Publications

Selected publications

2018

Alberti C, RA Manzenreither, I Sowemimo, TR Burkard, J Wang, K Mahofsky, SL Ameres, and L Cochella (2018) Cell-Type Specific Sequencing of microRNAs From Complex Animal Tissues. Nat Methods doi:10.1038/nmeth.4610.

Bian S, M Repic, Z Guo, A Kavirayani, T Burkard, JA Bagley, C Krauditsch and JA Knoblich (2018) Genetically engineered cerebral organoids model brain tumor formation. Nat Methods 1doi:10.1038/s41592-018-0070-7

Brackmann K, J Qi, M Gebert, V Jouannet, T Schlamp, K Grünwald, ES Wallner, DD Novikova, VG Levitsky, J Agustí, P Sanchez, JU Lohmann and T Greb. (2018) Spatial Specificity of Auxin Responses Coordinates Wood Formation Nat Commun doi:10.1038/s41467-018-03256-2.

Corsini NS, AM Peer, P Moeseneder, M Roiuk, TR Burkard, HC Theussl, I Moll, and JA Knoblich (2018) Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation. Cell Stem Cell doi:10.1016/j.stem.2018.03.002.

Ebner P, I Poetsch, L Deszcz, T Hoffmann, J Zuber, and F Ikeda (2018) The IAP Family Member BRUCE Regulates Autophagosome-Lysosome Fusion. Nat Commun doi:10.1038/s41467-018-02823-x.

Fitz J, T Neumann and R Pavri  (2018) Regulation of RNA Polymerase II Processivity by Spt5 Is Restricted to a Narrow Window During Elongation. EMBO J doi:10.15252/embj.201797965.

Gassler J, HB Brandão, M Imakaev, IM Flyamer, S Ladstätter, WA Bickmore, JM Peters, LA Mirny, and K Tachibana (2017) A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture. EMBO J doi:10.15252/embj.201798083.

Gstrein T, A Edwards, A Přistoupilová, I Leca, M Breuss, S Pilat-Carotta, AH Hansen, R Tripathy, AK Traunbauer, T Hochstoeger, G Rosoklija, M Repic, L Landler, V Stránecký, G Dürnberger, TM Keane, J Zuber, DJ Adams, J Flint, T Honzik, M Gut, S Beltran, K Mechtler, E Sherr, S Kmoch, I Gut and DA Keays (2018) Mutations in Vps15 Perturb Neuronal Migration in Mice and Are Associated with Neurodevelopmental Disease in Humans. Nat Neuroscience  doi:10.1038/s41593-017-0053-5.

Herberg S, KR Gert, A Schleiffer and A Pauli (2018) The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization. Science  doi:10.1126/science.aat7113

Kurzbauer MT, M Pradillo, C Kerzendorfer, J Sims, R Ladurner, C Oliver, MP Janisiw, M Mosiolek, D Schweizer, GP Copenhaver and P Schlogelhofer (2018) Arabidopsis Thaliana FANCD2 Promotes Meiotic Crossover Formation. Plant Cell doi:10.1105/tpc.17.00745.

Landskron L, V Steinmann, F Bonnay, TR Burkard, J Steinmann, I Reichardt, H Harzer, AS Laurenson, H Reichert, and JA Knoblich (2018) The Asymmetrically Segregating lncRNA Cherub Is Required for Transforming Stem Cells Into Malignant Cells. eLife doi:10.7554/eLife.31347.

Muhar M, A Ebert, T Neumann, C Umkehrer, J Jude, C Wieshofer, P Rescheneder, JJ Lipp, VA Herzog, B Reichholf, DA Cisneros, T Hoffmann, MF Schlapansky, P Bhat, A von Haeseler, T Köcher, AC Obenauf, J Popow, SL Ameres and J Zuber (2018) SLAM-Seq Defines Direct Gene-Regulatory Functions of the BRD4-MYC Axis. Science doi:10.1126/science.aao2793.

Nowoshilow S, S Schloissnig, JF Fei, A Dahl, AWC Pang, M Pippel, S Winkler,  AR Hastie, G Young, JG Roscito, F Falcon, D Knapp, S Powell, A Cruz, H Cao, B Habermann, M Hiller, EM Tanaka and EW Myers (2018) The Axolotl Genome and the Evolution of Key Tissue Formation Regulators. Nature doi:10.1038/nature25458.

Sasaki E, F Frommlet and M Nordborg (2018) GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data. G3 doi:10.1534/g3.118.200571

Skora S, F Mende and M Zimmer (2018) Energy Scarcity Promotes a Brain-Wide Sleep State Modulated by Insulin Signaling in C. Elegans Cell Reports doi:10.1016/j.celrep.2017.12.091.

Smakowska-Luzan E, GA Mott, K Parys, M Stegmann, TC Howton, M Layeghifard, J Neuhold,  A Lehner, J Kong, K Grünwald, N Weinberger, SB Satbhai, D Mayer, W Busch, M Madalinski, P Stolt-Bergner, NJ Provart, MS Mukhtar, C Zipfel, D Desveaux, DS Guttman and Y Belkhadir (2018) An Extracellular Network of Arabidopsis Leucine-Rich Repeat Receptor Kinases. Nature doi:10.1038/nature25184.

Stanyte R, J Nuebler, C Blaukopf, R Hoefler, R Stocsits, JM Peters and DW Gerlich  (2018) Dynamics of Sister Chromatid Resolution During Cell Cycle Progression. J Cell Biol doi:10.1083/jcb.201801157.

Uhse S, FG Pflug, A Stirnberg, K Ehrlinger, A von Haeseler, and A Djamei (2018). In Vivo Insertion Pool Sequencing Identifies Virulence Factors in a Complex Fungal-Host Interaction. PLoS Biology doi:10.1371/journal.pbio.2005129.

 

2017

Alberti C and Cochella L (2017) A Framework for understanding the roles of miRNAs in animal development. Development  doi:10.1242/dev.146613.

Andersen PR, L Tirian, M Vunjak, and J  Brennecke (2017) A heterochromatin-dependent transcription machinery drives piRNA expression. Nature doi:10.1038/nature23482.

Busslinger GA, Stocsits RR, van der Lelij P, Axelsson E, Tedeschi A, Galjart N and Peters J-M (2017) Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature 460: 410

Kerdaffrec E and M Nordborg (2017) The Maternal Environment Interacts with Genetic Variation in Regulating Seed Dormancy in Swedish Arabidopsis Thaliana. PLoS ONE doi:10.1371/journal.pone.0190242.

Lutzmayer S, B Enugutti, and MD Nodine (2017) Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data. Scientific Reports doi:10.1038/s41598-017-06174-3.

Mierzwa BE, Chiaruttini N, Redondo-Morata L, Moser von Filseck J, König J, Larios J, Poser I, Müller-Reichert T, Scheuring S, Roux A and Gerlich DW (2017) Dynamic subunit turnover in ESCRT-III assemblies is regulated by Vps4 to mediate membrane remodelling during cytokinesis. Nat. Cell Biology 545: 113

Muerdter F, ŁM Boryń, AR Woodfin, C Neumayr, M Rath, MA Zabidi, M Pagani, V Haberle, T Kazmar, RR Catarino, K Schernhuber, CD Arnold and A Stark (2017) Resolving Systematic Errors in Widely Used Enhancer Activity Assays in Human Cells. Nat Methods doi:10.1038/nmeth.4534.

Pisupati R, I Reichardt, U Seren, P Korte, V Nizhynska, E Kerdaffrec, K Uzunova, FA Rabanal, DL Filiault, and M Nordborg (2017) Verification of Arabidopsis Stock Collections Using SNPmatch, a Tool for Genotyping High-Plexed Samples. Scientific Data  doi:10.1038/sdata.2017.184.

Renner M, Lancaster MA, Bian S, Choi H, Ku T, Peer A, Chung K and Knoblich JA (2017) Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J doi:10.15252/embj.201694700

Rabanal FA, Mandáková T, Soto-Jiménez LM, Greenhalgh R, Parrott DL, Lutzmayer S, Steffen JG, Nizhynska V, Mott R, Lysak MA, Clark RM and Nordborg M (2017) Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thalianaGenome Biol. 18: 75

Samwer M, MWG Schneider, R Hoefler, PS Schmalhorst, JG Jude, J Zuber, and DW Gerlich (2017) DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell doi:10.1016/j.cell.2017.07.038

Schon MA and Nodine M (2017) Widespread contamination of Arabidopsis embryo and endosperm transcriptome datasets. Plant Cell doi:10.1105/tpc.16.00845

Stowers JR, M Hofbauer, R Bastien, J Griessner, P Higgins, S Farooqui, RM Fischer, K Nowikovsky, W Haubensak, ID Couzin, K Tessmar-Raible and AD Straw (2017) Virtual reality for freely moving animals. Nature Methods doi:10.1038/nmeth.4399

Suhren JH, Noto T, Kataoka K, Gao S, Liu Y and Mochizuki K (2017) Negative regulators of an RNAi-heterochromatin positive feedback loop safeguard somatic genome integrity in TetrahymenaCell Rep 18:2494–507 doi:10.1016/j.celrep.2017.02.024

van der Lelij, P, S Lieb, J Jude, G Wutz, CP Santos, K Falkenberg, A Schlattl, J Ban, R Schwentner, T Hoffmann, H Kovar, FX Real, T Waldman, MA Pearson, N Kraut, J-M Peters, J Zuber and  Mark Petronczki  (2017)  Synthetic Lethality Between the Cohesin Subunits STAG1 and STAG2 in Diverse Cancer Contexts. eLife doi:10.7554/eLife.26980

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 and Nordborg M (2017) Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol Biol Evol 2017:msw299

2016

Drexel T, Mahofsky K, Latham R, Zimmer M and Cochella L (2016) Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegansGenes Dev 30: 2042-7 

Gallego LD, Ghodgaonkar Steger M, Polyansky AA, Schubert T, Zagrovic B, Zheng N, Clausen T, Herzog F and Köhler A (2016) Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1. Proc Natl Acad Sci U S A 113:10553–8

Hums I, Riedl J, Mende F, Kato S, Kaplan HS, Latham R, Sonntag M, Traunmüller L and Zimmer M (2016) Regulation of two motor patterns enables the gradual adjustment of locomotion strategy in Caenorhabditis elegansElife 5: e14116

Kerdaffrec E, Filiault DL, Korte A, Sasaki E, Nizhynska V, Seren U and Nordborg M (2016) Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis. Elife 5: e22502

Ladstätter S and Tachibana-Konwalski K (2016) A Surveillance Mechanism Ensures Repair of DNA Lesions during Zygotic Reprogramming. Cell 167: 1774-87

Ladurner R, Kreidl E, Ivanov MP, Ekker H, Idarraga-Amado MH, Busslinger GA, Wutz G, Cisneros DA and Peters JM (2016) Sororin actively maintains sister chromatid cohesion. EMBO J 35:635-53

Minnich, M, Tagoh H, Bönelt P, Axelsson E, Fischer M, Cebolla B, Tarakhovsky A, Nutt SL, Jaritz M and Busslinger M (2016) Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation. Nat Immunol 17:331-43

Pekgöz Altunkaya G, Malvezzi F, Demianova Z, Zimniak T, Litos G, Weissmann F, Mechtler K, Herzog F and Westermann S (2016) CCAN Assembly configures composite binding interfaces to promote cross-linking of Ndc80 complexes at the kinetochore. Curr Biol 26:2370-8

Sigl V, Owusu-Boaitey K, Joshi PA, Kavirayani A, Wirnsberger G, Novatchkova M, Kozieradzki I, Schramek D, Edokobi N, Hersl J, Sampson A, Odai-Afotey A, Lazaro C, Gonzalez-Suarez E, Pujana MA, Cimba F, Heyn H, Vidal E, Cruickshank J, Berman H, Sarao R, Ticevic M, Uribesalgo I, Tortola L, Rao S, Tan Y, Pfeiler G, Lee EY, Bago-Horvath Z, Kenner L, Popper H, Singer C, Khokha R, Jones LP and Penninger JM (2016) RANKL/RANK control Brca1 mutation-driven mammary tumors. Cell Res 26:761-74

Trentini DB, Suskiewicz MJ, Heuck A, Kurzbauer R, Deszcz L, Mechtler K and Clausen T (2016) Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature 539: 48-53

Weissmann F, Petzold G, VanderLinden R, Huis In 't Veld PJ, Brown NG, Lampert F, Westermann S, Stark H, Schulman BA and Peters JM (2016) biGBac enables rapid gene assembly for the expression of large multisubunit protein complexes. Proc Natl Acad Sci U S A 113: E2564-9

2015

Kato S, Kaplan HS, Schrödel T, Skora S, Lindsay TH, Yemini E, Lockery S and Zimmer M (2015) Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegansCell 163:656-69

Laos T, Cabral G and Dammermann A (2015) Isotropic incorporation of SPD-5 underlies centrosome assembly in C. elegans. Curr Biol 25:R648-9

Mészáros N, Cibulka J, Mendiburo MJ, Romanauska A, Schneider M and Köhler A (2015) Nuclear pore basket proteins are tethered to the nuclear envelope and can regulate membrane curvature. Dev Cell 33:285-98

Mieck C, Molodtsov MI, Drzewicka K, van der Vaart B, Litos G, Schmauss G, Vaziri A and Westermann S (2015) Non-catalytic motor domains enable processive movement and functional diversification of the kinesin-14 Kar3. Elife 4:e04489

Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Bory? ?M, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR and Zuber J (2015) Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature  525:543-7

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

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

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

Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O and Stark A (2015) Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518:556-9

Wurzer B, Zaffagnini G, Fracchiolla D, Turco E, Abert C, Romanov J and Martens S (2015) Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy. ELife eLife.08941

2014

Bath DE, Stowers JR, Hörmann D, Poehlmann A, Dickson BJ, Straw AD (2014) FlyMAD: rapid thermogenetic control of neuronal activity in freely walking Drosophila. Nat Methods, Available online 25 May 2014, doi: 10.1038/nmeth.2973

Bidaye SS, Machacek C, Wu Y, Dickson BJ (2014) Neuronal Control of Drosophila Walking Direction. Science 344: 97-101

Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, et al. (2014) How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation. PLoS Genet 10: e1004115 

Eroglu E, Burkard TR, Jiang Y, Saini N, Homem CCF, Reichert H, Knoblich JA (2014) SWI/SNF Complex Prevents Lineage Reversion and Induces Temporal Patterning in Neural Stem Cells. Cell 156: 1259-73

Kvon EZ, Kazmar T, Stampfel G, Yáñez-Cuna JO, Pagani M , Schernhuber K, Dickson BJ, Stark A (2014) Genome-scale functional characterization of Drosophila developmental enhancers in vivoNature, Available online 1 June 2014

Radics J, Königsmaier L, Marlovits TC (2014) Structure of a pathogenic type 3 secretion system in action. Nat Struct Mol Biol 21:82-7

Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryn LM, Arnold CD, Stark A (2014) Hormone-Responsive Enhancer-Activity Maps Reveal Predictive Motifs, Indirect Repression, and Targeting of Closed Chromatin. Mol Cell, Available online 27 March 2014, 10.1016/j.molcel.2014.02.026

2013

Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A (2013) Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. Science 339: 1074-7

Bulankova P, Akimcheva S, Fellner N, Riha K (2013) Identification of Arabidopsis Meiotic Cyclins Reveals Functional Diversification among Plant Cyclin Genes. PLoS Genet 9: e1003508

Cabral G, Sans, Sanegre S, Cowan CR, Dammermann A (2013) Multiple mechanisms contribute to centriole separation in C. elegansCurr Biol 23: 1380-7

Dick AE, Gerlich DW (2013) Kinetic framework of spindle assembly checkpoint signalling. Nat Cell Biol 15: 1370–7

Dönertas D, Sienski G, Brennecke J (2013) Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev 27:1693-705 

Fischer RM, Fontinha BM, Kirchmaier S, Steger J, Bloch S , Inoue D, Panda S, Rumpel S, Tessmar-Raible K. (2013) Co-Expression of VAL- and TMT-Opsins Uncovers Ancient Photosensory Interneurons and Motorneurons in the Vertebrate Brain PLoS Biology 11: e1001585

Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45: 884–90

Schrödel T, Prevedel R, Aumayr K, Zimmer M, Vaziri A (2013) Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. Nat Methods 10: 1013-20

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