-86

Shlyueva, D., Stelzer, C., Gerlach, D., Yáñez-Cuna, JO., Rath, M., Boryń, LM., Arnold, CD., Stark, A. (2014). Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. Mol Cell. 54(1):180-92

Yáñez-Cuna, JO., Arnold, CD., Stampfel, G., Boryń, LM., Gerlach, D., Rath, M., Stark, A. (2014). Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res.

Karaca, E., Weitzer, S., Pehlivan, D., Shiraishi, H., Gogakos, T., Hanada, T., Jhangiani, SN., Wiszniewski, W., Withers, M., Campbell, IM., Erdin, S., Isikay, S., Franco, LM., Gonzaga-Jauregui, C., Gambin, T., Gelowani, V., Hunter, JV., Yesil, G., Koparir, E., Yilmaz, S., Brown, M., Briskin, D., Hafner, M., Morozov, P., Farazi, TA., Bernreuther, C., Glatzel, M., Trattnig, S., Friske, J., Kronnerwetter, C., Bainbridge, MN., Gezdirici, A., Seven, M., Muzny, DM., Boerwinkle, E., Ozen, M., Clausen, T., Tuschl, T., Yuksel, A., Hess, A., Gibbs, RA., Martinez, J., Penninger, JM., Lupski, JR. (2014). Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell. 157(3):636-50

Popow, J., Jurkin, J., Schleiffer, A., Martinez, J. (2014). Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. Nature. 511(7507):104-7

Noto, T., Kurth, HM., Mochizuki, K. (2014). Analysis of Piwi-loaded small RNAs in Terahymena. Methods Mol Biol. 1093:209-24

Vogt, A., Mochizuki, K. (2014). The taming of the shrew: Regulation of a catalytically active domesticated transposase. Mob Genet Elements. 4:e29383


Bannikova, Olga; Zywicki, Marek; Marquez, Yamile; Skrahina, Tatsiana; Kalyna, Maria; Barta, Andrea (2013). Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. NUCLEIC ACIDS RES;41(3):1783-96. PMID: 23248006

Bielewicz, Dawid; Kalak, Malgorzata; Kalyna, Maria; Windels, David; Barta, Andrea; Vazquez, Franck; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur (2013). Introns of plant pri-miRNAs enhance miRNA biogenesis. EMBO REP;14(7):622-8. PMID: 23681439

Dönertas, D., Sienski, G., Brennecke, J. (2013). Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev. 27(15):1693-705 (abstract)

Handler, D., Meixner, K., Pizka, M., Lauss, K., Schmied, C., Gruber, FS., Brennecke, J. (2013). The genetic makeup of the Drosophila piRNA pathway. Mol Cell. 50(5):762-77 (abstract)

Reddy, Anireddy S N; Marquez, Yamile; Kalyna, Maria; Barta, Andrea (2013). Complexity of the alternative splicing landscape in plants. PLANT CELL;25(10):3657-83. PMID: 24179125

Kaberdin, Vladimir R; Bläsi, Udo (2013). Bacterial helicases in post-transcriptional control. Biochimica et biophysica acta.;1829(8):878-83. PMID: 23291566

Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol. 2013; 11: 59.

Kulinski TM, Barlow DB, Hudson Q. Imprinted silencing is extended over broad chromosomal domains in mouse extra-embryonic lineages. Curr Opin Cell Biol. 2013 June; 25(3): 297–304.

Santoro F, Mayer D, Klement RM, Warczok KE, Stukalov A, Barlow DP, Pauler FM. Imprinted Igf2r silencing depends on continuous Airn lncRNA expression and is not restricted to a developmental window. Development. 2013 Mar;140(6):1184-95.

Santoro F, Pauler FM.  (Barlow lab) Silencing by the imprinted Airn macro lncRNA. Cell Cycle. 2013 March 1; 12(5): 711–712.

Evguenieva-Hackenberg, Elena; Bläsi, Udo (2013). Attack from both ends: mRNA degradation in the crenarchaeon Sulfolobus solfataricus. BIOCHEM SOC T;41(1):379-83. PMID: 23356315

La Teana, Anna; Benelli, Dario; Londei, Paola; Bläsi, Udo (2013). Translation initiation in the crenarchaeon Sulfolobus solfataricus: eukaryotic features but bacterial route. BIOCHEM SOC T;41(1):350-5. PMID: 23356310

Märtens, Birgit; Manoharadas, Salim; Hasenöhrl, David; Manica, Andrea; Bläsi, Udo (2013). Antisense regulation by transposon-derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. EMBO REP(14):527 – 533. PMID: 23579342

Milojevic, Tetyana; Grishkovskaya, Irina; Sonnleitner, Elisabeth; Djinovic-Carugo, Kristina; Bläsi, Udo (2013). The Pseudomonas aeruginosa Catabolite Repression Control Protein Crc Is Devoid of RNA Binding Activity. PLOS ONE;8(5):e64609. PMID: 23717639

Milojevic, Tetyana; Sonnleitner, Elisabeth; Romeo, Alessandra; Djinovic-Carugo, Kristina; Bläsi, Udo (2013). False positive RNA binding activities after Ni-affinity purification from Escherichia coli. RNA BIOL;10(6):1066-9. PMID: 23770724

Märtens, Birgit; Amman, Fabian; Manoharadas, Salim; Zeichen, Lukas; Orell, Alvaro; Albers, Sonja-Verena; Hofacker, Ivo; Bläsi, Udo (2013). Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2. PLOS ONE;8(10):e76569. PMID: 24116119

Märtens, Birgit; Manoharadas, Salim; Hasenöhrl, David; Zeichen, Lukas; Bläsi, Udo (2013). Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus. NUCLEIC ACIDS RES. PMID: 24271401

Hämmerle, Hermann; Ve?erek, Branislav; Resch, Armin; Bläsi, Udo (2013). Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature. RNA BIOL;10(12):1834-41. PMID: 24448230

Byrgazov, Konstantin; Vesper, Oliver; Moll, Isabella (2013). Ribosome heterogeneity: another level of complexity in bacterial translation regulation. CURR OPIN MICROBIOL;16(2):133-9. PMID: 23415603

Stampfl, Sabine; Doetsch, Martina; Beich-Frandsen, Mads; Schroeder, Renée (2013). Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA. RNA BIOL;10(1):149-56. PMID: 23291905

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Arnold, CD., Gerlach, D., Stelzer, C., Boryń, ŁM., Rath, M., Stark, A. (2013). Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 339(6123):1074-7 (abstract)

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Gebeshuber, CA., Martinez, J. (2013). miR-100 suppresses IGF2 and inhibits breast tumorigenesis by interfering with proliferation and survival signaling. Oncogene. 32(27):3306-10 (abstract)

Hanada, T., Weitzer, S., Mair, B., Bernreuther, C., Wainger, BJ., Ichida, J., Hanada, R., Orthofer, M., Cronin, SJ., Komnenovic, V., Minis, A., Sato, F., Mimata, H., Yoshimura, A., Tamir, I., Rainer, J., Kofler, R., Yaron, A., Eggan, KC., Woolf, CJ., Glatzel, M., Herbst, R., Martinez, J., Penninger, JM. (2013). CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature. 495(7442):474-80 (abstract)

Mair, B., Popow, J., Mechtler, K., Weitzer, S., Martinez, J. (2013). Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components. Biochem Soc Trans. 41(4):831-7 (abstract)

Chalker, DL., Meyer, E., Mochizuki, K. (2013). Epigenetics of ciliates. Cold Spring Harb Perspect Biol. 5(12):a017764 (abstract)

Mochizuki, K., Kurth, HM. (2013). Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena. Biochem Biophys Res Commun. 436(3):497-502 (abstract)

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Vogt, A., Mochizuki, K. (2013). A domesticated PiggyBac transposase interacts with heterochromatin and catalyzes reproducible DNA elimination in Tetrahymena. PLoS Genet. 9(12):e1004032 (abstract)


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Doyle M, Kiebler MA. (2012) A zipcode unzipped. Genes Dev. 2012, PMID: 22279044

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Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J. (2011). A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J.;30(19):3977-93.. PMID: 21863019

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Nguyen, Minh Anh Thi; Klaere, Steffen; von Haeseler, Arndt (2011). MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment. MOL BIOL EVOL:143-52. PMID: 20643866

Thi Nguyen, Minh Anh; Gesell, Tanja; von Haeseler, Arndt (2011). ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods. MOL BIOL EVOL. PMID: 21940641

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Manja Marz, Andreas R. Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H. Bernhart, Stephanie Beyer, Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L. Hofacker, and Peter F. Stadler. Animal snoRNAs and scaRNAs with exceptional structures. RNA Biology, 8:1–9, 2011. (doi:10.4161/rna.8.6.)

Jan Gorodkin and Ivo L Hofacker. From structure prediction to genomic screens for novel non-coding RNAs. PLoS computational biology, 7(8):e1002100, 2011. (doi:10.1371/journal.pcbi.1002100)

Christian Höner zu Siederdissen, Stephan H. Berhart, Peter F. Stadler, and Ivo L. Hofacker. A folding algorithm for extended RNA secondary structures. Bioinformatics, 27:i129–i136, 2011. (doi:10.1093/bioinformatics/btr220)

Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, and Ivo L. Hofacker. RNApredator: Fast accessibility-based prediction of sRNA targets. Nucleic Acids Res., 39:W149–W154, 2011. (doi:10.1093/nar/gkr467)

Hakim Tafer, Fabian Ammann, Florian Eggenhoffer, Peter F. Stadler, and Ivo L. Hofacker (2011). Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics, 27:1924–1940, 2011. (doi:10.1093/bioinformatics/btr281)

Matthias Hackl, Tobias Jakobi, Jochen Blom, Daniel Doppmeier, Karina Brinkrolff, Rafael Sczepanowski, Stephan Bernhart, Christian Höner zu Siederdissen, Juan Hernandez-Bort, Matthias Wieser, Renate Kunert, Simon Jeffs, Ivo L. Hofacker, Alexander Goesmann, Alfred Pühler, Nicole Borth, and Johannes Grillari (2011). Next-generation sequencing of the chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 2011. (doi:10.1016/j.jbiotec.2011.02.011)

Stefan Washietl, Sven Findeiß, Stephan Müller, Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, and Nick Goldman (2011). RNAcode: robust prediction of protein coding regions in comparative genomics data. RNA, 17:578–594. (doi:10.1261/rna.2536111)

Stephan H Bernhart, Ulrike Mückstein, and Ivo L Hofacker (2011). RNA accessibility in cubic time. Algorithms Mol Biol, 6(1):3. (doi:10.1186/1748-7188-6-3)

Andreas R Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, and Ivo L Hofacker (2011). AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res, 39:D66–69. (doi:10.1093/nar/gkq990)

Eun, C., Lorkovic, Z.J., Naumann, U., Long, Q., Havecker, E.R., Simon, S.A., Meyers, B.C., Matzke, A.J.M. and Matzke, M. (2011) AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One 6, e25730. PMID: 21998686

Schoeberl Ursula E, Mochizuki, Kazufumi (2011). Keeping the soma free of transposons: Programmed DNA elimination in ciliates. J Biol Chem, 286, 37045–37052. PMID: 21914793

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Doetsch, Martina; Fürtig, Boris; Gstrein, Thomas; Stampfl, Sabine; Schroeder, Renée (2011). The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealing-competent conformation. NUCLEIC ACIDS RES;39(10):4405-18. PMID: 21297117

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Mikl Martin, Vendra Georgia, Kiebler Michael A (2011). Independent localization of MAP2, CaMKIIα and β-actin RNAs in low copy numbers. EMBO Rep;12(10):1077-84. PMID: 21869818

Vesper, Oliver; Amitai, Shahar; Belitsky, Maria; Byrgazov, Konstantin; Kaberdina, Anna Chao; Engelberg-Kulka, Hanna; Moll, Isabella (2011). Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli. CELL(147):147-57. PMID: 21944167

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