RNA Biology

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis.
Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL.
Mol Cell. 2019 Jul 9. pii: S1097-2765(19)30474-5. [Epub ahead of print]

Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Nat Protoc. 2019 Jun 26. doi: 10.1038/s41596-019-0179-x. [Epub ahead of print] Erratum in: Nat Protoc. 2019 Jul 11;:.

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.
Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P.
BMC Bioinformatics. 2019 May 20;20(1):258.

Structural basis for acceptor RNA substrate selectivity of the 3′ terminal uridylyl transferase Tailor.
Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M.
Nucleic Acids Res. 2019 Jan 25;47(2):1030-1042.

Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus.
Bassani F, Zink IA, Pribasnig T, Wolfinger MT, Romagnoli A, Resch A, Schleper C, Bläsi U, La Teana A.
RNA Biol. 2019 May;16(5):675-685.

Architectural principles for Hfq/Crc-mediated regulation of gene expression.
Pei XY, Dendooven T, Sonnleitner E, Chen S, Bläsi U, Luisi BF.
Elife. 2019 Feb 13;8.

A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production.
ElMaghraby MF, Andersen PR, Pühringer F, Hohmann U, Meixner K, Lendl T, Tirian L, Brennecke J.
Cell. 2019 Aug 8;178(4):964-979.e20.

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J.
Nat Struct Mol Biol. 2019 Aug;26(8):720-731. Epub 2019 Aug 5.

Feedback regulation of small RNA processing by the cleavage product.
Durica-Mitic S, Görke B.
RNA Biol. 2019 Aug;16(8):1055-1065.

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL.
Version 2. F1000Res. 2019 Mar 14 [revised 2019 Jan 1];8. pii: ISCB Comm J-287.

Conserved Secondary Structures in Viral mRNAs.
Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D.
Viruses. 2019 Apr 29;11(5).

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.
Ochsenreiter R, Hofacker IL, Wolfinger MT.
Viruses. 2019 Mar 24;11(3).

Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.
Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Hart-Smith G, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y.
Plant Physiol. 2019 May;180(1):305-322.

RNA modifications in structure prediction – Status quo and future challenges.
Tanzer A, Hofacker IL, Lorenz R.
Methods. 2019 Mar 1;156:32-39.

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.
Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF.
Genome Res. 2019 Aug 19. [Epub ahead of print]

Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains.
Fablet M, Jacquet A, Rebollo R, Haudry A, Rey C, Salces-Ortiz J, Bajad P, Burlet N, Jantsch MF, Guerreiro MPG, Vieira C.
G3 (Bethesda). 2019 Mar 7;9(3):855-865.

Inosine induces context-dependent recoding and translational stalling.
Licht K, Hartl M, Amman F, Anrather D, Janisiw MP, Jantsch MF.
Nucleic Acids Res. 2019 Jan 10;47(1):3-14.

Transcriptional Activation of Arabidopsis Zygotes Is Required for Their Initial Division. (preprint)
Kao P and Nodine MD.
bioRivx:679035. 2019

MicroRNA Dynamics and Functions during Arabidopsis Embryogenesis. (preprint)
Plotnikova A, Kellner M, Mosiolek M, Schon M, Nodine MD.
bioRxiv:633735 2019

The embryonic transcriptome of Arabidopsis thaliana.
Hofmann F, Schon MA, Nodine MD.
Plant Reprod. 2019 Mar;32(1):77-91.

Transcriptional cofactors display specificity for distinct types of core promoters.
Haberle V, Arnold CD, Pagani M, Rath M, Schernhuber K, Stark A.
Nature. 2019 Jun;570(7759):122-126

Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.
Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ.
Dev Cell. 2018 Aug 20;46(4):481-494.e6.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF, Quattrone A, O’Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.
RNA Biol. 2018 May 9:1-3.

Analysis of 3′ End Modifications in microRNAs by High-Throughput Sequencing.
Reimão-Pinto MM, Rodrigues-Viana AM, Ameres SL.
Methods Mol Biol. 2018;1823:115-139.

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.
Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Development. 2018 Jul 11;145(13).

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.
Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J.
Science. 2018 May 18;360(6390):800-805.

Cell-type specific sequencing of microRNAs from complex animal tissues.
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.
Nat Methods. 2018 Apr;15(4):283-289.

Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa.
Pusic P, Sonnleitner E, Krennmayr B, Heitzinger DA, Wolfinger MT, Resch A, Bläsi U.
Front Microbiol. 2018 Nov 9;9:2709.

Negative Control of RpoS Synthesis by the sRNA ReaL in Pseudomonas aeruginosa.
Thi Bach Nguyen H, Romero A D, Amman F, Sorger-Domenigg T, Tata M, Sonnleitner E, Bläsi U.
Front Microbiol. 2018 Oct 29;9:2488.

Modification of translation factor aIF5A from Sulfolobus solfataricus.
Bassani F, Romagnoli A, Cacciamani T, Amici A, Benelli D, Londei P, Märtens B, Bläsi U, La Teana A.
Extremophiles. 2018 Jul 25. [Epub ahead of print]

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 XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FH, Luisi BF, Urlaub H, Bläsi U.
Nucleic Acids Res. 2018 Feb 16;46(3):1470-1485.

Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli.
Göpel Y, Görke B.
PLoS Genet. 2018 Jul 24;14(7):e1007547.

Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs.
Durica-Mitic S, Göpel Y, Görke B.
Microbiol Spectr. 2018 Mar;6(2).

CMV: visualization for RNA and protein family models and their comparisons.
Eggenhofer F, Hofacker IL, Backofen R, Höner Zu Siederdissen C.
Bioinformatics. 2018 Aug 1;34(15):2676-2678.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.
Wolfinger MT, Flamm C, Hofacker IL.
Methods. 2018 Jul 1;143:70-76.

In silico design of ligand triggered RNA switches.
Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL.
Methods. 2018 Jul 1;143:90-101.

RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure.
Jain M, Mann TD, Stulić M, Rao SP, Kirsch A, Pullirsch D, Strobl X, Rath C, Reissig L, Moreth K, Klein-Rodewald T, Bekeredjian R, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Pablik E, Cimatti L, Martin D, Zinnanti J, Graier WF, Sibilia M, Frank S, Levanon EY, Jantsch MF.
EMBO J. 2018 Aug 7. [Epub ahead of print]

Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system.
Czermak P, Amman F, Jantsch MF, Cimatti L.
RNA Biol. 2018 Jul 31:1-9. [Epub ahead of print]

Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells.
Avogaro L, Querido E, Dalachi M, Jantsch MF, Chartrand P, Cusanelli E.
RNA Biol. 2018 Apr 16:1-10.

Competition of Candida glabrata against Lactobacillus is Hog1 dependent.
Beyer R, Jandric Z, Zutz C, Gregori C, Willinger B, Jacobsen ID, Kovarik P, Strauss J, Schüller C.
Cell Microbiol. 2018 Aug 15:e12943.

The Bicarbonate Transporter SLC4A7 Plays a Key Role in Macrophage Phagosome Acidification.
Sedlyarov V, Eichner R, Girardi E, Essletzbichler P, Goldmann U, Nunes-Hasler P, Srndic I, Moskovskich A, Heinz LX, Kartnig F, Bigenzahn JW, Rebsamen M, Kovarik P, Demaurex N, Superti-Furga G.
Cell Host Microbe. 2018 Jun 13;23(6):766-774.e5.

Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!
Beck HJ, Moll I.
Microbiol Spectr. 2018 Jul;6(4).

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations.
Nikolic N, Bergmiller T, Vandervelde A, Albanese TG, Gelens L, Moll I.
Nucleic Acids Res. 2018 Apr 6;46(6):2918-2931.

Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation.
Corsini NS, Peer AM, Moeseneder P, Roiuk M, Burkard TR, Theussl HC, Moll I, Knoblich JA.
Cell Stem Cell. 2018 Apr 5;22(4):543-558.e12.

Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells. (preprint)
Gutzat R, Rembart K, Nussbaumer T, Pisupati R, Hofmann Falko, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine MD, Mittelsten Scheid O.
bioRxiv:430447. 2018

NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA.
Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD.
Genome Res. 2018 Dec;28(12):1931-1942.

Whole Mount in situ Localization of miRNAs and mRNAs During Somatic Embryogenesis in Arabidopsis.
Wójcik AM, Mosiolek M, Karcz J, Nodine MD, Gaj MD.
Front Plant Sci. 2018 Sep 4;9:1277.

A Common Pathway of Root Growth Control and Response to CLE Peptides Through Two Receptor Kinases in Arabidopsis.
Racolta A, Nodine MD, Davies K, Lee C, Rowe S, Velazco Y, Wellington R, Tax FE.
Genetics. 2018 Feb;208(2):687-704.

Nascent RNA signaling to yeast RNA Pol II during transcription elongation.
Klopf E, Moes M, Amman F, Zimmermann B, von Pelchrzim F, Wagner C, Schroeder R.
PLoS One. 2018 Mar 23;13(3):e0194438.

A high-throughput method to identify trans-activation domains within transcription factor sequences.
Arnold CD, Nemčko F, Woodfin AR, Wienerroither S, Vlasova A, Schleiffer A, Pagani M, Rath M, Stark A.
EMBO J. 2018 Aug 15;37(16).

Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle V, Stark A.
Nat Rev Mol Cell Biol. 2018 Jun 26. [Epub ahead of print]

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.
Catarino RR, Stark A.
Genes Dev. 2018 Feb 1;32(3-4):202-223.

Resolving systematic errors in widely used enhancer activity assays in human cells.
Muerdter F, Boryń ŁM, Woodfin AR, Neumayr C, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A.
Nat Methods. 2018 Feb;15(2):141-149.

Thiol-linked alkylation of RNA to assess expression dynamics.
Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL.
Nat Methods. 2017 Dec;14(12):1198-1204.

The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14.
Tata M, Amman F, Pawar V, Wolfinger MT, Weiss S, Häussler S, Bläsi U.
Front Microbiol. 2017 Nov 23;8:2312.

The SmAP2 RNA binding motif in the 3’UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus.
Märtens B, Sharma K, Urlaub H, Bläsi U.
Nucleic Acids Res. 2017 Sep 6;45(15):8957-8967.

The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts.
Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U.
Nucleic Acids Res. 2017 Jul 27;45(13):7938-7949.

The Pseudomonas aeruginosa CrcZ RNA interferes with Hfq-mediated riboregulation.
Sonnleitner E, Prindl K, Bläsi U.
PLoS One. 2017 Jul 7;12(7):e0180887.

A heterochromatin-dependent transcription machinery drives piRNA expression.
Andersen PR, Tirian L, Vunjak M, Brennecke J.
Nature. 2017 Sep 7;549(7670):54-59.

A framework for understanding the roles of miRNAs in animal development.
Alberti C, Cochella L.
Development. 2017 Jul 15;144(14):2548-2559.

Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.
Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Görke B, Luisi BF.
Nucleic Acids Res. 2017 Oct 13;45(18):10845-10860.

Non-canonical activation of histidine kinase KdpD by phosphotransferase protein PtsN through interaction with the transmitter domain.
Mörk-Mörkenstein M, Heermann R, Göpel Y, Jung K, Görke B.
Mol Microbiol. 2017 Oct;106(1):54-73.

Synthesis and antimicrobial activity of 6-sulfo-6-deoxy-D-glucosamine and its derivatives.
Skarbek K, Gabriel I, Szweda P, Wojciechowski M, Khan MA, Görke B, Milewski S, Milewska MJ.
Carbohydr Res. 2017 Aug 7;448:79-87.

Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets.
Dersch P, Khan MA, Mühlen S, Görke B.
Front Microbiol. 2017 May 5;8:803.

A framework for understanding the roles of miRNAs in animal development.
Alberti C, Cochella L.
Development. 2017 Jul 15;144(14):2548-2559.

RNAblueprint: flexible multiple target nucleic acid sequence design.
Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S.
Bioinformatics. 2017 Sep 15;33(18):2850-2858.

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.
Nucleic Acids Res. 2017 May 5;45(8):e60.

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.
Helmling C, Wacker A, Wolfinger MT, Hofacker IL, Hengesbach M, Fürtig B, Schwalbe H.
J Am Chem Soc. 2017 Feb 22;139(7):2647-2656.

The Other Face of an Editor: ADAR1 Functions in Editing-Independent Ways.
Licht K, Jantsch MF.
Bioessays. 2017 Nov;39(11).

A to I editing in disease is not fake news.
Bajad P, Jantsch MF, Keegan L, O’Connell M.
RNA Biol. 2017 Sep 2;14(9):1223-1231.

RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA.
Anantharaman A, Gholamalamdari O, Khan A, Yoon JH, Jantsch MF, Hartner JC, Gorospe M, Prasanth SG, Prasanth KV.
FEBS Lett. 2017 Sep;591(18):2890-2904.

RNA in Disease and development.
Barta A, Jantsch MF.
RNA Biol. 2017 May 4;14(5):457-459.

Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’.
Schaefer M, Kapoor U, Jantsch MF.
Open Biol. 2017 May;7(5). pii: 170077.

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, Öhman M, Jantsch MF, Conrad NK, Ma J, Gorospe M, Prasanth SG, Prasanth KV.
Nucleic Acids Res. 2017 Apr 20;45(7):4189-4201.

Natural killer cell-intrinsic type I IFN signaling controls Klebsiella pneumoniae growth during lung infection.
Ivin M, Dumigan A, de Vasconcelos FN, Ebner F, Borroni M, Kavirayani A, Przybyszewska KN, Ingram RJ, Lienenklaus S, Kalinke U, Stoiber D, Bengoechea JA, Kovarik P.
PLoS Pathog. 2017 Nov 7;13(11):e1006696.

The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt M, Kovarik P.
J Clin Invest. 2017 Jun 1;127(6):2051-2065.

HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis.
Lang M, Berry D, Passecker K, Mesteri I, Bhuju S, Ebner F, Sedlyarov V, Evstatiev R, Dammann K, Loy A, Kuzyk O, Kovarik P, Khare V, Beibel M, Roma G, Meisner-Kober N, Gasche C.
Cancer Res. 2017 May 1;77(9):2424-2438.

Posttranscriptional regulation of cytokine expression.
Kovarik P, Ebner F, Sedlyarov V.
Cytokine. 2017 Jan;89:21-26

The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli.
Temmel H, Müller C, Sauert M, Vesper O, Reiss A, Popow J, Martinez J, Moll I.
Nucleic Acids Res. 2017 May 5;45(8):4708-4721.

MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations.
Nikolic N, Didara Z, Moll I.
PeerJ. 2017 Sep 21;5:e3830.

miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
Wójcik AM, Nodine MD, Gaj MD1.
Front Plant Sci. 2017 Dec 11;8:2024.

Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data.
Lutzmayer S, Enugutti B, Nodine MD.
Sci Rep. 2017 Jul 19;7(1):5913.

Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets.
Schon MA, Nodine MD.
Plant Cell. 2017 Apr;29(4):608-617.

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.
Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E.
Mol Cell. 2017 Jul 6;67(1):30-43.e6.

In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.
Adams PP, Flores Avile C, Popitsch N, Bilusic I, Schroeder R, Lybecker M, Jewett MW.
Nucleic Acids Res. 2017 Jan 25;45(2):775-792.

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete.
Popitsch N, Bilusic I, Rescheneder P, Schroeder R, Lybecker M.
BMC Genomics. 2017 Jan 5;18(1):28.

A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.
Elling U, Wimmer RA, Leibbrandt A, Burkard T, Michlits G, Leopoldi A, Micheler T, Abdeen D, Zhuk S, Aspalter IM, Handl C, Liebergesell J, Hubmann M, Husa AM, Kinzer M, Schuller N, Wetzel E, van de Loo N, Martinez JAZ, Estoppey D, Riedl R, Yang F, Fu B, Dechat T, Ivics Z, Agu CA, Bell O, Blaas D, Gerhardt H, Hoepfner D, Stark A, Penninger JM.
Nature. 2017 Oct 5;550(7674):114-118.

Promoting transcription over long distances.
Catarino RR, Neumayr C, Stark A.
Nat Genet. 2017 Jun 28;49(7):972-973.

Probing the canonicity of the Wnt/Wingless signaling pathway.
Franz A, Shlyueva D, Brunner E, Stark A, Basler K.
PLoS Genet. 2017 Apr 3;13(4):e1006700.

Combinatorial function of transcription factors and cofactors.
Reiter F, Wienerroither S, Stark A.
Curr Opin Genet Dev. 2017 Apr;43:73-81.

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.
Arnold CD, Zabidi MA, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A.
Nat Biotechnol. 2017 Feb;35(2):136-144.

Genetic and mechanistic diversity of piRNA 3′-end formation.
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J.
Nature. 2016 Nov 24;539(7630):588-592.

Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.
Reimão-Pinto MM, Manzenreither RA, Burkard TR, Sledz P, Jinek M, Mechtler K, Ameres SL.
EMBO J. 2016 Nov 15;35(22):2417-2434.

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.

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, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U.
PLoS One. 2016 Jan 28;11(1):e0147811.

Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.
Drexel T, Mahofsky K, Latham R, Zimmer M, Cochella L.
Genes Dev. 2016 Sep 15;30(18):2042-2047.

Two Small RNAs Conserved in Enterobacteriaceae Provide Intrinsic Resistance to Antibiotics Targeting the Cell Wall Biosynthesis Enzyme Glucosamine-6-Phosphate Synthase.
Khan MA, Göpel Y, Milewski S, Görke B.
Front Microbiol. 2016 Jun 15;7:908.

Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage.
Göpel Y, Khan MA, Görke B.
Nucleic Acids Res. 2016 Jan 29;44(2):824-37.

Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.
Drexel T, Mahofsky K, Latham R, Zimmer M, Cochella L.
Genes Dev. 2016 Sep 15;30(18):2042-2047.

RNAlien – Unsupervised RNA family model construction.
Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.
Nucleic Acids Res. 2016 Sep 30;44(17):8433-41.

Predicting RNA secondary structures from sequence and probing data.
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL.
Methods. 2016 Jul 1;103:86-98.

RNA folding with hard and soft constraints.
Lorenz R, Hofacker IL, Stadler PF.
Algorithms Mol Biol. 2016 Apr 23;11:8.

Computational Design of a Circular RNA with Prionlike Behavior.
Badelt S, Flamm C, Hofacker IL.
Artif Life. 2016 Spring;22(2):172-84.

Pseudoknots in RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J.
Bioinformatics. 2016 Jan 15;32(2):187-94.

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
Fallmann J, Sedlyarov V, Tanzer A, Kovarik P, Hofacker IL.
Nucleic Acids Res. 2016 Jan 4;44(D1):D90-5.

SHAPE directed RNA folding.
Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT.
Bioinformatics. 2016 Jan 1;32(1):145-7.

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

Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA.
Anantharaman A, Jadaliha M, Tripathi V, Nakagawa S, Hirose T, Jantsch MF, Prasanth SG, Prasanth KV.
Sci Rep. 2016 Sep 26;6:34043.

Adenosine to Inosine editing frequency controlled by splicing efficiency.
Licht K, Kapoor U, Mayrhofer E, Jantsch MF.
Nucleic Acids Res. 2016 Jul 27;44(13):6398-408.

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications.
Licht K, Jantsch MF.
J Cell Biol. 2016 Apr 11;213(1):15-22.

The dynamic epitranscriptome: A to I editing modulates genetic information.
Tajaddod M, Jantsch MF, Licht K.
Chromosoma. 2016 Mar;125(1):51-63.

Type I Interferons in Bacterial Infections: A Balancing Act.
Kovarik P, Castiglia V, Ivin M, Ebner F.
Front Immunol. 2016 Dec 26;7:652.

The Influence of Programmed Cell Death in Myeloid Cells on Host Resilience to Infection with Legionella pneumophila or Streptococcus pyogenes.
Gamradt P, Xu Y, Gratz N, Duncan K, Kobzik L, Högler S, Kovarik P, Decker T, Jamieson AM.
PLoS Pathog. 2016 Dec 14;12(12):e1006032.

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 I, Kovarik P.
Mol Syst Biol. 2016 May 13;12(5):868

Type I Interferon Signaling Prevents IL-1β-Driven Lethal Systemic Hyperinflammation during Invasive Bacterial Infection of Soft Tissue.
Castiglia V, Piersigilli A, Ebner F, Janos M, Goldmann O, Damböck U, Kröger A, Weiss S, Knapp S, Jamieson AM, Kirschning C, Kalinke U, Strobl B, Müller M, Stoiber D, Lienenklaus S, Kovarik P.
Cell Host Microbe. 2016 Mar 9;19(3):375-87.

A code within a code: how codons influence mRNA stability.
Martinez J, Zagrovic B.
EMBO J. 2016 Oct 4;35(19):2064-2065.

A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli.
Oron-Gottesman A, Sauert M, Moll I, Engelberg-Kulka H.
MBio. 2016 Nov 15;7(6). pii: e01855-16.

The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.
Sauert M, Wolfinger MT, Vesper O, Müller C, Byrgazov K, Moll I.
Nucleic Acids Res. 2016 Aug 19;44(14):6660-75.

Insights into the Stress Response Triggered by Kasugamycin in Escherichia coli.
Müller C, Sokol L, Vesper O, Sauert M, Moll I.
Antibiotics (Basel). 2016 Jun 1;5(2).

Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation.
Kumar S, Kolodkin-Gal I, Vesper O, Alam N, Schueler-Furman O, Moll I, Engelberg-Kulka H.
MBio. 2016 Jan 26;7(1):e02034-15.

Sensitive whole mount in situ localization of small RNAs in plants.
Ghosh Dastidar M, Mosiolek M, Bleckmann A, Dresselhaus T, Nodine MD, Maizel A.
Plant J. 2016 Nov;88(4):694-702.

Mobile small RNAs: Sperm-companion communication.
Nodine MD.
Nat Plants. 2016 Apr 5;2:16041.

sRNA-Mediated Control of Transcription Termination in E. coli.
Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J, Gottesman S, Schroeder R, Nudler E.
Cell. 2016 Sep 22;167(1):111-121.e13.

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.
Nucleic Acids Res. 2016 Feb 29;44(4):1703-17.

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E.
RNA Biol. 2016;13(2):177-95.

Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.
Zabidi MA, Stark A.
Trends Genet. 2016 Dec;32(12):801-814.

RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2.
Stepien BK, Oppitz C, Gerlach D, Dag U, Novatchkova M, Krüttner S, Stark A, Keleman K.
Proc Natl Acad Sci U S A. 2016 Oct 24.

Gene Regulation: Activation through Space.
Muerdter F, Stark A.
Curr Biol. 2016 Oct 10;26(19):R895-R898.

Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation.
Shlyueva D, Meireles-Filho AC, Pagani M, Stark A.
PLoS One. 2016 Aug 30;11(8):e0161997.

Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila.
Reimão-Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Fariña-Lopez S, Ameres SL.
Mol Cell. 2015 Jul 16;59(2):203-16.

Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor.
Bortolamiol-Becet D, Hu F, Jee D, Wen J, Okamura K, Lin CJ, Ameres SL, Lai EC.
Mol Cell. 2015 Jul 16;59(2):217-28.

Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions.
Herzog VA, Ameres SL.
Mol Cell. 2015 Jul 2;59(1):4-7.

Binding of the 5′-Triphosphate End of mRNA to the γ-Subunit of Translation Initiation Factor 2 of the Crenarchaeon Sulfolobus solfataricus.
Arkhipova V, Stolboushkina E, Kravchenko O, Kljashtorny V, Gabdulkhakov A, Garber M, Nikonov S, Märtens B, Bläsi U, Nikonov O.
J Mol Biol. 2015 Sep 25;427(19):3086-95.

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.

Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.
Sienski G, Batki J, Senti KA, Dönertas D, Tirian L, Meixner K, Brennecke J.
Genes Dev. 2015 Nov 1;29(21):2258-71.

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.
Senti KA, Jurczak D, Sachidanandam R, Brennecke J.
Genes Dev. 2015 Aug 15;29(16):1747-62.

Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.
Mohn F, Handler D, Brennecke J.
Science. 2015 May 15;348(6236):812-817.

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.

Cross-Talk between the Canonical and the Nitrogen-Related Phosphotransferase Systems Modulates Synthesis of the KdpFABC Potassium Transporter in Escherichia coli.
Lüttmann D, Göpel Y, Görke B.
J Mol Microbiol Biotechnol. 2015;25(2-3):168-77.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.
Theis C, Zirbel CL, Zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J.
PLoS One. 2015 Oct 28;10(10):e0139900.

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.
Kerpedjiev P, Hammer S, Hofacker IL.
Bioinformatics. 2015 Oct 15;31(20):3377-9.

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

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.
Lavender CA, Lorenz R, Zhang G, Tamayo R, Hofacker IL, Weeks KM.
PLoS Comput Biol. 2015 May 20;11(5):e1004126.

Product Grammars for Alignment and Folding.
Höner Zu Siederdissen C, Hofacker IL, Stadler PF.
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):507-19.

Thermodynamic and kinetic folding of riboswitches.
Badelt S, Hammer S, Flamm C, Hofacker IL.
Methods Enzymol. 2015;553:193-213.

Tristetraprolin Limits Inflammatory Cytokine Production in Tumor-Associated Macrophages in an mRNA Decay-Independent Manner.
Kratochvill F, Gratz N, Qualls JE, Van De Velde LA, Chi H, Kovarik P, Murray PJ.
Cancer Res. 2015 Aug 1;75(15):3054-64.

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.
PLoS One. 2015 Mar 10;10(3):e0119727.

Promoter occupancy of STAT1 in interferon responses is regulated by processive transcription.
Wiesauer I, Gaumannmüller C, Steinparzer I, Strobl B, Kovarik P.
Mol Cell Biol. 2015 Feb;35(4):716-27.

CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.
Weitzer S, Hanada T, Penninger JM, Martinez J.
Wiley Interdiscip Rev RNA. 2015 Jan-Feb;6(1):47-63.

Heterogeneity of the translational machinery: Variations on a common theme.
Sauert M, Temmel H, Moll I.
Biochimie. 2015 Jul;114:39-47.

Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.
Byrgazov K, Grishkovskaya I, Arenz S, Coudevylle N, Temmel H, Wilson DN, Djinovic-Carugo K, Moll I.
Nucleic Acids Res. 2015 Jan;43(1):661-73.

Soups & SELEX for the origin of life.
Schroeder R.
RNA. 2015 Apr;21(4):729-32

Transcriptional regulators form diverse groups with context-dependent regulatory functions.
Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A.
Nature. 2015 Dec 3;528(7580):147-51.

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.
Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryń ŁM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR, Zuber J.
Nature. 2015 Sep 24;525(7570):543-547.

Coordinating the human looks.
Haberle V, Stark A.
Cell. 2015 Sep 24;163(1):24-6.

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.

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.

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.
J Virol. 2014 Sep;88(18):10501-10

Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression.
Sonnleitner E, Bläsi U.
PLoS Genet. 2014 Jun 19;10(6):e1004440.

Impact of Hfq on the Bacillus subtilis transcriptome.
Hämmerle H, Amman F, Večerek B, Stülke J, Hofacker I, Bläsi U.
PLoS One. 2014 Jun 16;9(6):e98661.

Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus.
Märtens B, Manoharadas S, Hasenöhrl D, Zeichen L, Bläsi U.
Nucleic Acids Res. 2014 Feb;42(4):2505-11

The exon junction complex is required for definition and excision of neighboring introns in Drosophila.
Hayashi R, Handler D, Ish-Horowicz D, Brennecke J.
Genes Dev. 2014 Aug 15;28(16):1772-85.

Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex.
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Genes Dev. 2013 Aug 1;27(15):1693-705.

The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila.
Mohn F, Sienski G, Handler D, Brennecke J.
Cell. 2014 Jun 5;157(6):1364-79.

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J.
Bioinformatics. 2014 Jul 15;30(14):2009-17.

TSSAR: TSS annotation regime for dRNA-seq data.
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S.
BMC Bioinformatics. 2014 Mar 27;15:89

Energy-directed RNA structure prediction.
Hofacker IL.
Methods Mol Biol. 2014;1097:71-84.

Predicting RNA structure: advances and limitations.
Hofacker IL, Lorenz R.
Methods Mol Biol. 2014;1086:1-19.

The RNA-editing enzyme ADAR1 controls innate immune responses to RNA.
Mannion NM, Greenwood SM, Young R, Cox S, Brindle J, Read D, Nellåker C, Vesely C, Ponting CP, McLaughlin PJ, Jantsch MF, Dorin J, Adams IR, Scadden AD, Ohman M, Keegan LP, O’Connell MA.
Cell Rep. 2014 Nov 20;9(4):1482-94.

ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.
Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF.
Nucleic Acids Res. 2014 Oct 29;42(19):12155-68.

Drosha protein levels are translationally regulated during Xenopus oocyte maturation.

Muggenhumer D, Vesely C, Nimpf S, Tian N, Yongfeng J, Jantsch MF.
Mol Biol Cell. 2014 Jul 1;25(13):2094-104.

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, Banerjee S, Mohamed WI, Jantsch MF, Allain FH.
Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1852-61.

The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells.
Jurkin J, Henkel T, Nielsen AF, Minnich M, Popow J, Kaufmann T, Heindl K, Hoffmann T, Busslinger M, Martinez J.
EMBO J. 2014 Dec 17;33(24):2922-36.

Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors.
Popow J, Jurkin J, Schleiffer A, Martinez J.
Nature. 2014 Jul 3;511(7507):104-7.

Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.
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; Baylor Hopkins Center for Mendelian Genomics, Clausen T, Tuschl T, Yuksel A, Hess A, Gibbs RA, Martinez J, Penninger JM, Lupski JR.
Cell. 2014 Apr 24;157(3):636-50.

MicroRNA functions in plant embryos.
Vashisht D, Nodine MD.
Biochem Soc Trans. 2014 Apr;42(2):352-7

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.

The double-stranded transcriptome of Escherichia coli.
Lybecker M, Zimmermann B, Bilusic I, Tukhtubaeva N, Schroeder R.
Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3134-9.

Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M.
RNA Biol. 2014;11(5):641-54.

Genomics: Hiding in plain sight.
Muerdter F, Stark A.
Nature. 2014 Aug 28;512(7515):374-5.

Genome-scale functional characterization of Drosophila developmental enhancers in vivo.
Kvon EZ, Kazmar T, Stampfel G, Yáñez-Cuna JO, Pagani M, Schernhuber K, Dickson BJ, Stark A.
Nature. 2014 Aug 7;512(7512):91-5.

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

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.
Yáñez-Cuna JO, Arnold CD, Stampfel G, Boryń LM, Gerlach D, Rath M, Stark A.
Genome Res. 2014 Jul;24(7):1147-56.

Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.
Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryń ŁM, Arnold CD, Stark A.
Mol Cell. 2014 Apr 10;54(1):180-192.

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

A conserved role for Snail as a potentiator of active transcription.
Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE.
Genes Dev. 2014 Jan 15;28(2):167-81.

cis-regulatory requirements for tissue-specific programs of the circadian clock.
Meireles-Filho ACA, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A.
Curr Biol. 2014 Jan 6;24(1):1-10.

Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature.
Hämmerle H, Večerek B, Resch A, Bläsi U.
RNA Biol. 2013 Dec;10(12):1834-41.

Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.
Märtens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Bläsi U.
PLoS One. 2013 Oct 7;8(10):e76569.

Bacterial helicases in post-transcriptional control.
Kaberdin VR, Bläsi U.
Biochim Biophys Acta. 2013 Aug;1829(8):878-83.

Antisense regulation by transposon-derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus.
Märtens B, Manoharadas S, Hasenöhrl D, Manica A, Bläsi U.
EMBO Rep. 2013 Jun;14(6):527-33.

False positive RNA binding activities after Ni-affinity purification from Escherichia coli.
Milojevic T, Sonnleitner E, Romeo A, Djinović-Carugo K, Bläsi U.
RNA Biol. 2013 Jun;10(6):1066-9.

The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity.
Milojevic T, Grishkovskaya I, Sonnleitner E, Djinovic-Carugo K, Bläsi U.
PLoS One. 2013 May 23;8(5):e64609.

Attack from both ends: mRNA degradation in the crenarchaeon Sulfolobus solfataricus.
Evguenieva-Hackenberg E, Bläsi U.
Biochem Soc Trans. 2013 Feb 1;41(1):379-83.

Translation initiation in the crenarchaeon Sulfolobus solfataricus: eukaryotic features but bacterial route.
La Teana A, Benelli D, Londei P, Bläsi U.
Biochem Soc Trans. 2013 Feb 1;41(1):350-5.

The genetic makeup of the Drosophila piRNA pathway.
Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber FS, Brennecke J.
Mol Cell. 2013 Jun 6;50(5):762-77.

Computational design of RNAs with complex energy landscapes.
Höner zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF.
Biopolymers. 2013 Dec;99(12):1124-36.

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.
Nucleic Acids Res. 2013 Dec;41(22):9999-10009.

2D meets 4G: G-quadruplexes in RNA secondary structure prediction.
Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):832-44.

CMCompare webserver: comparing RNA families via covariance models.
Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W499-503.

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.
Hum Mutat. 2013 Apr;34(4):546-56.

Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues.
Stulić M, Jantsch MF.
RNA Biol. 2013 Oct;10(10):1611-7.

RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation.
Tariq A, Garncarz W, Handl C, Balik A, Pusch O, Jantsch MF.
Nucleic Acids Res. 2013 Feb 1;41(4):2581-93.

A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing.
Garncarz W, Tariq A, Handl C, Pusch O, Jantsch MF.
RNA Biol. 2013 Feb;10(2):192-204.

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

miR-100 suppresses IGF2 and inhibits breast tumorigenesis by interfering with proliferation and survival signaling.
Gebeshuber CA, Martinez J.
Oncogene. 2013 Jul 4;32(27):3306-10.

Focal segmental glomerulosclerosis is induced by microRNA-193a and its downregulation of WT1.
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.
Nat Med. 2013 Apr;19(4):481-7.

CLP1 links tRNA metabolism to progressive motor-neuron loss.
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.
Nature. 2013 Mar 28;495(7442):474-80.

Ribosome heterogeneity: another level of complexity in bacterial translation regulation.
Byrgazov K, Vesper O, Moll I.
Curr Opin Microbiol. 2013 Apr;16(2):133-9.

Study of E. coli Hfq’s RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents.
Doetsch M, Stampfl S, Fürtig B, Beich-Frandsen M, Saxena K, Lybecker M, Schroeder R.
Nucleic Acids Res. 2013 Jan 7;41(1):487-97.

Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA.
Stampfl S, Doetsch M, Beich-Frandsen M, Schroeder R.
RNA Biol. 2013 Jan;10(1):149-56.

Identification of transcription factor binding sites from ChIP-seq data at high resolution.
Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A.
Bioinformatics. 2013 Nov 1;29(21):2705-13.

Regulatory Genomics – Decoding Drosophila Regulatory Sequences.
Stark A.
Biomed Tech (Berl). 2013 Sep 7.

Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A.
Science. 2013 Mar 1;339(6123):1074-7.

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

Structural flexibility of RNA as molecular basis for Hfq chaperone function.
Ribeiro Ede A Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K.
Nucleic Acids Res. 2012 Sep;40(16):8072-84.

Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon.
Romeo A, Sonnleitner E, Sorger-Domenigg T, Nakano M, Eisenhaber B, Bläsi U.
Microbiology. 2012 Jun;158(Pt 6):1543-52.

Small regulatory RNAs in Pseudomonas aeruginosa.
Sonnleitner E, Romeo A, Bläsi U.
RNA Biol. 2012 Apr;9(4):364-71.

Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq.
Hämmerle H, Beich-Frandsen M, Večerek B, Rajkowitsch L, Carugo O, Djinović-Carugo K, Bläsi U.
PLoS One. 2012;7(11):e50892.

Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression.
Sienski G, Dönertas D, Brennecke J.
Cell. 2012 Nov 21;151(5):964-80.

Preparation of small RNA libraries for high-throughput sequencing.
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ.
Cold Spring Harb Protoc. 2012 Oct 1;2012(10):1067-77.

The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.
Olivieri D, Senti KA, Subramanian S, Sachidanandam R, Brennecke J.
Mol Cell. 2012 Sep 28;47(6):954-69.

Folding RNA/DNA hybrid duplexes.
Lorenz R, Hofacker IL, Bernhart SH.
Bioinformatics. 2012 Oct 1;28(19):2530-1.

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs.
Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF.
Genome Res. 2012 Aug;22(8):1468-76.

Transcript diversification in the nervous system: a to I RNA editing in CNS function and disease development.
Tariq A, Jantsch MF.
Front Neurosci. 2012 Jul 9;6:99.

Diversity and roles of (t)RNA ligases.
Popow J, Schleiffer A, Martinez J.
Cell Mol Life Sci. 2012 Aug;69(16):2657-70.

Selective translation during stress in Escherichia coli.
Moll I, Engelberg-Kulka H.
Trends Biochem Sci. 2012 Nov;37(11):493-8.

Direct interaction of the N-terminal domain of ribosomal protein S1 with protein S2 in Escherichia coli.
Byrgazov K, Manoharadas S, Kaberdina AC, Vesper O, Moll I.
PLoS One. 2012;7(3):e32702.

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

A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.
Hnisz D, Bardet AF, Nobile CJ, Petryshyn A, Glaser W, Schöck U, Stark A, Kuchler K.
PLoS Genet. 2012;8(12):e1003118.

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.
Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A.
Genome Res. 2012 Oct;22(10):2018-30.

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature.
Kvon EZ, Stampfel G, Yáñez-Cuna JO, Dickson BJ, Stark A.
Genes Dev. 2012 May 1;26(9):908-13.

Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq.
Beich-Frandsen M, Vecerek B, Konarev PV, Sjöblom B, Kloiber K, Hämmerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA, Svergun DI, Konrat R, Bläsi U, Djinovic-Carugo K.
Nucleic Acids Res. 2011 Jun;39(11):4900-15.

Structural analysis of full-length Hfq from Escherichia coli.
Beich-Frandsen M, Večerek B, Sjöblom B, Bläsi U, Djinović-Carugo K.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 May 1;67(Pt 5):536-40.

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal.
Sonnleitner E, Gonzalez N, Sorger-Domenigg T, Heeb S, Richter AS, Backofen R, Williams P, Hüttenhofer A, Haas D, Bläsi U.
Mol Microbiol. 2011 May;80(4):868-85.

Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota.
Hasenöhrl D, Konrat R, Bläsi U.
RNA. 2011 Jan;17(1):99-107

A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors.
Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J.
EMBO J. 2011 Aug 23;30(19):3977-93.

A genome-scale shRNA resource for transgenic RNAi in Drosophila.
Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N.
Nat Methods. 2011 May;8(5):405-7.

ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.
Algorithms Mol Biol. 2011 Nov 24;6:26.

Animal snoRNAs and scaRNAs with exceptional structures.
Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.
RNA Biol. 2011 Nov-Dec;8(6):938-46.

From structure prediction to genomic screens for novel non-coding RNAs.
Gorodkin J, Hofacker IL.
PLoS Comput Biol. 2011 Aug;7(8):e1002100.

Fast accessibility-based prediction of RNA-RNA interactions.
Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL.

Bioinformatics. 2011 Jul 15;27(14):1934-40.

A folding algorithm for extended RNA secondary structures.
Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL.
Bioinformatics. 2011 Jul 1;27(13):i129-36.

RNApredator: fast accessibility-based prediction of sRNA targets.
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W149-54.

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering.
Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner Zu Siederdissen C, Bort JA, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J.
J Biotechnol. 2011 Apr 20;153(1-2):62-75.

AREsite: a database for the comprehensive investigation of AU-rich elements.
Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL.
Nucleic Acids Res. 2011 Jan;39(Database issue):D66-9.

A structural determinant required for RNA editing.
Tian N, Yang Y, Sachsenmaier N, Muggenhumer D, Bi J, Waldsich C, Jantsch MF, Jin Y.
Nucleic Acids Res. 2011 Jul;39(13):5669-81.

HSPC117 is the essential subunit of a human tRNA splicing ligase complex.
Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, Trowitzsch S, Will CL, Lührmann R, Söll D, Martinez J.
Science. 2011 Feb 11;331(6018):760-4.

Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.
Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I.
Cell. 2011 Sep 30;147(1):147-57.

Transient RNA-protein interactions in RNA folding.
Doetsch M, Schroeder R, Fürtig B.
FEBS J. 2011 May;278(10):1634-42.

The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealing-competent conformation.
Doetsch M, Fürtig B, Gstrein T, Stampfl S, Schroeder R.
Nucleic Acids Res. 2011 May;39(10):4405-18.

A computational pipeline for comparative ChIP-seq analyses.
Bardet AF, He Q, Zeitlinger J, Stark A.
Nat Protoc. 2011 Dec 15;7(1):45-61.

Forward and reverse genetics through derivation of haploid mouse embryonic stem cells.
Elling U, Taubenschmid J, Wirnsberger G, O’Malley R, Demers SP, Vanhaelen Q, Shukalyuk AI, Schmauss G, Schramek D, Schnuetgen F, von Melchner H, Ecker JR, Stanford WL, Zuber J, Stark A, Penninger JM.
Cell Stem Cell. 2011 Dec 2;9(6):563-74.

A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature. 2011 Oct 12;478(7370):476-82.

Neural-specific elongation of 3′ UTRs during Drosophila development.
Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B.
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15864-9.

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J.
Nat Genet. 2011 May;43(5):414-20.