Next Generation Sequencing

  • Genomics’ most flexible and powerful tool.
  • Genomics’ most flexible and powerful tool.
  • Genomics’ most flexible and powerful tool.

The goal of the Next Generation Sequencing (NGS) Core Facility is to provide cutting edge next generation sequencing technology to its users. Next Generation Sequencing has become a key analysis method for biological research. The capacity to expand analysis from more or less defined genomic regions to genome wide studies has boosted the pace of research discovery and enabled researchers to obtain a global view on biological processes. Advice and guidance of sequencing projects are offered by our team that relies on years of experience with sequencing systems and sequencing data analysis. All common sequencing applications are supported and the development of novel methods and protocols encouraged. For general inquiries please contact us at


    Library Preparation

    Library Preparation

    A prerequisite for NGS is the generation of so-called sequencing libraries out of the correspondent DNA or RNA sample. It consists mainly in the ligation of adaptors, which make the sequencing reaction possible. There are many protocols and kits available depending on sample source and biological question of interest.

    The Next Generation Sequencing Core Facility offers two major pipelines:

    • DNA preparation - suitable for all types of DNA samples e.g. ChIP, gDNA, cDNA, amplicons
    • RNA preparation - applications: sequencing of total RNA, purified mRNA or ribosomal-depleted RNA

    Preparation of libraries by user is encouraged and supported.

    Quality Control

    Quality Control

    Every sequencing library, prepared by facility or user has to be carefully quality checked. This includes three major steps:

    • Measurement of concentration (Fluorescence NanoDrop)
    • Measurement of size (Bioanalyzer, Fragment Analyzer)
    • Mimicking cluster formation (RT-PCR)



    Sequencing is performed on Illumina HiSeq 2500 instruments with the capacity to produce up to 70Gbp per lane. The request unit is one sequencing lane, which can be filled up (multiplexed) with as many samples as the user requires. Sequencing read length (50-500bp) and modus (single read or paired end) can be freely chosen depending on application.

    Currently we offer the following read length modes, the preferred mode is given in brackets:

    • Single Read 50 bp (V4)
    • Paired End 50 bp (Rapid Mode)
    • Single Read 100 bp (Rapid Mode)
    • Paired End 125 bp (V4)
    • Paired End 150 bp (Rapid Mode)

    Data Analysis

    Data Analysis

    Primary data output from the Illumina sequencers is converted to compressed BAM files that hold sequences from both reads (in case of paired end sequencing), quality information, index read barcodes and other information. We generate quality metrics from the sequencing process and analyse the reads using Fastqc (Basecalling quality, GC content, overrepresented sequences, …) and PreSeq (duplications and library complexity) to check successful sequencing and potential downstream analysis problems. Lanes running pools of multiple samples are demultiplexed by the index barcode into one file per sample and their quality is checked individually.

    On demand we offer mapping to reference genomes of model organisms either with Bowtie (ChIP-Seq), Tophat/STAR (RNA-Seq) or BWA (Whole Genome, genotyping and SNP calling). The alignment data can be visualized in a genome browser (IGB, IGV, UCSC) and further analyzed in Galaxy.



    Lab equipment

    Software and Data management

    • Forskalle - For submission and administration of your sequencing requests.
    • Queue - A page to check the progress of your requests and securely download finished sequencing data.
    • Galaxy - Galaxy allows our customers to perform basic bioinfomatics tasks. In collaboration with the GenAU bionformatics group we provide some custom tailored tools for groups adressing their research.
    • Reserva - Book a time slot for the Covaris DNA shearer.
    • BAM2FQ - A light-weight tool to convert unaligned BAM files to fastq format. Just drag and drop your BAM files into the window. It detects paired end runs and splits them automatically into two files. Runs on any operating system with Java installed.
    • VBCF-NGS Github - Illumina-related tools and snippets for quality metrics and file conversion.


    Resources available at Partner Institutions

    User Information


    The NGS Core Facility offers access to its services to all members of the Campus Vienna Biocenter. Unused capacity is offered to external Users. In order to estimate feasibility and allocable resources we strongly recommend to contact our team when planning a sequencing experiment. Queuing follows first come, first serves policy.

    All relevant information for Users can be found in our User Guide which can be downloaded from our sample management interface Forskalle at for registered users.

    Please create an account on if you don't already have one (it's free and painless!). If your research group is not listed there, contact us at to set it up for you.

    Citing the facility

    How should I acknowledge the NGSequencing Service?

    We all like to receive credit for the work we do don't we?

    Continuation of funding for the VBCF NGS facility by the city of Vienna and the ministry of science depends on documented evidence of contribution to scientific output.

    We therefore demand acknowledgement of utilization of the facility in publishing work.

    A simple statement is sufficient and can either be placed in the materials and methods section or at the end of your manuscript (acknowledgements) depending on journal format.

    Suggested minimal format:

    Solexa (Illumina, Deep, Next generation, or however you named it in your manuscript) Sequencing was performed at the VBCF NGS Unit (

    Your publication will be then listed on our website.

    Terms & Conditions

    All requests submitted to the CSF NGS are subject to the general cooperation conditions of the CSF as well as CSF NGS policy if no additional agreement exists.

    • User Guide
    • Price List
    • general Cooperation Conditions

    These documents are available as PDF for registered users. Please go to and create an account (if you don't already have one). After logging in, you will find them under the Important Documents tab.


    Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation.
    Söllinger A, Tveit AT, Poulsen M, Noel SJ, Bengtsson M, Bernhardt J, Frydendahl Hellwing AL, Lund P, Riedel K, Schleper C, Højberg O, Urich T
    mSystems 2018 Jul-Aug; 3 (4) (abstract)

    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; (abstract)

    Genetically engineered cerebral organoids model brain tumor formation.
    Bian S, Repic M, Guo Z, Kavirayani A, Burkard T, Bagley JA, Krauditsch C, Knoblich JA
    Nat. Methods 2018 Aug; 15 (8) (abstract)

    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) (abstract)

    The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi.
    Drecktrah D, Hall LS, Rescheneder P, Lybecker M, Samuels DS
    Front Cell Infect Microbiol 2018; 8 (abstract)

    The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.
    Ivanov MP, Ladurner R, Poser I, Beveridge R, Rampler E, Hudecz O, Novatchkova M, Hériché JK, Wutz G, van der Lelij P, Kreidl E, Hutchins JR, Axelsson-Ekker H, Ellenberg J, Hyman AA, Mechtler K, Peters JM
    EMBO J. 2018 Aug 01; 37 (15) (abstract)

    In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction.
    Uhse S, Pflug FG, Stirnberg A, Ehrlinger K, von Haeseler A, Djamei A
    PLoS Biol. 2018 Apr; 16 (4) (abstract)

    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 05; 22 (4) (abstract)

    Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.
    Simon L, Rabanal FA, Dubos T, Oliver C, Lauber D, Poulet A, Vogt A, Mandlbauer A, Le Goff S, Sommer A, Duborjal H, Tatout C, Probst AV
    Nucleic Acids Res. 2018 Apr 06; 46 (6) (abstract)

    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 Apr 05; (abstract)

    The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells.
    Landskron L, Steinmann V, Bonnay F, Burkard TR, Steinmann J, Reichardt I, Harzer H, Laurenson AS, Reichert H, Knoblich JA
    Elife 2018 Mar 27; 7 (abstract)

    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; 13 (3) (abstract)

    Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.
    Fitz J, Neumann T, Pavri R
    EMBO J. 2018 Apr 13; 37 (8) (abstract)

    Spatial specificity of auxin responses coordinates wood formation.
    Brackmann K, Qi J, Gebert M, Jouannet V, Schlamp T, Grünwald K, Wallner ES, Novikova DD, Levitsky VG, Agustí J, Sanchez P, Lohmann JU, Greb T
    Nat Commun 2018 Feb 28; 9 (1) (abstract)

    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) (abstract)

    The IAP family member BRUCE regulates autophagosome-lysosome fusion.
    Ebner P, Poetsch I, Deszcz L, Hoffmann T, Zuber J, Ikeda F
    Nat Commun 2018 Feb 09; 9 (1) (abstract)

    Human tripartite motif protein 52 is required for cell context-dependent proliferation.
    Benke S, Agerer B, Haas L, Stöger M, Lercher A, Gabler L, Kiss I, Scinicariello S, Berger W, Bergthaler A, Obenauf AC, Versteeg GA
    Oncotarget 2018 Mar 02; 9 (17) (abstract)

    Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids.
    Bateman RM, Sramkó G, Paun O
    Ann. Bot. 2018 Jan 25; 121 (1) (abstract)

    The axolotl genome and the evolution of key tissue formation regulators.
    Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW
    Nature 2018 Jan 24; (abstract)

    Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria.
    Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S
    Front Microbiol 2018; 9 (abstract)

    Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria.
    Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S
    Front Microbiol 2018; 9 (abstract)

    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. 2017 Dec 13; (abstract)

    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 2017 Dec 11; (abstract)

    Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
    Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM
    EMBO J. 2017 Dec 07; (abstract)

    A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.
    Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters JM, Mirny LA, Tachibana K
    EMBO J. 2017 Dec 07; (abstract)

    Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia.
    Fulgione A, Koornneef M, Roux F, Hermisson J, Hancock AM
    Mol. Biol. Evol. 2017 Dec 05; (abstract)

    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; 8 (abstract)

    Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction.
    Mann E, Stouthamer CM, Kelly SE, Dzieciol M, Hunter MS, Schmitz-Esser S
    mSystems 2017 Nov-Dec; 2 (6) (abstract)

    CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens.
    Michlits G, Hubmann M, Wu SH, Vainorius G, Budusan E, Zhuk S, Burkard TR, Novatchkova M, Aichinger M, Lu Y, Reece-Hoyes J, Nitsch R, Schramek D, Hoepfner D, Elling U
    Nat. Methods 2017 Oct 16; (abstract)

    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 05; 550 (7674) (abstract)

    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 Sep 25; (abstract)

    The splicing co-factor Barricade/Tat-SF1 is required for cell cycle and lineage progression in Drosophila neural stem cells.
    Abramczuk MK, Burkard TR, Rolland V, Steinmann V, Duchek P, Jiang Y, Wissel S, Reichert H, Knoblich JA
    Development 2017 Nov 01; 144 (21) (abstract)

    A heterochromatin-dependent transcription machinery drives piRNA expression.
    Andersen PR, Tirian L, Vunjak M, Brennecke J
    Nature 2017 Sep 07; 549 (7670) (abstract)

    DNA replication-coupled histone modification maintains Polycomb gene silencing in plants.
    Jiang D, Berger F
    Science 2017 Sep 15; 357 (6356) (abstract)

    The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals.
    Jenull S, Tscherner M, Gulati M, Nobile CJ, Chauhan N, Kuchler K
    Sci Rep 2017 Aug 16; 7 (1) (abstract)

    Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae).
    Trucchi E, Frajman B, Haverkamp THA, Schönswetter P, Paun O
    New Phytol. 2017 Oct; 216 (1) (abstract)

    Overrepresentation Analyses of Differentially Expressed Genes in the Smut Fungus Ustilago bromivora during Saprophytic and in planta Growth.
    Czedik-Eysenberg A, Rabe F, Ekker H, Czepe C, Djamei A
    Bio Protoc 2017 Aug 05; 7 (15) (abstract)

    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) (abstract)

    Two different, mutually exclusively distributed, TP53 mutations in ovarian and peritoneal tumor tissues of a serous ovarian cancer patient: indicative for tumor origin?
    Sukhbaatar N, Bachmayr-Heyda A, Auer K, Aust S, Deycmar S, Horvat R, Pils D
    Cold Spring Harb Mol Case Stud 2017 Jul; 3 (4) (abstract)

    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 06; 67 (1) (abstract)

    Guided self-organization and cortical plate formation in human brain organoids.
    Lancaster MA, Corsini NS, Wolfinger S, Gustafson EH, Phillips AW, Burkard TR, Otani T, Livesey FJ, Knoblich JA
    Nat. Biotechnol. 2017 Jul; 35 (7) (abstract)

    Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont.
    König L, Siegl A, Penz T, Haider S, Wentrup C, Polzin J, Mann E, Schmitz-Esser S, Domman D, Horn M
    mSystems 2017 May-Jun; 2 (3) (abstract)

    The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana.
    Wollmann H, Stroud H, Yelagandula R, Tarutani Y, Jiang D, Jing L, Jamge B, Takeuchi H, Holec S, Nie X, Kakutani T, Jacobsen SE, Berger F
    Genome Biol. 2017 May 18; 18 (1) (abstract)

    Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana.
    Rabanal FA, Mandáková T, Soto-Jiménez LM, Greenhalgh R, Parrott DL, Lutzmayer S, Steffen JG, Nizhynska V, Mott R, Lysak MA, Clark RM, Nordborg M
    Genome Biol. 2017 May 03; 18 (1) (abstract)

    Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl.
    Busslinger GA, Stocsits RR, van der Lelij P, Axelsson E, Tedeschi A, Galjart N, Peters JM
    Nature 2017 Apr 19; (abstract)

    Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants.
    Lorković ZJ, Park C, Goiser M, Jiang D, Kurzbauer MT, Schlögelhofer P, Berger F
    Curr. Biol. 2017 Apr 05; (abstract)

    Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana.
    Rabanal FA, Nizhynska V, Mandáková T, Novikova PY, Lysak MA, Mott R, Nordborg M
    G3 (Bethesda) 2017 Apr 03; 7 (4) (abstract)

    Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima.
    Balao F, Trucchi E, Wolfe T, Hao BH, Lorenzo MT, Baar J, Sedman L, Kosiol C, Amman F, Chase MW, Hedrén M, Paun O
    Mol. Ecol. 2017 Mar 30; (abstract)

    Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.
    Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K
    Nature 2017 Mar 29; (abstract)

    Negative Regulators of an RNAi-Heterochromatin Positive Feedback Loop Safeguard Somatic Genome Integrity in Tetrahymena.
    Suhren JH, Noto T, Kataoka K, Gao S, Liu Y, Mochizuki K
    Cell Rep 2017 Mar 07; 18 (10) (abstract)

    Absence of PD-L1 on tumor cells is associated with reduced MHC I expression and PD-L1 expression increases in recurrent serous ovarian cancer.
    Aust S, Felix S, Auer K, Bachmayr-Heyda A, Kenner L, Dekan S, Meier SM, Gerner C, Grimm C, Pils D
    Sci Rep 2017 Mar 07; 7 (abstract)

    Essential role for the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells.
    Kreslavsky T, Vilagos B, Tagoh H, Poliakova DK, Schwickert TA, Wöhner M, Jaritz M, Weiss S, Taneja R, Rossner MJ, Busslinger M
    Nat. Immunol. 2017 Feb 27; (abstract)

    Molecular role of the PAX5-ETV6 oncoprotein in promoting B-cell acute lymphoblastic leukemia.
    Smeenk L, Fischer M, Jurado S, Jaritz M, Azaryan A, Werner B, Roth M, Zuber J, Stanulla M, den Boer ML, Mullighan CG, Strehl S, Busslinger M
    EMBO J. 2017 Feb 20; (abstract)

    Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota.
    Loy A, Pfann C, Steinberger M, Hanson B, Herp S, Brugiroux S, Gomes Neto JC, Boekschoten MV, Schwab C, Urich T, Ramer-Tait AE, Rattei T, Stecher B, Berry D
    mSystems 2017 Jan-Feb; 2 (1) (abstract)

    Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica.
    Yu Novikova P, Tsuchimatsu T, Simon S, Nizhynska V, Voronin V, Burns R, Fedorenko OM, Holm S, Säll T, Prat E, Marande W, Castric V, Nordborg M
    Mol. Biol. Evol. 2017 Jan 12; (abstract)

    Temperature-dependent sRNA transcriptome of the Lyme disease spirochete.
    Popitsch N, Bilusic I, Rescheneder P, Schroeder R, Lybecker M
    BMC Genomics 2017 Jan 05; 18 (1) (abstract)

    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. 2016 Dec 26; (abstract)

    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 (abstract)

    Comparative transcriptome analysis links distinct peritoneal tumor spread types, miliary and non-miliary, with putative origin, tubes and ovaries, in high grade serous ovarian cancer.
    Auer K, Bachmayr-Heyda A, Aust S, Grunt TW, Pils D
    Cancer Lett. 2016 Dec 07; 388 (abstract)

    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. 2016 Dec 01; (abstract)

    The genomic basis of circadian and circalunar timing adaptations in a midge.
    Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K
    Nature 2016 Nov 21; (abstract)

    Genetic and mechanistic diversity of piRNA 3'-end formation.
    Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J
    Nature 2016 Nov 16; (abstract)

    A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem.
    Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CM, Mannhaupt G, Güldener U, Kahmann R, Djamei A
    Elife 2016 Nov 11; 5 (abstract)

    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; (abstract)

    Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis.
    Watson JM, Platzer A, Kazda A, Akimcheva S, Valuchova S, Nizhynska V, Nordborg M, Riha K
    Proc. Natl. Acad. Sci. U.S.A. 2016 Oct 25; 113 (43) (abstract)

    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 Oct 11; (abstract)

    Linear ubiquitination by LUBEL has a role in Drosophila heat stress response.
    Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F
    EMBO Rep. 2016 Oct 4; (abstract)

    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) (abstract)

    CCAN Assembly Configures Composite Binding Interfaces to Promote Cross-Linking of Ndc80 Complexes at the Kinetochore.
    Pekgöz Altunkaya G, Malvezzi F, Demianova Z, Zimniak T, Litos G, Weissmann F, Mechtler K, Herzog F, Westermann S
    Curr. Biol. 2016 Sep 12; 26 (17) (abstract)

    Phosphorylation of an HP1-like protein is a prerequisite for heterochromatin body formation in Tetrahymena DNA elimination.
    Kataoka K, Noto T, Mochizuki K
    Proc. Natl. Acad. Sci. U.S.A. 2016 Jul 27; (abstract)

    Phytohormone sensing in the biotrophic fungus Ustilago maydis- the dual role of the transcription factor Rss1.
    Rabe F, Seitner D, Bauer L, Navarrete F, Czedik-Eysenberg A, Rabanal FA, Djamei A
    Mol. Microbiol. 2016 Jul 8; (abstract)

    Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function
    Valli M, Tatto NE, Peymann A, Gruber C, Landes N, Ekker H, Thallinger GG, Mattanovich D, Gasser B, Graf AB
    FEMS Yeast Research 2016 July 6; (abstract)

    Small RNAs and the competing endogenous RNA network in high grade serous ovarian cancer tumor spread.
    Bachmayr-Heyda A, Auer K, Sukhbaatar N, Aust S, Deycmar S, Reiner AT, Polterauer S, Dekan S, Pils D
    Oncotarget 2016 Jun 28; 7 (26) (abstract)

    Molecular functions of the transcription factors E2A and E2-2 in controlling germinal center B cell and plasma cell development.
    Wöhner M, Tagoh H, Bilic I, Jaritz M, Poliakova DK, Fischer M, Busslinger M
    J. Exp. Med. 2016 Jun 3; (abstract)

    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; 12 (5) (abstract)

    Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence.
    Turner B, Paun O, Munzinger J, Chase MW, Samuel R
    Ann. Bot. 2016 Jun; 117 (7) (abstract)

    Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time.
    Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N
    Biotechnol. Bioeng. 2016 Apr 12; (abstract)

    Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex.
    Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O
    Heredity (Edinb) 2016 Apr; 116 (4) (abstract)

    Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance.
    Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V
    PLoS Biol. 2016 Mar; 14 (3) (abstract)

    MOL1 is required for cambium homeostasis in Arabidopsis.
    Gursanscky NR, Jouannet V, Grünwald K, Sanchez P, Laaber-Schwarz M, Greb T
    Plant J. 2016 Mar 17; (abstract)

    Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot.
    Paun O, Turner B, Trucchi E, Munzinger J, Chase MW, Samuel R
    Syst. Biol. 2016 Mar; 65 (2) (abstract)

    Sororin actively maintains sister chromatid cohesion.
    Ladurner R, Kreidl E, Ivanov MP, Ekker H, Idarraga-Amado MH, Busslinger GA, Wutz G, Cisneros DA, Peters JM
    EMBO J. 2016 Feb 22; (abstract)

    Response to interferons and antibacterial innate immunity in the absence of tyrosine-phosphorylated STAT1.
    Majoros A, Platanitis E, Szappanos D, Cheon H, Vogl C, Shukla P, Stark GR, Sexl V, Schreiber R, Schindler C, Müller M, Decker T
    EMBO Rep. 2016 Feb 12; (abstract)

    BsRADseq: screening DNA methylation in natural populations of non-model species.
    Trucchi E, Mazzarella AB, Gilfillan GD, Romero ML, Schönswetter P, Paun O
    Mol. Ecol. 2016 Jan 28; (abstract)

    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; 11 (1) (abstract)

    A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha.
    Gesson K, Rescheneder P, Skoruppa MP, von Haeseler A, Dechat T, Foisner R
    Genome Res. 2016 Jan 21; (abstract)

    Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation.
    Minnich M, Tagoh H, Bönelt P, Axelsson E, Fischer M, Cebolla B, Tarakhovsky A, Nutt SL, Jaritz M, Busslinger M
    Nat. Immunol. 2016 Jan 18; (abstract)

    Phosphorylation of an HP1-like Protein Regulates Heterochromatin Body Assembly for DNA Elimination.
    Kataoka K, Mochizuki K
    Dev. Cell 2015 Dec 21; 35 (6) (abstract)

    The histone chaperone CAF-1 safeguards somatic cell identity.
    Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K
    Nature 2015 Dec 10; 528 (7581) (abstract)

    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) (abstract)

    Transcriptional regulators form diverse groups with context-dependent regulatory functions.
    Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A
    Nature 2015 Nov 9; (abstract)

    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 Oct 22; (abstract)

    The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.
    Tscherner M, Zwolanek F, Jenull S, Sedlazeck FJ, Petryshyn A, Frohner IE, Mavrianos J, Chauhan N, von Haeseler A, Kuchler K
    PLoS Pathog. 2015 Oct; 11 (10) (abstract)

    Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot.
    Paun O, Turner B, Trucchi E, Munzinger J, Chase MW, Samuel R
    Syst. Biol. 2016 Mar; 65 (2) (abstract)

    The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.
    Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS
    PLoS Pathog. 2015 Sep; 11 (9) (abstract)

    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 14; (abstract)

    The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.
    Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A
    Cell 2015 Aug 27; 162 (5) (abstract)

    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) (abstract)

    Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia.
    Grebien F, Vedadi M, Getlik M, Giambruno R, Grover A, Avellino R, Skucha A, Vittori S, Kuznetsova E, Smil D, Barsyte-Lovejoy D, Li F, Poda G, Schapira M, Wu H, Dong A, Senisterra G, Stukalov A, Huber KV, Schönegger A, Marcellus R, Bilban M, Bock C, Brown PJ, Zuber J, Bennett KL, Al-Awar R, Delwel R, Nerlov C, Arrowsmith CH, Superti-Furga G
    Nat. Chem. Biol. 2015 Jul 13; (abstract)

    Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex.
    Wienerroither S, Shukla P, Farlik M, Majoros A, Stych B, Vogl C, Cheon H, Stark GR, Strobl B, Müller M, Decker T
    Cell Rep 2015 Jul 1 (abstract)

    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 1 (abstract)

    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) (abstract)

    Peritoneal tumor spread in serous ovarian cancer-epithelial mesenchymal status and outcome.
    Auer K, Bachmayr-Heyda A, Aust S, Sukhbaatar N, Reiner AT, Grimm C, Horvat R, Zeillinger R, Pils D
    Oncotarget 2015 May 11; (abstract)

    DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
    Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M
    Elife 2015; 4 (abstract)

    Noncanonical Effects of IRF9 in Intestinal Inflammation: More than Type I and Type III Interferons.
    Rauch I, Rosebrock F, Hainzl E, Heider S, Majoros A, Wienerroither S, Strobl B, Stockinger S, Kenner L, Müller M, Decker T
    Mol. Cell. Biol. 2015 Jul; 35 (13) (abstract)

    General and miRNA-mediated mRNA degradation occurs on ribosome complexes in Drosophila cells.
    Antic S, Wolfinger MT, Skucha A, Hosiner S, Dorner S
    Mol. Cell. Biol. 2015 Apr 27; (abstract)

    Inosine modifications in human tRNAs are incorporated at the precursor tRNA level.
    Torres AG, Piñeyro D, Rodríguez-Escribà M, Camacho N, Reina O, Saint-Léger A, Filonava L, Batlle E, Ribas de Pouplana L
    Nucleic Acids Res. 2015 Apr 27; (abstract)

    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) (abstract)

    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) (abstract)

    Correlation of circular RNA abundance with proliferation--exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues.
    Bachmayr-Heyda A, Reiner AT, Auer K, Sukhbaatar N, Aust S, Bachleitner-Hofmann T, Mesteri I, Grunt TW, Zeillinger R, Pils D
    Sci Rep 2015; 5 (abstract)

    A DEK Domain-Containing Protein Modulates Chromatin Structure and Function in Arabidopsis.
    Waidmann S, Kusenda B, Mayerhofer J, Mechtler K, Jonak C.
    Plant Cell. 2014 Nov;26(11):4328-44. (abstract)

    Role of STN1 and DNA Polymerase α in Telomere Stability and Genome-Wide Replication in Arabidopsis.
    Derboven E, Ekker H, Kusenda B, Bulankova P, Riha K.
    PLoS Genet. 2014 Oct. 9. (abstract)

    SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs.
    van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM.
    EMBO J. 2014 Nov 18. (abstract)

    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 Sept. (abstract)

    Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense.
    Gloggnitzer J, Akimcheva S, Srinivasan A, Kusenda B, Riehs N, Stampfl H, Bautor J, Dekrout B, Jonak C, Jiménez-Gómez JM, Parker JE, Riha K
    Cell Host Microbe 2014 Sep 10; 16 (3) (abstract)

    Alternative 3' UTR Selection Controls PAR-5 Homeostasis and Cell Polarity in C. elegans Embryos.
    Mikl M, Cowan CR
    Cell Rep. 2014 Sep 11;8(5) (abstract)

    H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.
    Sawicka A, Hartl D, Goiser M, Pusch O, Stocsits RR, Tamir IM, Mechtler K, Seiser C
    Genome Res. 2014 Nov; 24 (11) (abstract)

    Ecdysone and mediator change energy metabolism to terminate proliferation in Drosophila neural stem cells.
    Homem CC, Steinmann V, Burkard TR, Jais A, Esterbauer H, Knoblich JA
    Cell 2014 Aug 14; 158 (4) (abstract)

    A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element.
    Herzog VA, Lempradl A, Trupke J, Okulski H, Altmutter C, Ruge F, Boidol B, Kubicek S, Schmauss G, Aumayr K, Ruf M, Pospisilik A, Dimond A, Senergin HB, Vargas ML, Simon JA, Ringrose L
    Nat. Genet. 2014 Sep; 46 (9) (abstract)

    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) (abstract)

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

    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) (abstract)

    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) (abstract)

    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) (abstract)

    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) (abstract)

    Gene expression of lactobacilli in murine forestomach biofilms.
    Schwab C, Tveit AT, Schleper C, Urich T
    Microb Biotechnol 2014 Jul; 7 (4) (abstract)

    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 LM, Arnold CD, Stark A
    Mol. Cell 2014 Apr 10; 54 (1) (abstract)

    Genome wide identification of fruitless targets suggests a role in upregulating genes important for neural circuit formation.
    Vernes SC
    Sci Rep 2014; 4 (abstract)

    Evolutionary conservation of the eumetazoan gene regulatory landscape.
    Schwaiger M, Schönauer A, Rendeiro AF, Pribitzer C, Schauer A, Gilles AF, Schinko JB, Renfer E, Fredman D, Technau U
    Genome Res. 2014 Apr; 24 (4) (abstract)

    SWI/SNF complex prevents lineage reversion and induces temporal patterning in neural stem cells.
    Eroglu E, Burkard TR, Jiang Y, Saini N, Homem CC, Reichert H, Knoblich JA
    Cell 2014 Mar 13; 156 (6) (abstract)

    Stage-specific control of early B cell development by the transcription factor Ikaros.
    Schwickert TA, Tagoh H, Gültekin S, Dakic A, Axelsson E, Minnich M, Ebert A, Werner B, Roth M, Cimmino L, Dickins RA, Zuber J, Jaritz M, Busslinger M
    Nat Immunol. 2014 Mar;15(3) (abstract)

    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) (abstract)

    A dual role for autophagy in a murine model of lung cancer.
    Rao S, Tortola L, Perlot T, Wirnsberger G, Novatchkova M, Nitsch R, Sykacek P, Frank L, Schramek D, Komnenovic V, Sigl V, Aumayr K, Schmauss G, Fellner N, Handschuh S, Glösmann M, Pasierbek P, Schlederer M, Resch GP, Ma Y, Yang H, Popper H, Kenner L, Kroemer G, Penninger JM
    Nat Commun. 2014;5:3056 (abstract)

    Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery.
    Schwab C, Berry D, Rauch I, Rennisch I, Ramesmayer J, Hainzl E, Heider S, Decker T, Kenner L, Müller M, Strobl B, Wagner M, Schleper C, Loy A, Urich T
    ISME J 2014 May; 8 (5) (abstract)

    Cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock.
    Meireles-Filho AC, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A.
    Curr Biol. 2013 Dez. (Epub) (abstract)

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

    Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation.
    Jüschke C, Dohnal I, Pichler P, Harzer H, Swart R, Ammerer G, Mechtler K, Knoblich JA.
    Genome Biol. 2013 Nov. (abstract)

    Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana.
    Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N
    New Phytol. 2014 Feb; 201 (3) (abstract)

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

    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; 8 (10) (abstract)

    Whole-genome sequences of two turkey adenovirus types reveal the existence of two unknown lineages that merit the establishment of novel species within the genus Aviadenovirus.
    Marek A, Ballmann MZ, Kosiol C, Harrach B, Schlötterer C, Hess M
    J. Gen. Virol. 2014 Jan; 95 (Pt 1) (abstract)

    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) (abstract)

    Wapl is an essential regulator of chromatin structure and chromosome segregation.
    Tedeschi A, Wutz G, Huet S, Jaritz M, Wuensche A, Schirghuber E, Davidson IF, Tang W, Cisneros DA, Bhaskara V, Nishiyama T, Vaziri A, Wutz A, Ellenberg J, Peters JM
    Nature 2013 Sep 26; 501 (7468) (abstract)

    Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.
    Medvedovic J, Ebert A, Tagoh H, Tamir IM, Schwickert TA, Novatchkova M, Sun Q, Huis In 't Veld PJ, Guo C, Yoon HS, Denizot Y, Holwerda SJ, de Laat W, Cogné M, Shi Y, Alt FW, Busslinger M
    Immunity 2013 Aug 22; 39 (2) (abstract)

    Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex.
    Dönertas D, Sienski G, Brennecke J
    Genes Dev. 2013 Aug 1;27(15) (abstract)

    Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.
    Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M
    Nat. Genet. 2013 Aug; 45 (8) (abstract)

    The first whole genome sequence of a Fowl adenovirus B strain enables interspecies comparisons within the genus Aviadenovirus.
    Marek A, Kosiol C, Harrach B, Kaján GL, Schlötterer C, Hess M
    Vet. Microbiol. 2013 Sep 27; 166 (1-2) (abstract)

    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) (abstract)

    FACS purification of Drosophila larval neuroblasts for next-generation sequencing.
    Harzer H, Berger C, Conder R, Schmauss G, Knoblich JA
    Nat Protoc 2013 Jun; 8 (6) (abstract)

    The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems.
    Chylinski K, Le Rhun A, Charpentier E
    RNA Biol 2013 May; 10 (5) (abstract)

    Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.
    Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G
    PLoS One. 2013;8(4) (abstract)

    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) (abstract)

    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) (abstract)

    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) (abstract)

    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) (abstract)

    Unusual case of apparent hypermutation in Arabidopsis thaliana.
    Sasaki T, Naumann U, Forai P, Matzke AJ, Matzke M
    Genetics 2012 Dec; 192 (4) (abstract)

    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) (abstract)

    FACS purification and transcriptome analysis of drosophila neural stem cells reveals a role for Klumpfuss in self-renewal.
    Berger C, Harzer H, Burkard TR, Steinmann J, van der Horst S, Laurenson AS, Novatchkova M, Reichert H, Knoblich JA
    Cell Rep 2012 Aug 30; 2 (2) (abstract)

    Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena.
    Schoeberl UE, Kurth HM, Noto T, Mochizuki K
    Genes Dev. 2012 Aug 1; 26 (15) (abstract)

    Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.
    Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A
    PLoS ONE 2012; 7 (7) (abstract)

    Blunt-ended telomeres: an alternative ending to the replication and end protection stories.
    Nelson AD, Shippen DE, Kazda A, Zellinger B, Rössler M, Derboven E, Kusenda B, Riha K
    Genes Dev. 2012 Aug 1; 26 (15) (abstract)

    Chromosome end protection by blunt-ended telomeres.
    Nelson AD, Shippen DE, Kazda A, Zellinger B, Rössler M, Derboven E, Kusenda B, Riha K
    Genes Dev. 2012 Aug 1; 26 (15) (abstract)

    The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis.
    Revilla-I-Domingo R, Bilic I, Vilagos B, Tagoh H, Ebert A, Tamir IM, Smeenk L, Trupke J, Sommer A, Jaritz M, Busslinger M
    EMBO J. 2012 Jul 18; 31 (14) (abstract)

    Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.
    Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M
    Genome Res. 2012 Jun; 22 (6) (abstract)

    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) (abstract)

    Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells.
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    Cell Stem Cell 2011 Dec. (abstract)

    A computational pipeline for comparative ChIP-seq analyses.
    Bardet AF, He Q, Zeitlinger J, Stark A.
    Nat. Protoc. 2011 Dec. (abstract)

    An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
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    PLoS ONE 2011; 6 (11) (abstract)

    Genetic rearrangements can modify chromatin features at epialleles.
    Foerster AM, Dinh HQ, Sedman L, Wohlrab B, Mittelsten Scheid O
    PLoS Genet. 2011 Oct; 7 (10) (abstract)

    AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana.
    Eun C, Lorkovic ZJ, Naumann U, Long Q, Havecker ER, Simon SA, Meyers BC, Matzke AJ, Matzke M
    PLoS ONE 2011; 6 (10) (abstract)

    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 Oct 5; 30 (19) (abstract)

    The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.
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    Nat. Cell Biol. 2011 Sep; 13 (9) (abstract)

    High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm.
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    PLoS Genet. 2011 Jun; 7 (6) (abstract)

    The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells.
    McManus S, Ebert A, Salvagiotto G, Medvedovic J, Sun Q, Tamir I, Jaritz M, Tagoh H, Busslinger M
    EMBO J. 2011 Jun 15; 30 (12) (abstract)


    Andreas Sommer

    Andreas Sommer

    Core Facility Head
    VBC2 / PG4

    Claudia Stocsits

    Claudia Stocsits

    VBC2 / PG4

    Alexander Vogt

    Alexander Vogt

    Sequencing Specialist
    VBC2 / 1OG-10

    Laura-Maria Bayer

    Laura-Maria Bayer

    Sequencing Specialist
    VBC2 / 1OG-10

    Carmen Czepe

    Carmen Czepe

    VBC2 / 1OG-10

    Heinz Ekker

    Heinz Ekker

    VBC2 / PG4

    Bartlomiej Gebarski

    Bartlomiej Gebarski

    Sequencing Specialist
    VBC2 / 1OG-10

    Renate Landwehr

    Renate Landwehr

    Sequencing Specialist
    VBC2 / 1OG-10

    Miriam Schalamun

    Miriam Schalamun

    Volodymyr Shubchynskyy

    Volodymyr Shubchynskyy

    Sequencing Specialist
    VBC2 / 1OG-10

    Lisa Slama

    Lisa Slama

    Ido Tamir

    Ido Tamir

    VBC2 / PG4