Bioinformatics Core Facility
Overview Head of the Core Facility Core Facility Members PublicationsPublications co-authored by the Bioinformatics Core Facility
2024
Hirth A*, Fatti E*, Netz E*, Acebron SP, Papageorgiou D, Švorinić A, Cruciat CM, Karaulanov E, Gopanenko A, Zhu T, Sinning I, Krijgsveld J, Kohlbacher O and Niehrs C (2024) DEAD box RNA helicases are pervasive protein kinase interactors and activators. Genome Res, doi: 10.1101/gr.278264.123 Link
Jörg M*, Plehn JE*, Kristen M, Lander M, Walz L, Lietz C, Wijns J, Pichot F, Rojas-Charry L, Wirtz Martin KM, Ruffini N, Kreim N, Gerber S, Motorin Y, Endres K, Rossmanith W, Methner A, Helm M and Friedland K (2024) N1-methylation of adenosine (m1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer's disease. Mol Psychiatry, 29:1427-1439 Link
Longo GMC*, Sayols S*, Kotini AG, Heinen S, Möckel MM, Beli P and Roukos V (2024) Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol, doi: 10.1038/s41587-024-02238-8 Link
Parasyraki E*, Mallick M*, Hatch V*, Vastolo V, Musheev MU, Karaulanov E, Gopanenko A, Moxon S, Méndez-Lago M, Han D, Schomacher L, Mukherjee D and Niehrs C (2024) 5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming. Cell, doi: 10.1016/j.cell.2024.08.011 (*indicates joint contribution) Link
2023
Ceron-Noriega A, Schoonenberg VAC, Butter F* and Levin M* (2023) AlexandrusPS: A user-friendly pipeline for the automated detection of orthologous gene clusters and subsequent positive selection analysis. Genome Biol Evol, 15:evad187 (*indicates joint contribution) Link
Chan YC*, Kienle E*, Oti M*, Di Liddo A, Mendez-Lago M, Aschauer DF, Peter M, Pagani M, Arnold C, Vonderheit A, Schön C, Kreuz S, Stark A and Rumpel S (2023) An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Sci Rep, 13:6745 (*indicates joint contribution) Link
Ebersberger S*, Hipp C*, Mulorz MM*, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K#, Sattler M# and König J# (2023) FUBP1 is a general splicing factor facilitating 3’ splice site recognition and splicing of long introns. Mol Cell, 83:2653–2672.e15 (*indicates joint contribution, #indicates joint correspondence) Link
Kalita AI, Marois E*, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF* and Keller Valsecchi CI* (2023) The sex-specific factor SOA controls dosage compensation in Anopheles mosquitos. Nature, 623:175-182 (*indicates joint contribution) Link
Kong KYE*, Shankar S*, Rühle F and Khmelinskii A (2023) Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun, 14:8363 (*indicates joint contribution) Link
Molitor L*, Klostermann M*, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck SM, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K# and Niessing D# (2023) Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res, 51:1297–1316 (*indicates joint contribution, #indicates joint correspondence) Link
Podvalnaya N*, Bronkhorst AW*, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S# and Ketting RF# (2023) piRNA processing by a trimeric Schlafen-domain nuclease. Nature, 622:402–409 (*indicates joint contribution, #indicates joint correspondence) Link
Rücklé C*, Körtel N*, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI and König J (2023) RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol, 30:1207–1215 (*indicates joint contribution) Link
Sayols S (2023) rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biol, doi: 10.17912/micropub.biology.000811 Link
Seistrup AS, Choppin M, Govind S, Feldmeyer B, Kever M, Karaulanov E, Séguret A, Karunanithi S, Almeida M V, Ketting RF# and Foitzik S# (2023) Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus. Mol Ecol, doi: 10.1111/mec.17162 (#indicates joint correspondence) Link
Zinina VV, Sauer M, Nigmatullina L, Kreim N and Soshnikova N (2023) TCF7L1 controls the differentiation of tuft cells in mouse small intestine. Cells, 12:1452 Link
2022
Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S and König J (2022) High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun, 13:5570 Link
Drews F, Salhab A, Karunanithi S, Cheaib M, Jung M, Schulz MH and Simon M (2022) Broad domains of histone marks in the highly compact Paramecium macronuclear genome. Genome Res, 32:710 Link
Gehrke N, Hofmann LJ, Straub BK, Rühle F, Waisman A, Galle PR and Schattenberg JM (2022) Hepatic interleukin-1 receptor type 1 signalling regulates insulin sensitivity in the early phases of nonalcoholic fatty liver disease. Clin Transl Med, 12:e1048 Link
Marnik EA*, Almeida MV*, Cipriani PG*, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF#, Gunsalus KC# and Updike DL# (2022) The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLOS Genet, 18:e1010245 (*indicates joint contribution, #indicates joint correspondence) Link
Misino S, Busch A, Wagner CB, Bento F and Luke B (2022) TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res, 50:12829–12843 Link
Petrosino G, Ponte G, Volpe M, Zarrella I, Ansaloni F, Langella C, Di Cristina G, Finaurini S, Russo MT, Basu S, Musacchia F, Ristoratore F, Pavlinic D, Benes V, Ferrante MI, Albertin C, Simakov O, Gustincich S, Fiorito G and Sanges R (2022) Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. BMC Biol, 20:116 Link
Zinina VV, Ruehle F, Winkler P, Rebmann L, Lukas H, Möckel S, Diefenbach A, Mendez-Lago M and Soshnikova N (2022) ID2 controls differentiation of enteroendocrine cells in mouse small intestine. Acta Physiol, 234:e13773 Link
2021
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
Bawankar P*, Lence T*, Paolantoni C*, Haussmann IU, Kazlauskiene M, Jacob D, Heidelberger JB, Richter FM, Nallasivan MP, Morin V, Kreim N, Beli P, Helm M, Jinek M, Soller M# and Roignant JY# (2021) Hakai is required for stabilization of core components of the m6A mRNA methylation machinery. Nat Commun, 12:3778 (*indicates joint contribution, #indicates joint correspondence) Link
García-Valverde A, Rosell J, Sayols S, Gómez-Peregrina D, Pilco-Janeta DF, Olivares-Rivas I, de Álava E, Maurel J, Rubió-Casadevall J, Esteve A, Gut M, Valverde C, Barretina J, Carles J, Demetri GD, Fletcher JA, Arribas J and Serrano C (2021) E3 ubiquitin ligase Atrogin-1 mediates adaptive resistance to KIT-targeted inhibition in gastrointestinal stromal tumor. Oncogene, 40:6614-6626 Link
Hernandez-Meza G, von Felden J, Gonzalez-Kozlova EE, Garcia-Lezana T, Peix J, Portela A, Craig AJ, Sayols S, Schwartz M, Losic B, Mazzaferro V, Esteller M, Llovet JM and Villanueva A (2021) DNA methylation profiling of human hepatocarcinogenesis. Hepatology, 74:183 Link
Kong KYE*, Fischer B*, Meurer M*, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M# and Khmelinskii A# (2021) Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. Mol Cell, 81:2460–2476.e11 (*indicates joint contribution, #indicates joint correspondence) Link
Körtel N*, Rücklé C*, Zhou Y*, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J# and Zarnack K# (2021) Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Res, 49:e92 (*indicates joint contribution, #indicates joint correspondence) Link
Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V and Beli P (2021) R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun, 12:7314 Link
Perez-Borrajero C, Podvalnaya N*, Holleis K*, Lichtenberger R, Karaulanov E, Simon B, Basquin J, Hennig J#, Ketting RF# and Falk S# (2021) Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev, 35:1304–1323 (*indicates joint contribution, #indicates joint correspondence) Link
Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A#, Soldano A# and Roignant JY# (2021) Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J, 40:e104975 (#indicates joint correspondence) Link
2020
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
Petrosino G*, Zilio N*, Sriramachandran AM and Ulrich HD (2020) Preparation and analysis of GLOE-Seq libraries for genome-wide mapping of DNA replication patterns, single-strand breaks, and lesions. STAR Protoc, 1:100076 (*indicates joint contribution) 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
2019
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
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
2018
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
2017
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
2016
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
2015
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
2014
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
2013
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
2012
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
2024
Arnold B, Riegger RJ, Okuda EK, Slišković I, Keller M, Bakisoglu C, McNicoll F, Zarnack K and Müller-McNicoll M (2024) hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. J Cell Biol, 223:e202304030 Link
Lee CY, Hubrich D, Varga JK, Schäfer C, Welzel M, Schumbera E, Djokic M, Strom JM, Schönfeld J, Geist JL, Polat F, Gibson TJ, Keller Valsecchi CI, Kumar M, Schueler-Furman O and Luck K (2024) Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Mol Syst Biol, 20:75-97 Link
2023
Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F and Kappei D (2023) ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun, 14:8252 Link
Fan W, Jurado-Arjona J, Alanis-Lobato G, Péron S, Berger C, Andrade-Navarro MA, Falk S and Berninger B (2023) The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation. EMBO J, 42:e110384 Link
Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J and Beli P (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell, 83:4272-4289.e10 Link
Yakoub G, Choi YS, Wong RP, Strauch T, Ann KJ, Cohen RE and Ulrich HD (2023) Avidity-based biosensors for ubiquitylated PCNA reveal choreography of DNA damage bypass. Sci Adv, 9:eadf3041 Link
2022
Gruijs da Silva LA, Simonetti F, Hutten S, Riemenschneider H, Sternburg EL, Pietrek LM, Gebel J, Dötsch V, Edbauer D, Hummer G, Stelzl LS and Dormann D (2022) Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO J, 41:e108443 Link
Mkrtchian S, Ebberyd A, Veerman RE, Mendez-Lago M, Gabrielsson S, Eriksson LI and Gómez-Galán M (2022) Surgical trauma in mice modifies the content of circulating extracellular vesicles. Front Immunol, 12:824696 Link
Musheev MU, Schomacher L, Basu A, Han D, Krebs L, Scholz C and Niehrs C (2022) Mammalian N1-adenosine PARylation is a reversible DNA modification. Nat Commun, 13:6138 Link
Öztürk M, Freiwald A, Cartano J, Schmitt R, Dejung M, Luck K, Al-Sady B, Braun S, Levin M and Butter F (2022) Proteome effects of genome-wide single gene perturbations. Nat Commun, 13:6153 Link
Rose R, Peschke N, Nigi E, Gelléri M, Ritz S, Cremer C, Luhmann HJ and Sinning A (2022) Chromatin compaction precedes apoptosis in developing neurons. Commun Biol, 5:797 Link
2021
Placentino M, Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, Albuquerque BF, Butter F and Ketting RF (2021) Intrinsically disordered protein PID‐2 modulates Z granules and is required for heritable piRNA‐induced silencing in the Caenorhabditis elegans embryo. EMBO J, 40:e105280
Redl S*, de Jesus Domingues AM*, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2021) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development, 148:dev193060 (*indicates joint contribution)
Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J and Thomas-Tikhonenko A (2021) Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol, 22:190 Link
2020
Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL and Roignant JY (2020) The 18S ribosomal RNA m6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep, 21:e49443
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
2018
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
2017
Lebedeva S, de Jesus Domingues AM, Butter F and Ketting RF (2017) Characterization of genetic loss-of-function of Fus in zebrafish. RNA Biol, 14:29-35 Link
Navandar M, Garding A, Kumar Sahu S, Pataskar A, Schick S and Tiwari VK (2017) ERK signalling modulates epigenome to drive epithelial to mesenchymal transition. Oncotarget, 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 development. Nat 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. Elegans. Genes Dev, 31: 1561–1572
2016
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 development. Genome 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 program. EMBO 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 myelin. Sci Rep, 6: 25828
2015
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 fate. EMBO 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 damage. J 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
2013
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