Publications co-authored by the Bioinformatics Core Facility


Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K# and Eizirik DL# (2021) The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance, 4:e202000825 (#indicates joint correspondence) Link


Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V and Crosetto N (2020) Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc, 15:3894–3941 Link

Buchbender A, Mutter H, Sutandy FXR, Körtel N, Hänel H, Busch A, Ebersberger S and König J (2020) Improved library preparation with the new iCLIP2 protocol. Methods, 178:33–48 Link

Busch A, Brüggemann M, Ebersberger S and Zarnack K (2020) iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods, 178:49–62 Link

Casas-Vila N, Sayols S, Pérez-Martínez L, Scheibe M and Butter F (2020) The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae. Nat Commun, 11:2789 Link

De Majo F, Hegenbarth JC, Rühle F, Bär C, Thum T, de Boer M, Duncker DJ, Schroen B, Armand AS, Stoll M and De Windt LJ (2020) Dichotomy between the transcriptomic landscape of naturally versus accelerated aged murine hearts. Sci Rep, 10:8136 Link

Dold A*, Han H*, Liu N*, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY# and Lasko P# (2020) Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLOS Genet, 16:e1008581 (*indicates joint contribution, #indicates joint correspondence) Link

Enculescu M#, Braun S, Thonta Setty S, Busch A, Zarnack K, König J# and Legewie S# (2020) Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene. Biophys J, 118:2027–2041 Link

Kang HS*, Sánchez-Rico C*, Ebersberger S, Sutandy FXR, Busch A, Welte T, Stehle R, Hipp C, Schulz L, Buchbender A, Zarnack K, König J# and Sattler M# (2020) An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proc Natl Acad Sci, 117:7140–7149 (*indicates joint contribution, #indicates joint correspondence) Link

Sayols S, Klassek J, Werner C, Möckel S, Ritz S, Mendez-Lago M and Soshnikova N (2020) Signalling codes for the maintenance and lineage commitment of embryonic gastric epithelial progenitors. Development, 147:dev188839 Link

Sriramachandran AM, Petrosino G, Méndez-Lago M, Schäfer AJ, Batista-Nascimento LS, Zilio N# and Ulrich HD# (2020) Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks, and lesions by GLOE-Seq. Mol Cell, 78:975-985.e7 (#indicates joint correspondence) Link

Vydzhak O*, Bender K*, Klermund J, Busch A, Reimann S and Luke B (2020) Checkpoint adaptation in recombination-deficient cells drives aneuploidy and resistance to genotoxic agents. DNA Repair, 95:102939 (*indicates joint contribution) Link


Akhtar J, Kreim N, Marini F, Mohana G, Brüne D, Binder H and Roignant JY (2019) Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun, 10:521 Link

Aparisi Rey A, Karaulanov E, Sharopov S, Arab K, Schäfer A, Gierl M, Guggenhuber S, Brandes C, Pennella L, Gruhn WH, Jelinek R, Maul C, Conrad A, Kilb W, Luhmann HJ, Niehrs C and Lutz B (2019) Gadd45α modulates aversive learning through post‐transcriptional regulation of memory‐related mRNAs. EMBO Rep, 20:e46022 Link

Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt I# and Niehrs C# (2019) GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet, 51:217–223 (#indicates joint correspondance) Link

Auber M, Fröhlich D, Drechsel O, Karaulanov E and Krämer-Albers EM (2019) Serum-free media supplements carry miRNAs that co-purify with extracellular vesicles. J Extracell Vesicles, 8:1656042 Link

Buchbender A, Mutter H, FX Sutandy R, Körtel N, Hänel H, Busch A, Ebersberger S and König J (2019) Improved library preparation with the new iCLIP2 protocol. Methods, doi:10.1016/j.ymeth.2019.10.003 Link

Gothe HJ, Bouwman BAM, Gusmao EG, Piccinno R, Petrosino G, Sayols S, Drechsel O, Minneker V, Josipovic N, Mizi A, Nielsen CF, Wagner EM, Takeda S, Sasanuma H, Hudson DF, Kindler T, Baranello L, Papantonis A, Crosetto N and Roukos V (2019) Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations. Mol Cell, 75:267-283.e12 Link

Han D*, Schomacher L*#, Schüle KM*, Mallick M, Musheev MU, Karaulanov E, Krebs L, von Seggern A and Niehrs C# (2019) NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress. eLife, e49044 (*indicates joint contribution #indicates joint correspondance) Link

Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K#, König J# and Beli P# (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol, 20:216 (#indicates joint correspondence) Link

Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M and Zarnack K (2019) The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep, 20:e46588 Link

Schüle KM*, Leichsenring M*, Andreani T, Vastolo V, Mallick M, Musheev MU, Karaulanov E and Niehrs C (2019) GADD45 promotes locus-specific DNA demethylation and 2C cycling in embryonic stem cells. Genes Dev, 33:782–798 (*indicates joint contribution) Link

Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH and Das PP (2019) TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network. Mol Cell, 74:1148-1163.e7 Link

Uhrig S and Klein H (2019) PingPongPro: A tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data. Bioinformatics, 2:335–336 Link


Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF (2018) GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J, 37:e99325 Link

Becker K, Bluhm A*, Casas-Vila N*, Dinges N*, Dejung M, Sayols S, Kreutz C, Roignant JY, Butter F# and Legewie S#. (2018). Quantifying post-transcriptional regulation in the development of Drosophila melanogaster. Nat Commun, 9: 4970 (*indicates joint contribution, #indicates joint correspondence) Link

Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA and Beli P (2018) p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun, 9:1017 Link

Braun S*, Enculescu M*, Setty ST*, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S#, König J# and Zarnack K# (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun, 9:3315 (*indicates joint contribution, #indicates joint correspondence) Link

Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA and Beli P (2018) Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc function. EMBO Rep, 19:e44754 Link

Kaymak A, Sayols S, Papadopoulu T and Richly H (2018) Role for the transcriptional activator ZRF1 in early metastatic events in breast cancer progression and endocrine resistance. Oncotarget, 9:28666–28690 Link

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M and Roignant J-Y (2018) Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes Dev, 32:415–429 Link

Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR and Backofen R (2018) Freiburg RNA tools: A central online resource for RNA-focused research and teaching. Nucleic Acids Res, 46:W25–W29 Link

Sanchez-Mut J V., Heyn H, Silva BA, Dixsaut L, Garcia-Esparcia P, Vidal E, Sayols S, Glauser L, Monteagudo-Sánchez A, Perez-Tur J, Ferrer I, Monk D, Schneider B, Esteller M and Gräff J (2018) PM20D1 is a quantitative trait locus associated with Alzheimer’s disease. Nat Med, 24:598–603 Link

Schäfer A, Mekker B, Mallick M, Vastolo V, Karaulanov E, Sebastian D, von der Lippen C, Epe B, Downes DJ, Scholz C and Niehrs C (2018) Impaired DNA demethylation of C/EBP sites causes premature aging. Genes Dev, 32:742–762 Link

Sutandy FXR*, Ebersberger S*, Huang L*, Busch A, Bach M, Kang H-S, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S# and König J# (2018) In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res, 28:699–713 (*indicates joint contribution, #indicates joint correspondence) Link

Tristán-Flores FE, Guzmán P, Ortega-Kermedy MS, Cruz-Torres G, de la Rocha C, Silva-Martínez GA, Rodríguez-Ríos D, Alvarado-Caudillo Y, Barbosa-Sabanero G, Sayols S, Lund G and Zaina S (2018) Liver X receptor-binding DNA motif associated with atherosclerosis-specific DNA methylation profiles of Alu elements and neighboring CpG islands.J Am Heart Assoc, 7:e007686 Link


Borriello F, Iannone R, Di Somma S, Vastolo V, Petrosino G, Visconte F, Raia M, Scalia G, Loffredo S, Varricchi G, Galdiero MR, Granata F, Del Vecchio L, Portella G and Marone G (2017) Lipopolysaccharide-elicited TSLPR expression enriches a functionally discrete subset of human CD14+ CD1c+ monocytes. J Immunol, 198:3426–3435 Link

Casas-Vila N*, Bluhm A*, Sayols S*, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY and Butter F (2017) The developmental proteome of Drosophila melanogaster.Genome Res, 27:1273–1285 (*indicates joint contribution) Link

Dinges N, Morin V, Kreim N, Southall TD and Roignant J-Y (2017) Comprehensive characterization of the complex lola locus reveals a novel role in the octopaminergic pathway via tyramine beta-hydroxylase regulation. Cell Rep, 21:2911–2925 Link

Dzama MM, Nigmatullina L, Sayols S, Kreim N and Soshnikova N (2017) Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells. Dev Biol, 432:258–264 Link

Jahn A*, Rane G*, Paszkowski‐Rogacz M, Sayols S, Bluhm A, Han C, Draškovič I, Londoño‐Vallejo JA, Kumar AP, Buchholz F#, Butter F# and Kappei D# (2017) ZBTB48 is both a vertebrate telomere‐binding protein and a transcriptional activator. EMBO Rep, 18:929–946 (*indicates joint contribution, #indicates joint correspondence) Link

Kazakevych J, Sayols S, Messner B, Krienke C and Soshnikova N (2017) Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells. Nucleic Acids Res, 45:5770–5784 Link

Nigmatullina L, Norkin M, Dzama MM, Messner B, Sayols S and Soshnikova N (2017) Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development.EMBO J, 36:869–885 Link

Sanchez-Mut JV, Heyn H, Vidal E, Delgado-Morales R, Moran S, Sayols S, Sandoval J, Ferrer I, Esteller M and Gräff J (2017) Whole genome grey and white matter DNA methylation profiles in dorsolateral prefrontal cortex. Synapse, 71:e21959 Link

Zapata L, Susak H, Drechsel O, Friedländer MR, Estivill X and Ossowski S (2017) Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes. Sci Rep, 7:13124 Link


Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U and Garnett MJ (2016) A landscape of pharmacogenomic interactions in cancer. Cell, 166:740–754 Link

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M and Roignant JY (2016) m6A modulates neuronal functions and sex determination in Drosophila. Nature, 540:242–247 Link

Movassat M, Crabb TL, Busch A, Yao C, Reynolds DJ, Shi Y and Hertel KJ (2016) Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns.RNA Biol, 13:646–655 Link

Papadopoulou T, Kaymak A, Sayols S and Richly H (2016) Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation. Cell Cycle, 15:1479–1493 Link

Sayols S, Scherzinger D and Klein H (2016) DupRadar: A bioconductor package for the assessment of PCR artifacts in RNA-Seq data. BMC Bioinformatics, 17:428 Link


Busch A and Hertel KJ (2015) Splicing predictions reliably classify different types of alternative splicing. RNA, 21:813–823 Link

Simon M, Richard EM, Wang X, Shahzad M, Huang VH, Qaiser TA, Potluri P, Mahl SE, Davila A, Nazli S, Hancock S, Yu M, Gargus J, Chang R, Al-Sheqaih N, Newman WG, Abdenur J, Starr A, Hegde R, Dorn T, Busch A, Park E, Wu J, Schwenzer H, Flierl A, Florentz C, Sissler M, Khan SN, Li R, Guan M-X, Friedman TB, Wu DK, Procaccio V, Riazuddin S, Wallace DC, Ahmed ZM, Huang T and Riazuddin S (2015) Mutations of human NARS2, encoding the mitochondrial asparaginyl-tRNA synthetase, cause nonsyndromic deafness and Leigh syndrome.PLOS Genet, 11:e1005097 Link

Villanueva A, Portela A, Sayols S, Battiston C, Hoshida Y, Méndez-González J, Imbeaud S, Letouzé E, Hernandez-Gea V, Cornella H, Pinyol R, Solé M, Fuster J, Zucman-Rossi J, Mazzaferro V, Esteller M, Llovet JM and HEPTROMIC Consortium (2015) DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma.Hepatology, 61:1945–1956 Link


Acebron SP, Karaulanov E, Berger BS, Huang YL and Niehrs C (2014) Mitotic Wnt signaling promotes protein stabilization and regulates cell size. Mol Cell, 54:663–674 Link

de Albuquerque BFM, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJT, Klein H, Boxem M and Ketting RF (2014) PID-1 is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegans. Genes Dev, 28:683–688 Link

Fröhlich D, Kuo WP, Frühbeis C, Sun J-J, Zehendner CM, Luhmann HJ, Pinto S, Toedling J, Trotter J and Krämer-Albers E-M (2014) Multifaceted effects of oligodendroglial exosomes on neurons: Impact on neuronal firing rate, signal transduction and gene regulation.Philos Trans R Soc Lond B Biol Sci, 369:20130510 Link

Malone CD, Mestdagh C, Akhtar J, Kreim N, Deinhard P, Sachidanandam R, Treisman J and Roignant JY (2014) The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript. Genes Dev, 28:1786–1799 Link

Simonetti M, Agarwal N, Stösser S, Bali KK, Karaulanov E, Kamble R, Pospisilova B, Kurejova M, Birchmeier W, Niehrs C, Heppenstall P and Kuner R (2014) Wnt-fzd signaling sensitizes peripheral sensory neurons via distinct noncanonical pathways. Neuron, 83:104–121 Link


Schäfer A, Karaulanov E, Stapf U, Döderlein G and Niehrs C (2013) Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3. Genes Dev, 27:261–273 Link


Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C and Barillot E (2012) ncPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data.Bioinformatics, 28:3147–3149 Link

Publications acknowledging the Bioinformatics Core Facility


Wong RP, García-Rodríguez N, Zilio N, Hanulová M and Ulrich HD (2020) Processing of DNA Polymerase-Blocking Lesions during Genome Replication Is Spatially and Temporally Segregated from Replication Forks. Mol Cell, 77:3–16.e4


Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF (2018) Tdrd6a regulates the aggregation of buc into functional subcellular compartments that drive germ cell specification. Dev Cell, 46: 285–301.e9

Tiwari N, Pataskar A, Péron S, Thakurela S, Sahu SK, Figueres-Oñate M, Marichal N, López-Mascaraque L, Tiwari VK and Berninger B (2018) Stage-specific transcription factors drive astrogliogenesis by remodeling gene regulatory landscapes. Cell Stem Cell, 23: 557–571.e8


Navandar M, Garding A, Kumar Sahu S, Pataskar A, Schick S and Tiwari VK (2017) ERK signalling modulates epigenome to drive epithelial to mesenchymal transitionOncotarget, 8: 29269–29281

Sahu SK, Tiwari N, Pataskar A, Zhuang Y, Borisova M, Diken M, Strand S, Beli P and Tiwari VK (2017) FBXO32 promotes microenvironment underlying epithelial-mesenchymal transition via CtBP1 during tumour metastasis and brain developmentNat Commun, 8: 1523

Wilhelm T, Byrne J, Medina R, Kolundžić E, Geisinger J, Hajduskova M, Tursun B and Richly H (2017) Neuronal inhibition of the autophagy cucleation complex extends life span in post-reproductive C. ElegansGenes Dev, 31: 1561–1572


Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD and Ketting RF (2016) Enhancers reside in a unique epigenetic environment during early zebrafish developmentGenome Biol, 17: 146

Pataskar A, Jung J, Smialowski P, Noack F, Calegari F, Straub T and Tiwari VK (2016)  NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal programEMBO J, 35: 24–45.

Thakurela S, Garding A, Jung RB, Müller C, Goebbels S, White R, Werner HB and Tiwari VK (2016)  The transcriptome of mouse central nervous system myelinSci Rep, 6: 25828


de Albuquerque BF, Placentino M and Ketting RF (2015) Maternal piRNAs are essential for germline development following de novo establishment of endo-siRNAs in Caenorhabditis elegans. Dev Cell, 34: 448-56

Sahu SK, Garding A, Tiwari N, Thakurela S, Toedling J, Gebhard S, Ortega F, Schmarowski N, Berninger B, Nitsch R, Schmidt M and Tiwari VK (2015) JNK-dependent gene regulatory circuitry governs mesenchymal fateEMBO J, 34: 2162–2181

Schick S, Fournier D, Thakurela S, Sahu SK, Garding A and Tiwari VK (2015) Dynamics of chromatin accessibility and epigenetic state in response to UV damageJ Cell Sci, 128: 4380–4394

Thakurela S, Sahu SK, Garding A and Tiwari VT (2015) Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Genome Res, 25: 1309-24


de Albuquerque BFM, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJT, Klein H, Boxem M and Ketting RF (2014) PID-1 Is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegansGenes Dev, 28: 683–688