2015

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. Genome Res. 2015 May 1. pii: gr.186585.114. [Epub ahead of print]

Predicting RNA 3D structure using a coarse-grain helix-centered model.
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL. RNA. 2015 Apr 22. [Epub ahead of print]  PMID: 25904133

Thermodynamic and kinetic folding of riboswitches.
Badelt S, Hammer S, Flamm C, Hofacker IL. Methods Enzymol. 2015;553:193-213. doi: 10.1016/bs.mie.2014.10.060. Epub 2015 Feb 12. PMID: 25726466

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 U. Life (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

A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms.
Woehrer SL, Aronica L, Suhren JH, Busch CJ, Noto T, Mochizuki K. EMBO J. 2015 Feb 12;34(4):559-77. doi: 10.15252/embj.201490062. Epub 2015 Jan 14. PMID: 25588944

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.
J Virol. 2014 Sep;88(18):10501-10. doi: 10.1128/JVI.01347-14. Epub 2014 Jun 25. PMID: 24965474

Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.
Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R.
Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):591-600. doi: 10.1002/wrna.1243. Epub 2014 Jul 9. PMID: 25045147

The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.
Spletter ML, Barz C, Yeroslaviz A, Schönbauer C, Ferreira IR, Sarov M, Gerlach D, Stark A, Habermann BH, Schnorrer F.
EMBO Rep. 2015 Feb;16(2):178-91. doi: 10.15252/embr.201439791. Epub 2014 Dec 22. PMID: 25532219

ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
Cornelia Vesely, Stefanie Tauber, Fritz J. Sedlazeck, Mansoureh Tajaddod, Arndt von Haeseler, Michael F. Jantsch. Nucleic Acids Res. 2014 October 29; 42(19): 12155–12168. Published online 2014 September 26. doi: 10.1093/nar/gku844  PMCID: PMC4231736

Shedding light on the chloroplast as a remote control of nuclear gene expression.
Godoy Herz MA, Kornblihtt AR, Barta A, Kalyna M, Petrillo E.
Plant Signal Behav. 2014;9(11):e976150. doi: 10.4161/15592324.2014.976150.

Let there be light: regulation of gene expression in plants.
Petrillo E1, Godoy Herz MA, Barta A, Kalyna M, Kornblihtt AR. RNA Biol. 2014;11(10):1215-20. doi: 10.4161/15476286.2014.972852.

Barraud, Pierre; Banerjee, Silpi; Mohamed, Weaam I; Jantsch, Michael F; Allain, Frédéric H-T (2014). A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1. P NATL ACAD SCI USA;111(18):E1852-61. PMID: 24753571

Suitable transfection methods for single particle tracing in plant suspension cells.
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.

Muggenhumer, Dominik; Vesely, Cornelia; Nimpf, Simon; Tian, Nan; Yongfeng, Jin; Jantsch, Michael F (2014). Drosha protein levels are translationally regulated during Xenopus oocyte maturation. MOL BIOL CELL;25(13):2094-104. PMID: 24829383

Petrillo, Ezequiel; Herz, Micaela A Godoy; Fuchs, Armin; Reifer, Dominik; Fuller, John; Yanovsky, Marcelo J; Simpson, Craig; Brown, John W S; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R (2014). A chloroplast retrograde signal regulates nuclear alternative splicing. SCIENCE;344(6182):427-30. PMID: 24763593

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

2013

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

Doetsch, Martina; Stampfl, Sabine; Fürtig, Boris; Beich-Frandsen, Mads; Saxena, Krishna; Lybecker, Meghan; Schroeder, Renée (2013). Study of E. coli Hfq’s RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents. NUCLEIC ACIDS RES;41(1):487-97. PMID: 23104381

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)

Bardet, AF., Steinmann, J., Bafna, S., Knoblich, JA., Zeitlinger, J., Stark, A. (2013). Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 29(21):2705-13 (abstract)

Stark, A. (2013). Regulatory Genomics – Decoding Drosophila Regulatory Sequences. Biomed Tech (Berl). (abstract)

Yáñez-Cuna, JO., Kvon, EZ., Stark, A. (2013). Deciphering the transcriptional cis-regulatory code. Trends Genet. 29(1):11-22 (

Tariq, Aamira; Garncarz, Wojciech; Handl, Cornelia; Balik, Ales; Pusch, Oliver; Jantsch, Michael F (2013). RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation. NUCLEIC ACIDS RES;41(4):2581-93. PMID: 23275536

Garncarz, Wojciech; Tariq, Aamira; Handl, Cornelia; Pusch, Oliver; Jantsch, Michael F (2013). A high throughput screen to identify enhancers of ADAR-mediated RNA-editing. RNA BIOL;10(2):190-202. PMID: 23353575

Jantsch, Michael F (2013). Editing the flow of information. RNA BIOL;10(10):1609-1610.

Stuli?, Maja; Jantsch, Michael F (2013). Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues. RNA BIOL;10(10):1611-7. PMID: 24025532

Gebeshuber, CA., Kornauth, C., Dong, L., Sierig, R., Seibler, J., Reiss, M., Tauber, S., Bilban, M., Wang, S., Kain, R., Böhmig, GA., Moeller, MJ., Gröne, HJ., Englert, C., Martinez, J., Kerjaschki, D. (2013). Focal segmental glomerulosclerosis is induced by microRNA-193a and its downregulation of WT1. Nat Med. 19(4):481-7 (abstract)

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)

Vogt, A., Goldman, AD., Mochizuki, K., Landweber, LF. (2013). Transposon domestication versus mutualism in ciliate genome rearrangements. PLoS Genet. 9(8):e1003659 (abstract)

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)

2012

de Ameida Ribeiro E Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinovic-Carugo K. (2012) Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res. 2012 Jun. PMID 22718981

Ebersberger I, de Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A. (2012) A Consistent Backbone for the Funi. Mol.Biol.Evol. PMID: 22114356

Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R. (2012) LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA. 2012 May. PMID: 22450757

Sonnleitner E, Romeo A, Bläsi U. (2012) Small regulatory RNAs in Pseudomonas aeruginosa. RNA Biol. 2012 Apr. PMID: 22336763

Byrgazov K, Manoharadas S, Kaberdina AC, Vesper O, Moll I. (2012) Direct interaction of the N-terminal domain of ribosomal protein S1 with protein S2 in Escherichia coli. PLoS One. PMID: 22412910

Guenzl P, Barlow D. (2012) Macro IncRNAs: A new layer of cis-regulatory information in the mammalian genome. RNA Biol. 2012 Jun. PMID: 22617879

Tolino M, Köhrmann M, Kiebler MA. (2012) RNA-binding proteins involved in RNA localization and their implications in neuronal diseases. Eur J Neurosci 2012 Jun. PMID: 22708593

Tariq A, Jantsch MF. (2012) Transcript Diversification in the Nervous System: A to I RNA Editing in CNS Function and Disease Development. Front Neurosci. 2012, PMID: 22787438

Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW. (2012) Alternative splicing in plants – coming of age. Trends Plant Sci. 2012 Jun 26, PMID: 2743067

Koerner MV, Pauler FM, Hudson QJ, Santoro F, Sawicka A, Guenzl PM, Stricker SH, Schichl YM, Latos PA, Klement RM, Warczok KE, Wojciechowski J, Seiser C, Kralovics R, Barlow DP. (2012) A downstream CpG island controls transcript initiation and elongation and the methylation state of the imprinted Airn macro ncRNA promoter. PLoS Genet. 2012. PMID: 22396659

Pauler FM, Barlow DP, Hudson QJ. (2012) Mechanisms of long range silencing by imprinted macro non-coding RNAs. Curr Opin Genet Dev. 2012. PMID: 22386265

Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JW. (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 2012 March, PMID: 22127866

Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF. (2012) Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 2012, PMID: 22310477

Doyle M, Kiebler MA. (2012) A numbers game underpins cytoplasmic mRNA transport. Nat Cell Biol. 2012 Apr 2. PMID 22469827

Marquez Y, Brown JW, Simpson CG, Barta A, Kalyna M. (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 2012 Mar 5, PMID: 22391557

Washietl S, Hofacker IL, Stadler PF, Kellis M. (2012) RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res. 2012. PMID: 22287623

Sarto-Jackson I, Milenkovic I, Smalla KH, Gundelfinger ED, Kaehne T, Herrera-Molina R, Kiebler MA, Thoams S, Sieghart W. (2012) The cell adhesion molecule neuroplastin-65 is a novel interaction partner of y-Aminobutyric acid type A receptors. J Biol Chem, 2012, PMID: 22389504

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

Ivo L. Hofacker, Christian M. Reidys, and Peter F. Stadler. (2012). Symmetric circular matchings and RNA folding. Discr. Math., 312:100–112. (doi:10.1016/j.disc.2011.06.004)

Mochizuki, Kazufumi(2012). Developmentally Programmed, RNA-directed Genome Rearrangement in Tetrahymena. Dev Growth Differ, in press. PMID: 22103557

Matylla-Kulinska K, Boots JL, Zimmermann B, Schroeder R. (2012). Finding aptamers and small ribozymes in unexpected places. Wiley Interdiscip Rev RNA. 2012 Jan-Feb;3(1);73-91. PMID: 21853532

Reddy AS, Day IS, Göhring J, Barta A. (2012). Localization and dynamics of nuclear speckles in plants. PLANT PHYSIOL. PMID: 22045923

 

2011

 

Kalyna M, Simpson CG, Sed NH, Lewandowska D, Marquez y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JW. (2011 – Epub ahead of print). Nucleic Acids Res. PMID: 22127866

Huang R, Jaritz M, Guenzl P, Vlatkovic I, Sommer A, Tamir IM, Marks H, Klampfl T, Kralovics R, Stunnenberg HG, Barlow DP, Pauler FM. (2011). An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One. 2011;6(11):e27288. PMID: 22102886

Barlow Denise P (2011). Genomic imprinting: a mammalian epigenetic discovery model. Annu Rev Genet. 2011;45:379-403. PMID: 21942369

Hudson QJ, Seidl CI, Kulinski TM, Huang R, Warczok KE, Bittner R, Bartolomei MS, Barlow DP. (2011). Extra-embryonic-specific imprinted expression is restricted to defined lineages in the post-implantation embryo. Dev Biol. 2011 May 15;353(2):420-31. PMID: 21354127

Santoro Federica, Barlow Denise P (2011). Developmental control of imprinted expression by macro non-coding RNAs. Semin Cell Dev Biol. 2011 Jun;22(4):328-35. PMID: 21333747

Hasenöhrl, David; Konrat, Robert; Bläsi, Udo (2011). Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota. RNA. PMID: 21115637

Beich-Frandsen, Mads; Vecerek, Branislav; Konarev, Petr V; Sjöblom, Björn; Kloiber, Karin; Hämmerle, Hermann; Rajkowitsch, Lukas; Miles, Andrew J; Kontaxis, Georg; Wallace, B A; Svergun, Dimitri I; Konrat, Robert; Bläsi, Udo; Djinovic-Carugo, Kristina (2011). Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. NUCLEIC ACIDS RES. PMID: 21330354

Sonnleitner, Elisabeth; Gonzalez, Nicolas; Sorger-Domenigg, Theresa; Heeb, Stephan; Richter, Andreas S; Backofen, Rolf; Williams, Paul; Hüttenhofer, Alexander; Haas, Dieter; Bläsi, Udo (2011). The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal. MOL MICROBIOL. PMID: 21375594

Beich-Frandsen, Mads; Vecerek, Branislav; Sjöblom, Björn; Bläsi, Udo; Djinovic-Carugo, Kristina (2011). Structural analysis of full-length Hfq from Escherichia coli. ACTA CRYSTALLOGR F;67(Pt 5):536-40. PMID: 21543856

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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)

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