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 more than 10 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.


Library preparation

A prerequisite for NGS is the generation of sequencing libraries from the corresponding DNA or RNA sample. 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.

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 is performed on Illumina (NovaSeq, NextSeq, MiSeq, iSeq), PacBio (Sequel II, in collabration), and ONT (MinION, PromethION) instruments depending on the application and biological question. The available instruments cover short, long and ultra-long sequencing as well as a broad range of output, from a few million of reads to Terabases.

Data analysis

We generate quality metrics from the sequencing process and analyze the reads to ensure successful sequencing. 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. Additional, standardized analysis pipelines are available for most common applications (ChIP-seq, RNA-seq, SNP-mapping, small genome assembly).


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.

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

VBCF-NGS GitHub – Illumina-related tools and snippets for quality metrics and file conversion.


In general, we offer four types of access to our shared research infrastructure:

  1. Research projects
  2. Full research services
  3. Trained user access | user labs
  4. Shared technology platform

Typically, these are set but not limited by the offered technology or instrument, and differ in the required user expertise, the usability of a technology, the user’s pre- and postprocessing input, and the underlying operational models.

Research project

Research projects are the equivalent of contract research organizations (CRO). The customer submits the starting material/sample and receives the ready-to-use data for publication. Hence, core facility members are often co-authoring and involved in the entire publication process.

Full research service

The user submits the sample, we perform a pre-defined workflow (incl. QC) and process the raw data. Data interpretation or contributions to publications cannot be offered in this service mode.

Trained user access | User labs

VBCF experts maintain an instrument park and train users to operate it. This requires a certain level of expertise, maturity of the offered technology, a hands-on attitude and reliability from the user.

Shared technology platform | Instrument park

These technologies require expert knowledge to run the offered instruments. Experts are hired by one of the research institutes on the Vienna BioCenter Campus. The experts maintain an instrument park, run the experiments and train other trainers. Machines can only be operated by experts.


The VBCF NGS facility provides full research service only. 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 (User Guide, Price List, and General Cooperation Conditions) can be found in our sample management interface Forskalle for registered users. Please create an account on if you don't already have one. If your research group is not listed there, contact us to set it up for you.

In general, the VBCF’s general cooperation conditions apply. Please contact the NGS team for further information and to discuss your specific project needs.

We require acknowledgement of facility use in publications. 
A simple statement is sufficient and can be placed in the Materials and Methods section or in the Acknowledgments section, depending on the journal format.

Suggested format:

The XXXXXX was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

In case of (co-)authorship:

The Vienna BioCenter Core Facilities (VBCF) Next Generation Sequencing Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna.



Intron-mediated induction of phenotypic heterogeneity. Lukačišin M, Espinosa-Cantú A, Bollenbach T. Nature. 2022 605(7908):113-118.

Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, Haberle V, Serebreni L, Karner K, Hendy O, Boija A, Henninger JE, Li CH, Stejskal K, Lin G, Bergauer K, Pagani M, Rath M, Mechtler K, Arnold CD, Stark A. Nature. 2022 606(7913):406-413.

Amplification of human interneuron progenitors promotes brain tumors and neurological defects. Eichmüller OL, Corsini NS, Vértesy Á, Morassut I, Scholl T, Gruber VE, Peer AM, Chu J, Novatchkova M, Hainfellner JA, Paredes MF, Feucht M, Knoblich JA. Science. 2022 375(6579):eabf5546.

Zygotic genome activation by the totipotency pioneer factor Nr5a2. Gassler J, Kobayashi W, Gáspár I, Ruangroengkulrith S, Mohanan A, Gómez Hernández L, Kravchenko P, Kümmecke M, Lalic A, Rifel N, Ashburn RJ, Zaczek M, Vallot A, Cuenca Rico L, Ladstätter S, Tachibana K. Science. 2022 378(6626):1305-1315

For the full list of scientific contributions, click here.

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level. Mazzucco R, Schlötterer C. Proc Biol Sci. 2021 288(1965):20212193.

Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. Bajaj S, Bagley JA, Sommer C, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. EMBO J. 2021 40(23):e108714.

An inhibitor-mediated beta-cell dedifferentiation model reveals distinct roles for FoxO1 in glucagon repression and insulin maturation. Casteels T, Zhang Y, Frogne T, Sturtzel C, Lardeau CH, Sen I, Liu X, Hong S, Pauler FM, Penz T, Brandstetter M, Barbieux C, Berishvili E, Heuser T, Bock C, Riedel CG, Meyer D, Distel M, Hecksher-Sørensen J, Li J, Kubicek S. Mol Metab. 2021 54:101329.

Anammox bacteria drive fixed nitrogen loss in hadal trench sediments. Thamdrup B, Schauberger C, Larsen M, Trouche B, Maignien L, Arnaud-Haond S, Wenzhöfer F, Glud RN. Proc Natl Acad Sci U S A. 2021 118(46):e2104529118.

Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation. Burny C, Nolte V, Dolezal M, Schlötterer C. Genome Biol Evol. 2021 13(11):evab239.

PhosphoFlowSeq - A High-throughput Kinase Activity Assay for Screening Drug Resistance Mutations in EGFR. Wagner A, Teufl M, Gold L, Lehner M, Obinger C, Sykacek P, Traxlmayr MW. J Mol Biol. 2021 433(22):167210.

Autochthonous fungi are central components in microbial community structure in raw fermented sausages. Zwirzitz B, Thalguter S, Wetzels SU, Stessl B, Wagner M, Selberherr E.  Microb Biotechnol. 2021, doi: 10.1111/1751-7915.13950. Epub ahead of print.

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. Nat Commun. 2021 12(1):6078.

miR-1 sustains muscle physiology by controlling V-ATPase complex assembly. Gutiérrez-Pérez P, Santillán EM, Lendl T, Wang J, Schrempf A, Steinacker TL, Asparuhova M, Brandstetter M, Haselbach D, Cochella L. Sci Adv. 2021 7(42):eabh1434.

The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Xue Z, Greimler J, Paun O, Ford KA, Barfuss MHJ, Chiapella JO. Endemism, and Hybridization. Biology (Basel). 2021 10(10):1001.

Gradual evolution of allopolyploidy in Arabidopsis suecica. Burns R, Mandáková T, Gunis J, Soto-Jiménez LM, Liu C, Lysak MA, Novikova PY, Nordborg M. Nat Ecol Evol. 2021 5(10):1367-1381.

Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology. Guenay-Greunke Y, Bohan DA, Traugott M, Wallinger C. Sci Rep. 2021 11(1):19510.

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat. Romanauska A, Köhler A. Dev Cell. 2021 56(18):2562-2578.e3.

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements. Stelzer CP, Blommaert J, Waldvogel AM, Pichler M, Hecox-Lea B, Mark Welch DB.  BMC Biol. 2021 19(1):206.

Copy Number Changes and Allele Distribution Patterns of Chromosome 21 in B Cell Precursor Acute Lymphoblastic Leukemia. Abbasi MR, Nebral K, Haslinger S, Inthal A, Zeitlhofer P, König M, Schinnerl D, Köhrer S, Strehl S, Panzer-Grümayer R, Mann G, Attarbaschi A, Haas OA. Cancers (Basel). 2021 13(18):4597.

A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis. Capitao C, Tanasa S, Fulnecek J, Raxwal VK, Akimcheva S, Bulankova P, Mikulkova P, Crhak Khaitova L, Kalidass M, Lermontova I, Mittelsten Scheid O, Riha K. PLoS Genet. 2021 17(9):e1009779.

A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. Schmieder V, Novak N, Dhiman H, Nguyen LN, Serafimova E, Klanert G, Baumann M, Kildegaard HF, Borth N. Biotechnol Rep (Amst). 2021 31:e00649.

Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants. Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pĕnčík A, Novák O, Kalyna M, Mouille G, Benková E, P Bhalerao R, Mravec J, Kleine-Vehn J. Int J Mol Sci. 2021 22(17):9222.

Quinoa genome assembly employing genomic variation for guided scaffolding. Bodrug-Schepers A, Stralis-Pavese N, Buerstmayr H, Dohm JC, Himmelbauer H. Theor Appl Genet. 2021 134(11):3577-3594.

LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line. Yotova I, Hudson QJ, Pauler FM, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. Int J Mol Sci. 2021 22(16):8385.

Ecdysis-related neuropeptide expression and metamorphosis in a non-ecdysozoan bilaterian. Zieger E, Calcino AD, Robert NSM, Baranyi C, Wanninger A. Evolution. 2021 75(9):2237-2250.

Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis. Papareddy RK, Páldi K, Smolka AD, Hüther P, Becker C, Nodine MD. Elife. 2021 10:e69396.

Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation. Calderón L, Schindler K, Malin SG, Schebesta A, Sun Q, Schwickert T, Alberti C, Fischer M, Jaritz M, Tagoh H, Ebert A, Minnich M, Liston A, Cochella L, Busslinger M. Sci Immunol. 2021 6(61):eabg5003.

The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime. Otte KA, Nolte V, Mallard F, Schlötterer C. Genome Biol. 2021 22(1):211.

Expression of RUNX1-JAK2 in Human Induced Pluripotent Stem Cell-Derived Hematopoietic Cells Activates the JAK-STAT and MYC Pathways. Fortschegger K, Husa AM, Schinnerl D, Nebral K, Strehl S. Int J Mol Sci. 2021 22(14):7576.

Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris. Lecaudey LA, Singh P, Sturmbauer C, Duenser A, Gessl W, Ahi EP. BMC Genomics. 2021 22(1):506.

Gene expression variation in Arabidopsis embryos at single-nucleus resolution. Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD. Development. 2021 148(13):dev199589.

Ovulation suppression protects against chromosomal abnormalities in mouse eggs at advanced maternal age. Chatzidaki EE, Powell S, Dequeker BJH, Gassler J, Silva MCC, Tachibana K. Curr Biol. 2021 31(18):4038-4051.e7.

The histone chaperone HIR maintains chromatin states to control nitrogen assimilation and fungal virulence. Jenull S, Mair T, Tscherner M, Penninger P, Zwolanek F, Silao FS, de San Vicente KM, Riedelberger M, Bandari NC, Shivarathri R, Petryshyn A, Chauhan N, Zacchi LF, -Landmann SL, Ljungdahl PO, Kuchler K. Cell Rep. 2021 36(3):109406.

Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells. Marx N, Dhiman H, Schmieder V, Freire CM, Nguyen LN, Klanert G, Borth N. Metab Eng. 2021 66:268-282.

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar S, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A. Nat Microbiol. 2021 6(7):885-898.

Bacteria of eleven different species isolated from biofilms in a meat processing environment have diverse biofilm forming abilities. Wagner EM, Fischel K, Rammer N, Beer C, Palmetzhofer AL, Conrady B, Roch FF, Hanson BT, Wagner M, Rychli K. Int J Food Microbiol. 2021 349:109232.

Favorable outcome of NUTM1-rearranged infant and pediatric B cell precursor acute lymphoblastic leukemia in a collaborative international study. Boer JM, Valsecchi MG, Hormann FM, Antić Ž, Zaliova M, Schwab C, Cazzaniga G, Arfeuille C, Cavé H, Attarbaschi A, Strehl S, Escherich G, Imamura T, Ohki K, Grüber TA, Sutton R, Pastorczak A, Lammens T, Lambert F, Li CK, Carrillo de Santa Pau E, Hoffmann S, Möricke A, Harrison CJ, Den Boer ML, De Lorenzo P, Stam RW, Bergmann AK, Pieters R. Leukemia. 2021 35(10):2978-2982.

Soil fertility relates to fungal-mediated decomposition and organic matter turnover in a temperate mountain forest. Mayer M, Rewald B, Matthews B, Sandén H, Rosinger C, Katzensteiner K, Gorfer M, Berger H, Tallian C, Berger TW, Godbold DL. New Phytol. 2021 231(2):777-790.

A non-viral and selection-free COL7A1 HDR approach with improved safety profile for dystrophic epidermolysis bullosa. Kocher T, Bischof J, Haas SA, March OP, Liemberger B, Hainzl S, Illmer J, Hoog A, Muigg K, Binder HM, Klausegger A, Strunk D, Bauer JW, Cathomen T, Koller U. Mol Ther Nucleic Acids. 2021 25:237-250.

Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Qi Q, Angermayr SA, Bollenbach T. Front Microbiol. 2021 12:760017.

Antagonistic activities of cotranscriptional regulators within an early developmental window set FLC expression level. Schon M, Baxter C, Xu C, Enugutti B, Nodine MD, Dean C. Proc Natl Acad Sci U S A. 2021 118(17):e2102753118.

Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces. Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L. mSystems. 2021 6(3):e0118620

Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Nat Commun. 2021 12(1):3804

Central amygdala circuitry modulates nociceptive processing through differential hierarchical interaction with affective network dynamics. Wank, I., Pliota, P., Badurek, S., Kraitsy, K., Kaczanowska J., Griessner J., Kreitz S., Hess A., Haubensak W. Commun Biol 2021 4, 732.

Cardioids reveal self-organizing principles of human cardiogenesis. Hofbauer P, Jahnel SM, Papai N, Giesshammer M, Deyett A, Schmidt C, Penc M, Tavernini K, Grdseloff N, Meledeth C, Ginistrelli LC, Ctortecka C, Salic S, Novatchkova M, Mendjan S (2021) Cell 184 (12) 3299-3317.e22.

Subcloning induces changes in the DNA-methylation pattern of outgrowing Chinese hamster ovary cell colonies. Weinguny M, Klanert G, Eisenhut P, Lee I, Timp W, Borth N. Biotechnol J. 2021 16(6):e2000350.

Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq. Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar JC, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaeffer J, Hufnagl P, Zoufaly A, Seitz T; VCDI, Födinger M, Allerberger F, Stark A, Cochella L, Elling U. Nat Commun. 2021 12(1):3132

Fibroblast dedifferentiation as a determinant of successful regeneration. Lin TY, Gerber T, Taniguchi-Sugiura Y, Murawala P, Hermann S, Grosser L, Shibata E, Treutlein B, Tanaka EM. Dev Cell. 2021 56(10):1541-1551.

Selective requirement of MYB for oncogenic hyperactivation of a translocated enhancer in leukemia. Smeenk L, Ottema S, Mulet-Lazaro R, Ebert A, Havermans M, Arricibita Varea A, Fellner M, Pastoors D, van Herk S, Erpelinck-Verschueren C, Grob T, Hoogenboezem RM, Kavelaars FG, Matson DR, Bresnick EH, Bindels EM, Kentsis A, Zuber J, Delwel R. Cancer Discov. 2021 doi: 10.1158/2159-8290.CD-20-1793. Epub ahead of print.

A tale of two morphs: developmental patterns and mechanisms of seed coat differentiation in the dimorphic diaspore model Aethionema arabicum (Brassicaceae). Arshad W, Lenser T, Wilhelmsson PKI, Chandler JO, Steinbrecher T, Marone F, Pérez M, Collinson ME, Stuppy W, Rensing SA, Theißen G, Leubner-Metzger G. Plant J. 2021 107(1):166-181

The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. Schloissnig S, Kawaguchi A, Nowoshilow S, Falcon F, Otsuki L, Tardivo P, Timoshevskaya N, Keinath MC, Smith JJ, Voss SR, Tanaka EM. Proc Natl Acad Sci U S A. 2021 118(15):e2017176118

Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. Fernandez-Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner-Metzger G, Rensing SA. Plant J. 2021 106(1):275-293

The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Osakabe A, Jamge B, Axelsson E, Montgomery SA, Akimcheva S, Kuehn AL, Pisupati R, Lorković ZJ, Yelagandula R, Kakutani T, Berger F.  Nat Cell Biol. 2021 23(4):391-400.

Data of de novo transcriptome assembly of the myxozoan parasite Tetracapsuloides bryosalmonae. Kumar G, Ertl R, Nilsen F, Bartholomew JL, El-Matbouli M. Data Brief. 2021 35:106831

Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Krenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A, Salata C, Rilo Christoff R, Pestana Garcez P, Mirazimi A, Knoblich JA. Cell Stem Cell. 2021 28(8):1362-1379.e7.

High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest. Gorfer M, Mayer M, Berger H, Rewald B, Tallian C, Matthews B, Sandén H, Katzensteiner K, Godbold DL. Microb Ecol. 2021 82(1):243-256.

Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species. Madritsch S, Burg A, Sehr EM. BMC Bioinformatics. 2021 22(1):146

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Thomas HF, Kotova E, Jayaram S, Pilz A, Romeike M, Lackner A, Penz T, Bock C, Leeb M, Halbritter F, Wysocka J, Buecker C. Mol Cell. 2021 81(5):969-982

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure. Bente H, Foerster AM, Lettner N, Mittelsten Scheid O. PLoS Genet. 2021 17(3):e1009444.

Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex. Schnabl J, Wang J, Hohmann U, Gehre M, Batki J, Andreev VI, Purkhauser K, Fasching N, Duchek P, Novatchkova M, Mechtler K, Plaschka C, Patel DJ, Brennecke J. Genes Dev. 2021 35(5-6):392-409

Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment. Pelikan C, Wasmund K, Glombitza C, Hausmann B, Herbold CW, Flieder M, Loy A. ISME J. 2021 15(3):833-847

Identification of gene targets of mutant C/EBPα reveals a critical role for MSI2 in CEBPA-mutated AML. Heyes E, Schmidt L, Manhart G, Eder T, Proietti L, Grebien F. Leukemia. 2021 doi: 10.1038/s41375-021-01169-6. Epub ahead of print.

ATM controls meiotic DNA double-strand break formation and recombination and affects synaptonemal complex organization in plants. Kurzbauer MT, Janisiw MP, Paulin LF, Prusén Mota I, Tomanov K, Krsicka O, Haeseler AV, Schubert V, Schlögelhofer P. Plant Cell. 2021 33(5):1633-1656

Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression.Terlecki-Zaniewicz S, Humer T, Eder T, Schmoellerl J, Heyes E, Manhart G, Kuchynka N, Parapatics K, Liberante FG, Müller AC, Tomazou EM, Grebien F. Nat Struct Mol Biol. 2021 28(2):190-201

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition. Cabrera-Quio LE, Schleiffer A, Mechtler K, Pauli A. PLoS Genet. 2021 17(2):e1009390.

Central amygdala circuit dynamics underlying the benzodiazepine anxiolytic effect. Griessner J, Pasieka M, Böhm V, Grössl F, Kaczanowska J, Pliota P, Kargl D, Werner B, Kaouane N, Strobelt S, Kreitz S, Hess A, Haubensak W. Mol Psychiatry 2021 26(2):534-544.

Novel Identified Circular Transcript of RCAN2, circ-RCAN2, Shows Deviated Expression Pattern in Pig Reperfused Infarcted Myocardium and Hypoxic Porcine Cardiac Progenitor Cells In Vitro. Mester-Tonczar J, Einzinger P, Winkler J, Kastner N, Spannbauer A, Zlabinger K, Traxler D, Lukovic D, Hasimbegovic E, Goliasch G, Pavo N, Gyöngyösi M. Int J Mol Sci. 2021 22(3):1390

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Elife. 2021 10:e61894

Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants. Sims J, Sestini G, Elgert C, von Haeseler A, Schlögelhofer P. Nat Commun. 2021 12(1):387

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb. Ahmad M, Leroy T, Krigas N, Temsch EM, Weiss-Schneeweiss H, Lexer C, Sehr EM, Paun O. Front Plant Sci. 2021 12:706574

Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia. Matsusaka D, Filiault D, Sanchez DH, Botto JF. Front Plant Sci. 2021 12:677728

Evidence for Glacial Refugia of the Forest Understorey Species Helleborus niger (Ranunculaceae) in the Southern as Well as in the Northern Limestone Alps. Záveská E, Kirschner P, Frajman B, Wessely J, Willner W, Gattringer A, Hülber K, Lazić D, Dobeš C, Schönswetter P. Front Plant Sci. 2021 12:683043

Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin. Cianciulli Sesso A, Lilić B, Amman F, Wolfinger MT, Sonnleitner E, Bläsi U. Front Microbiol. 2021 12:626715

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events. Zwirzitz B, Wetzels SU, Dixon ED, Fleischmann S, Selberherr E, Thalguter S, Quijada NM, Dzieciol M, Wagner M, Stessl B. Front Microbiol. 2021 12:632935

TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. Fontinha BM, Zekoll T, Al-Rawi M, Gallach M, Reithofer F, Barker AJ, Hofbauer M, Fischer RM, von Haeseler A, Baier H, Tessmar-Raible K.  PLoS Biol. 2021 19(1):e3001012

Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets. Bhat P, Burkard TR, Herzog VA, Pauli A, Ameres SL. Methods Enzymol. 2021;655:205-223

A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans. Hagelkruys A, Wirnsberger G, Stadlmann J, Wöhner M, Horrer M, Vilagos B, Jonsson G, Kogler M, Tortola L, Novatchkova M, Bönelt P, Hoffmann D, Koglgruber R, Steffen U, Schett G, Busslinger M, Bergthaler A, Klein C, Penninger JM. J Exp Med. 2021 218(1):e20200559.

Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W. Lei B, Capella M, Montgomery SA, Borg M, Osakabe A, Goiser M, Muhammad A, Braun S, Berger F. A. Curr Biol. 2021 31(1):182-191.e5.


Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae). Brandrud MK, Baar J, Lorenzo MT, et al. Syst Biol. 2020 69(1):91-109.

High activation of STAT5A drives peripheral T-cell lymphoma and leukemia. Maurer B, Nivarthi H, Wingelhofer B, et al. Haematologica. 2020 105(2):435-447.

Early diversification and permeable species boundaries in the Mediterranean firs. Balao F, Lorenzo MT, Sánchez-Robles JM, Paun O, García-Castaño JL, Terrab A. Ann Bot. 2020 125(3):495-507. 

Predictable CRISPR/Cas9-Mediated COL7A1 Reframing for Dystrophic Epidermolysis Bullosa. Kocher T, March OP, Bischof J, Liemberger B, Hainzl S, Klausegger A, Hoog A, Strunk D, Bauer JW, Koller U. J Invest Dermatol. 2020 Mar 3.

An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species. Pan D, Hülber K, Willner W, Schneeweiss GM. Mol Ecol. 2020 29(1):172-183.

Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish. Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Glabonjat R, Goessler W, Hois V, Wagner C, Lass A, Sefc KM. BMC Genomics. 2020 16;21(1):54. 

Podocyte RNA sequencing reveals Wnt- and ECM-associated genes as central in FSGS. Bukosza EN, Kratochwill K, Kornauth C, Schachner H, Aufricht C, Gebeshuber CA.  PLoS One. 2020;15(4):e0231898.

Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. Laukoter S, Beattie R, Pauler FM, Amberg N, Nakayama KI, Hippenmeyer S. Nat Commun. 2020;11(1):195

Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes. Silva MCC, Powell S, Ladstätter S, et al.  J Cell Biol. 2020;219(4):e201906100

Bioinformatic Identification of Chinese Hamster Ovary (CHO) Cold-Shock Genes and Biological Evidence of their Cold-Inducible Promoters. Nguyen LN, Novak N, Baumann M, Koehn J, Borth N. Biotechnol J. 2020;15(3):e1900359.

Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells. Weinguny M, Klanert G, Eisenhut P, et al. Comput Struct Biotechnol J. 2020;18:1320-1329. 

Rbfox1 Is Expressed in the Mouse Brain in the Form of Multiple Transcript Variants and Contains Functional E Boxes in Its Alternative Promoters. Casanovas S, Schlichtholz L, Mühlbauer S, et al.  Front Mol Neurosci. 2020;13:66.

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Montgomery SA, Tanizawa Y, Galik B, et al. Curr Biol. 2020;30(4):573-588.e7.

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Borg M, Jacob Y, Susaki D, et al.  Nat Cell Biol. 2020;22(6):621-629. 

Soil microbial community structure and function mainly respond to indirect effects in a multifactorial climate manipulation experiment. Deltedesco E, Keiblinger KM, iepho HP, Soil Biology and Biochemistry,  2020,142,107704

Benchmarking of long-read correction methods. Dohm JC, Peters P, Stralis-Pavese N, Himmelbauer H, NAR Genomics and Bioinformatics 2020, 2 (2), lqaa037

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato. Herpell JB, Schindler F, Bejtović M, et al. Front Microbiol. 2020;11:581.

Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae). McCann J, Macas J, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Front Plant Sci. 2020;11:362. 

First transcriptome analysis of bryozoan Fredericella sultana, the primary host of myxozoan parasite Tetracapsuloides bryosalmonae. Kumar G, Ertl R, Bartholomew JL, El-Matbouli M. PeerJ. 2020;8:e9027. 

Prevalence and risk factors of Leptospira infection in urban brown rats (Rattus norvegicus), Vienna, Austria. Desvars-Larrive, A., Smith, S., Munimanda, G. et al. Urban Ecosyst 23, 775–784 (2020). 

Transcriptional profiling of human macrophages during infection with Bordetella pertussis. Petráčková D, Farman MR, Amman F, et al.  RNA Biol. 2020;17(5):731-742.

Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Fitz J, Neumann T, Steininger M, et al. Nat Genet. 2020;52(5):505-515.

Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq. Sonnleitner E, Pusic P, Wolfinger MT, Bläsi U. Front Microbiol. 2020;11:1001. 

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome. Wu G, Schmid M, Rib L, et al. Cell Rep. 2020;30(7):2387-2401.e5.

A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells. Kainov YA, Makeyev EV. Nat Commun. 2020;11(1):361.

Lactuca dregeana DC. (Asteraceae: Chicorieae) – A South African crop relative under threat from hybridization and climate change. Sochor M, Manning,JC, Šarhanová P, et al. South African Journal of Botany 2020, 132, 146-154.

Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters. Zhang X, Adamowski M, Marhava P, et al. Plant Cell. 2020;32(5):1644-1664.

The sources and transmission routes of microbial populations throughout a meat processing facility. Zwirzitz B, Wetzels SU, Dixon ED, et al. NPJ Biofilms Microbiomes. 2020;6(1):26.

ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Kapoor U, Licht K, Amman F, et al. Genome Res. 2020;30(8):1107-1118.

The evolution and functional divergence of the histone H2B family in plants. Jiang D, Borg M, Lorković ZJ, et al. PLoS Genet. 2020;16(7):e1008964

Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. Gutzat R, Rembart K, Nussbaumer T, et al. EMBO J. 2020;e103667.

Adaptor protein RapZ activates endoribonuclease RNase E by protein-protein interaction to cleave a small regulatory RNA. Durica-Mitic S, Göpel Y, Amman F, Görke B.  RNA. 2020;26(9):1198-1215.

Repression of the B cell identity factor Pax5 is not required for plasma cell development. Liu GJ, Jaritz M, Wöhner M, et al. J Exp Med. 2020;217(11):e20200147.

Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion. Hill L, Ebert A, Jaritz M, et al.  Nature. 2020;584(7819):142-147. 

CDK6 is an essential direct target of NUP98 fusion proteins in acute myeloid leukemia. Schmoellerl J, Barbosa IAM, Eder T, et al.Blood. 2020;136(4):387-400.

Context-Dependent IL-1 mRNA-Destabilization by TTP Prevents Dysregulation of Immune Homeostasis Under Steady State Conditions. Sneezum L, Eislmayr K, Dworak H, et al.Front Immunol. 2020;11:1398. 

Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles. Michlits G, Jude J, Hinterndorfer M, et al. Nat Methods. 2020;17(7):708-716.

Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis. Bonnay F, Veloso A, Steinmann V, et al. Cell. 2020;S0092-8674(20)30947-8.

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii. Palmieri N, Hess C, Hess M, Alispahic M. BMC Genomics. 2020;21(1):579.

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. Reyes C, Hodgskiss LH, Kerou M, et al. ISME J. 2020

Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. De S, Rebnegger C, Moser J, et al. FEMS Yeast Res. 2020;20(5):foaa044.

Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. Laukoter S, Pauler FM, Beattie R, et al. Neuron. 2020;S0896-6273(20)30485-2.

Integrative transcriptomics reveals genotypic impact on sugar beet storability. Madritsch S, Bomers S, Posekany A, et al. Plant Mol Biol. 2020

Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells. Zepeda-Martinez JA, Pribitzer C, Wang J, Bsteh D, Golumbeanu S, Zhao Q, Burkard TR, Reichholf B, Rhie SK, Jude J, Moussa HF, Zuber J, Bell O. Sci Adv. 2020 6(14):eaax5692.

A human tissue screen identifies a regulator of ER secretion as a brain-size determinant. Esk C, Lindenhofer D, Haendeler S, Wester RA, Pflug F, Schroeder B, Bagley JA, Elling U, Zuber J, von Haeseler A, Knoblich JA. Science. 2020 Nov 20;370(6519):935-941

Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Papareddy RK, Páldi K, Paulraj S, Kao P, Lutzmayer S, Nodine MD. Genome Biol. 2020 Sep 17;21(1):251.

Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont. Herrera P, Schuster L, Wentrup C, König L, Kempinger T, Na H, Schwarz J, Köstlbacher S, Wascher F, Zojer M, Rattei T, Horn M. Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21658-21666.

An internal deletion of ADAR rescued by MAVS deficiency leads to a minute phenotype. Bajad P, Ebner F, Amman F, Szabó B, Kapoor U, Manjali G, Hildebrandt A, Janisiw MP, Jantsch MF. Nucleic Acids Res. 2020 Apr 6;48(6):3286-3303.

Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts. Mazzucco R, Nolte V, Vijayan T, Schlötterer C. Front Genet. 2020 May 14;11:482.

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature. Langmüller AM, Nolte V, Galagedara R, Poupardin R, Dolezal M, Schlötterer C. BMC Biol. 2020 Oct 30;18(1):157.

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value. Piñar G, Tafer H, Schreiner M, Miklas H, Sterflinger K. Environ Microbiol. 2020 Aug;22(8):3218-3233.

Adaptive Evolution in Producing Microtiter Cultivations Generates Genetically Stable Escherichia coli Production Hosts for Continuous Bioprocessing. Schuller A, Cserjan-Puschmann M, Köppl C, Grabherr R, Wagenknecht M, Schiavinato M, Dohm JC, Himmelbauer H, Striedner G. Biotechnol J. 2020 Oct 20:e2000376.

Comparative genome characterization of the periodontal pathogen Tannerella forsythia. Zwickl NF, Stralis-Pavese N, Schäffer C, Dohm JC, Himmelbauer H. BMC Genomics. 2020 Feb 11;21(1):150.

Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. De S, Rebnegger C, Moser J, Tatto N, Graf AB, Mattanovich D, Gasser B. FEMS Yeast Res. 2020 Aug 1;20(5):foaa044.

Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion. Herzog VA, Fasching N, Ameres SL. Methods Mol Biol. 2020;2062:169-189.

Combinatorial Action of Temporally Segregated Transcription Factors. Charest J, Daniele T, Wang J, Bykov A, Mandlbauer A, Asparuhova M, Röhsner J, Gutiérrez-Pérez P, Cochella L. Dev Cell. 2020 Nov 23;55(4):483-499.e7.

Draft Genome Sequences of Three Strains of Verticillium nonalfalfae Exhibiting Different Levels of Aggressiveness on Ailanthus altissima. Berger H, Maschek O, Halmschlager E. Microbiol Resour Announc. 2020 Jan 9;9(2):e01384-19.

Evaluation of Transcriptomic Regulations behind Metabolic Syndrome in Obese and Lean Subjects. Paczkowska-Abdulsalam M, Niemira M, Bielska A, Szałkowska A, Raczkowska BA, Junttila S, Gyenesei A, Adamska-Patruno E, Maliszewska K, Citko A, Szczerbiński Ł, Krętowski A. Int J Mol Sci. 2020 Feb 20;21(4):1455.

Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. Vilardo E, Amman F, Toth U, Kotter A, Helm M, Rossmanith W. Nucleic Acids Res. 2020 Jun 19;48(11):6157-6169.

Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen. Abdelhamid MK, Quijada NM, Dzieciol M, Hatfaludi T, Bilic I, Selberherr E, Liebhart D, Hess C, Hess M, Paudel S. Front Microbiol. 2020 Oct 30;11:586437.

Expression levels of the tetratricopeptide repeat protein gene <i>ttc39b</i> covary with carotenoid-based skin colour in cichlid fish. Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Goessler W, Sefc KM. Biol Lett. 2020 Nov;16(11):20200629.

Experimental determination of evolutionary barriers to horizontal gene transfer. Acar Kirit H, Lagator M, Bollback JP. BMC Microbiol. 2020 Oct 28;20(1):326.

Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi. Quijada NM, Schmitz-Esser S, Zwirzitz B, Guse C, Strachan CR, Wagner M, Wetzels SU, Selberherr E, Dzieciol M. Foods. 2020 Dec 11;9(12):1851.

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos. Du Z, Zheng H, Kawamura YK, Zhang K, Gassler J, Powell S, Xu Q, Lin Z, Xu K, Zhou Q, Ozonov EA, Véron N, Huang B, Li L, Yu G, Liu L, Au Yeung WK, Wang P, Chang L, Wang Q, He A, Sun Y, Na J, Sun Q, Sasaki H, Tachibana K, Peters AHFM, Xie W. Mol Cell. 2020 Feb 20;77(4):825-839.e7.

PHF3 Regulates Neuronal Gene Expression Through the New Pol II CTD Reader Domain SPOC. Appel LM et al. 2020

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. doi: 10.1038/s41586-019-1210-7. Epub 2019 May 15.

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 Aug 22;75(4):756-768.e7. doi: 10.1016/j.molcel.2019.06.018. Epub 2019 Jul 23.

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. doi: 10.1016/j.cell.2019.07.007.

HERE you can browse the document containing all 57 acknowledgements in 2019.


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) 

Draft Genome Resource for the Potato Powdery Scab Pathogen Spongospora subterranea.
Ciaghi S, Neuhauser S, Schwelm A, Mol Plant Microbe Interact. 2018 Dec;31(12):1227-1229.

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.

Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes.
Heckenhauer J, Paun O, Chase MW, Ashton PS, Kamariah AS, Samuel R, Ann Bot. 2018 Dec 12.

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture.
Hernandez I, Dhiman H, Klanert G, Jadhav V, Auer N, Hanscho M, Baumann M, Esteve-Codina A, Dabad M, Gómez J, Alioto T, Merkel A, Raineri E, Heath S, Rico D, Borth N, Biotechnol Bioeng. 2018 Dec 4.

Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants.
Higo A, Kawashima T, Borg M, Zhao M, López-Vidriero I, Sakayama H, Montgomery SA, Sekimoto H, Hackenberg D, Shimamura M, Nishiyama T, Sakakibara K, Tomita Y, Togawa T, Kunimoto K, Osakabe A, Suzuki Y, Yamato KT, Ishizaki K, Nishihama R, Kohchi T, Franco-Zorrilla JM, Twell D, Berger F, Araki T, Nat Commun. 2018 Dec 11;9(1):5283

Central amygdala circuit dynamics underlying the benzodiazepine anxiolytic effect.
Griessner J, Pasieka M, Böhm V, Grössl F, Kaczanowska J, Pliota P, Kargl D, Werner B, Kaouane N, Strobelt S, Kreitz S, Hess A, Haubensak W, Mol Psychiatry. 2018 Nov 30

Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae).
Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H, Syst Biol. 2018 Nov 1;67(6):1010-1024.

Integrating phylogenomics, phylogenetics, morphometrics, relative genome size and ecological niche modelling disentangles the diversification of Eurasian Euphorbia seguieriana s. l. (Euphorbiaceae).
Frajman B, Záveská E, Gamisch A, Moser T; STEPPE Consortium, Schönswetter P, Mol Phylogenet Evol. 2018 Nov 8.

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.

Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae (Dipterocarpaceae).
Heckenhauer J, Samuel R, Ashton PS, Abu Salim K, Paun O, Mol Phylogenet Evol. 2018 Oct;127:1-13.

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.

The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history.
Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, Lysak MA, Hodges SA, Nordborg M, Elife. 2018 Oct 16;7.

Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians.
Dnyansagar R, Zimmermann B, Moran Y, Praher D, Sundberg P, Møller LF, Technau U, Mol Phylogenet Evol. 2018 Sep;126:346-355.

A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila.
Mallard F, Nolte V, Tobler R, Kapun M, Schlötterer C, Genome Biol. 2018 Aug 20;19(1):119.

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)

Identification and characterization of the Komagataella phaffii mating pheromone genes.
Heistinger L, Moser J, Tatto NE, Valli M, Gasser B, Mattanovich D, FEMS Yeast Res. 2018 Aug 1;18(5).

Dorsal tegmental dopamine neurons gate associative learning of fear. 
Groessl F, Munsch T, Meis S, Griessner J, Kaczanowska J, Pliota P, Kargl D, Badurek S, Kraitsy K, Rassoulpour A, Zuber J, Lessmann V, Haubensak W, Nat Neurosci. 2018 Jul;21(7):952-962

Evolution of gene dosage on the Z-chromosome of schistosome parasites.
Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding CG, Couté Y, Vicoso B, Elife. 2018 Jul 25;7.

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; 

Hypothesis on monochromatic vision in scorpionflies questioned by new transcriptomic data.
Böhm A, Meusemann K, Misof B, Pass G, Sci Rep. 2018 Jun 29;8(1):9872.

Small RNA-Mediated trans-Nuclear and trans-Element Communications in Tetrahymena DNA Elimination.
Noto T, Mochizuki K, Curr Biol. 2018 Jun 18;28(12):1938-1949.e5.

Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity.
Liutkevičiūtė Z, Gil-Mansilla E, Eder T, Casillas-Pérez B, Di Giglio MG, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber CW, FASEB J. 2018 Jun 25:fj201800443.

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 

A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle.
Spletter ML, Barz C, Yeroslaviz A, Zhang X, Lemke SB, Bonnard A, Brunner E, Cardone G, Basler K, Habermann BH, Schnorrer F, Elife. 2018 May 30;7.

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia).
Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, T Domyan E, Suh A, Warren WC, Yandell M, Gilbert MTP, Shapiro MD, G3 (Bethesda), 2018 May 4;8(5):1391-1398

Polarization-resolved microscopy reveals a muscle myosin motor-independent mechanism of molecular actin ordering during sarcomere maturation.
Loison O, Weitkunat M, Kaya-Çopur A, Nascimento Alves C, Matzat T, Spletter ML, Luschnig S, Brasselet S, Lenne PF, Schnorrer F, PLoS Biol. 2018 Apr 27;16(4):e2004718.

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;

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) 

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 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

Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae).
Michalik A, Schulz F, Michalik K, Wascher F, Horn M, Szklarzewicz T, Environ Microbiol. 2018 Mar;20(3):1148-1157.

Comparative transcriptome analysis of a Trichoplusia ni cell line reveals distinct host responses to intracellular and secreted protein products expressed by recombinant baculoviruses.
Koczka K, Peters P, Ernst W, Himmelbauer H, Nika L, Grabherr R, J Biotechnol. 2018 Mar 20;270:61-69.

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) 

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) 

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) 

New Aspects on Listeria monocytogenes ST5-ECVI Predominance in a Heavily Contaminated Cheese Processing Environment.
Muhterem-Uyar M, Ciolacu L, Wagner KH, Wagner M, Schmitz-Esser S, Stessl B, Front Microbiol. 2018 Feb 1;9:64.

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) 

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.
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Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria.
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Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome.
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Pham HTT, Maurer B, Prchal-Murphy M, Grausenburger R, Grundschober E, Javaheri T, Nivarthi H, Boersma A, Kolbe T, Elabd M, Halbritter F, Pencik J, Kazemi Z, Grebien F, Hengstschläger M, Kenner L, Kubicek S, Farlik M, Bock C, Valent P, Müller M, Rülicke T, Sexl V, Moriggl R, J Clin Invest. 2018 Jan 2;128(1):387-401.

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

Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.
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Resolving systematic errors in widely used enhancer activity assays in human cells.
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Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
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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.
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The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14.
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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.
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A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.
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Thiol-linked alkylation of RNA to assess expression dynamics.
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The splicing co-factor Barricade/Tat-SF1 is required for cell cycle and lineage progression in Drosophila neural stem cells.
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A heterochromatin-dependent transcription machinery drives piRNA expression.
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DNA replication-coupled histone modification maintains Polycomb gene silencing in plants.
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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).
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Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data.
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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.
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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.
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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) 

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; 

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.
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Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa.
Pusic P, Tata M, Wolfinger MT, Sonnleitner E, Häussler S, Bläsi U, Sci Rep 2016 Dec 21; 6 

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.
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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.
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Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis.
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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.
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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.
Tata M, Wolfinger MT, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U, PLoS ONE 2016; 11 (1) 

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.
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) 

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.
Sienski G, Batki J, Senti KA, Dönertas D, Tirian L, Meixner K, Brennecke J, Genes Dev. 2015 Oct 22; 

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) 

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)

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) 

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; 

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) 

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.
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; 

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 

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.
Mohn F, Handler D, Brennecke J, Science 2015 May 15; 348 (6236) 

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.
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 

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) 

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.
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;

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

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)

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.