Next Generation Sequencing

Genomics’ most flexible and powerful tool to accelerate your research!

Next Generation Sequencing (NGS) has become a key analysis method for biological research, enabling researchers to obtain a global view of biological processes.

Advice and guidance for sequencing projects are offered by our team, which relies on years of experience with sequencing systems, high-throughput data analysis, and cutting-edge NGS technology. All common sequencing applications are supported, and the development of novel methods and protocols is encouraged.

SERVICES

Library preparation

A prerequisite for NGS is the generation of sequencing libraries from the corresponding DNA or RNA sample. During library preparation, adaptors are added, which makes the sequencing reaction possible. There are many protocols and kits available depending on the sequencing technology, sample source, and biological question of interest. The Next Generation Sequencing Core Facility offers a broad range of library preparation methods; you can find them listed here (Link to pdf).

Quality control

There is a careful quality check of each sequencing library prepared by facility staff or users. This includes three major steps:

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

Sequencing

Sequencing is performed on Illumina (HiSeq 2500, NextSeq, MiSeq), PacBio (Sequel), and ONT instruments depending on the application and biological question. Please refer to our list of sequencing services (Link to pdf).

Data analysis

Primary data output from the sequencing instruments is converted to compressed BAM files that hold sequence quality information, index read barcodes, and other information. We generate quality metrics from the sequencing process and analyze the reads to ensure successful sequencing and avoid 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. The alignment data can be visualized in available genome browsers and further analyzed in Galaxy.

RESOURCES

2 × HiSeq2500

1 × NextSeq

1 × MiSeq

1 × PacBio Sequel Please see here (link to pdf) for sample requirements.

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 bioinformatics tasks. In collaboration with the GenAU bioinformatics group, we provide custom-tailored tools.

Reserva – Book a time slot for the Covaris DNA shearer and MiSeq.

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.

USER INFORMATION

The VBCF NGS facility offers access to its services to all members of the Vienna BioCenter. Free capacity is offered to external users (academic and industry). To estimate feasibility and allocable resources, we strongly recommend contacting our team when planning a sequencing experiment. Queuing follows a first come, first served policy.

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

Please create an account on https://ngs.vbcf.ac.at/forskalle3/signup if you don't already have one (it's free and painless!). If your research group is not listed there, contact us to set it up for you.

 

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 Education, Science and Research depends on documented evidence of contribution to scientific output. We therefore require acknowledgement of use of the facility in published 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 the journal format.

Suggested minimal format:

“Sequencing was performed at the VBCF NGS Unit (www.viennabiocenter.org/facilities).” Your publication will be also listed on our website.

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

User Guide, Price List, and General Cooperation Conditions are available as PDFs for registered users. Please go to https://ngs.vbcf.ac.at/forskalle3 and create an account (if you don't already have one). After logging in, you will find them under the ‘Important Documents’ tab.

PUBLICATIONS

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)

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) 

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 

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; 

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; 

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.

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)

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)

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)

ACKNOWLEDGEMENTS

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) 

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; 

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)

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)

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 

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)

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)

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;

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

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) 

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) 

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) 

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) 

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) 

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) 

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)

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; 

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 

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;

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;

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; 

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; 

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;

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 

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) 

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;

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) 

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; 

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)

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

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

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) 

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) 

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)

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) 

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)

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) 

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) 

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) 

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) 

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; 

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)

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;

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; 

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) 

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 

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;

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;

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) 

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; 

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) 

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) 

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;

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 

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 

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; 

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; 

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; 

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;

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) 

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; 

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; 

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)

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) 

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; 

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;

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) 

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; 

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) 

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)

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)

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)

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;

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) 

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;

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; 

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.
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A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha.
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Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation.
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The histone chaperone CAF-1 safeguards somatic cell identity.
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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;

Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.
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The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.
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Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot.
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The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.
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Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.
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The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.
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piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.
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Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia.
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Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex.
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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

Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.
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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; 

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
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Noncanonical Effects of IRF9 in Intestinal Inflammation: More than Type I and Type III Interferons.
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General and miRNA-mediated mRNA degradation occurs on ribosome complexes in Drosophila cells.
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Inosine modifications in human tRNAs are incorporated at the precursor tRNA level.
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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)

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) 

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