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  (*indicates joint contribution)  Link

Papadopoulos D, Ha SA, Fleischhauer D, Uhl L, Russell TJ, Mikicic I, Schneider K, Brem A, Valanju OR, Cossa G, Gallant P, Schuelein-Voelk C, Maric HM, Beli P, Büchel G, Vos SM and Eilers M ( 2024 ) The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex. Mol Cell , S1097-2765:00285-5 Link

Schmidt A*, Allmann S*, Schwarzenbach C, Snyder P, Chen JX, Nagel G, Schöneis A, Rasenberger B, Beli P, Loewer A, Hofmann TG, Tomicic MT and Christmann M ( 2024 ) The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence. Nucleic Acids Res , doi: 10.1093/nar/gkae426  (*indicates joint contribution)  Link


D'Alessandro G#, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G# and Jackson SP# ( 2023 ) RAD54L2 counters TOP2-DNA adducts to promote genome stability. Sci Adv , 9:eadl2108  (#indicates joint correspondence)  Link

Lampersberger L, Conte F*, Ghosh S*, Xiao Y*, Price J*, Jordan D, Matus DQ, Sarkies P, Beli P, Miska EA# and Burton NO# ( 2023 ) Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function. Proc Natl Acad Sci USA , 120:e2217992120  (*indicates joint contribution, #indicates joint correspondence)  Link

Oliveira CAB*, Isaakova E*, Beli P* and Xirodimas DP* ( 2023 ) A mass spectrometry-based strategy for mapping modification sites for the ubiquitin-like modifier NEDD8. Methods Mol Biol , 2602:137–149  (*indicates joint contribution)  Link

Rahmanto AS*, 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  (*indicates joint contribution)  Link

Schindler N*, Tonn M*, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B ( 2023 ) Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun , 14:1227  (* indicates joint contribution)  Link

Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD# and Wollscheid HP# ( 2023 ) Nuclear myosin VI maintains replication fork stability. Nat Commun , 14:3787  (#indicates joint correspondence)  Link

Stier A*, Gilberto S*, Mohamed WI, Royall LN, Helenius J, Mikicic I, Sajic T, Beli P, Müller DJ, Jessberger S and Peter M ( 2023 ) The CUL4B-based E3 ubiquitin ligase regulates mitosis and brain development by recruiting phospho-specific DCAFs. EMBO J , 42:e112847  (*indicates joint contribution)  Link


Gräf JF*, Mikicic I*, Ping X, Scalera C, Mayr K, Stelzl LS, Beli P and Wagner SA ( 2022 ) Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks. iScience , 25:104892  (*indicates joint contribution)  Link

Mosler T*, Baymaz HI*, Gräf JF, Mikicic I, Blattner G, Bartlett E, Ostermaier M, Piccinno R, Yang J, Voigt A, Gatti M, Pellegrino S, Altmeyer M, Luck K, Ahel I, Roukos V and Beli P ( 2022 ) PARP1 proximity proteomics reveals interaction partners at stressed replication forks. Nucleic Acids Res , 50:11600–11618  (*indicates joint contribution)  Link

Solvie D*, Baluapuri A*, Uhl L*, Fleischhauer D, Endres T, Papadopoulos D, Aziba A, Gaballa A, Mikicic I, Isaakova E, Giansanti C, Jansen J, Jungblut M, Klein T, Schülein-Völk C, Maric H, Doose S, Sauer M, Beli P, Rosenwald A, Dobbelstein M, Wolf E# and Eilers M# ( 2022 ) MYC multimers shield stalled replication forks from RNA polymerase. Nature , 612:148–155  (*indicates joint contribution, #indicates joint correspondence)  Link

Szczęśniak PP, Heidelberger JB, Serve H, Beli P and Wagner SA ( 2022 ) VCP inhibition induces an unfolded protein response and apoptosis in human acute myeloid leukemia cells. PLOS One , 17:e0266478 Link

Wegmann S*, Meister C*, Renz C, Yakoub G, Wollscheid HP, Takahashi DT, Mikicic I, Beli P and Ulrich HD ( 2022 ) Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass. Mol Cell , 82:1589–1602.e5  (*indicates joint contribution)  Link

Winkler R*, Mägdefrau AS*, Piskor EM, Kleemann M, Beyer M, Linke K, Hansen L, Schaffer AM, Hoffmann ME, Poepsel S, Heyd F, Beli P, Möröy T, Mahboobi S, Krämer OH and Kosan C ( 2022 ) Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition. Oncogene , 41:4560–4572  (*indicates joint contribution)  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

Bufe A, García del Arco A, Hennecke M, de Jaime-Soguero A, Ostermaier M, Lin YC, Ciprianidis A, Hattemer J, Engel U, Beli P, Bastians H and Acebrón SP ( 2021 ) Wnt signaling recruits KIF2A to the spindle to ensure chromosome congression and alignment during mitosis. Proc Natl Acad Sci USA , 118:e2108145118 Link

Endres T*, Solvie D*, Heidelberger JB, Andrioletti V, Baluapuri A, Ade CP, Muhar M, Eilers U, Vos SM, Cramer P, Zuber J, Beli P, Popov N, Wolf E, Gallant P and Eilers M ( 2021 ) Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol Cell , 81:830-844.e13  (*indicates joint contribution)  Link

Juretschke T and Beli P ( 2021 ) Causes and consequences of DNA damage-induced autophagy. Matrix Biology , 100–101:39–53 Link

Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P# and Xirodimas DP# ( 2021 ) Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation. Cell Rep , 34:108635  (#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

Reich TR*, Schwarzenbach C, Vilar JB, Unger S, Mühlhäusler F, Nikolova T, Poplawski A, Baymaz HI, Beli P, Christmann M and Tomicic MT* ( 2021 ) Localization matters: nuclear-trapped Survivin sensitizes glioblastoma cells to temozolomide by elevating cellular senescence and impairing homologous recombination. Cell Mol Life Sci , 78:5587–5604  (*indicates joint contribution)  Link

Roedig J, Kowald L, Juretschke T, Karlowitz R, Ahangarian Abhari B, Roedig H, Fulda S, Beli P and Wijk SJ ( 2021 ) USP22 controls necroptosis by regulating receptor-interacting protein kinase 3 ubiquitination. EMBO Rep , 22:e50163 Link

Roeschert I*, Poon E*, Henssen AG, Dorado Garcia H, Gatti M, Giansanti C, Jamin Y, Ade CP, Gallant P, Schülein-Völk C, Beli P, Richards M, Rosenfeldt M, Altmeyer M, Anderson J, Eggert A, Dobbelstein M, Bayliss R, Chesler L#, Büchel G# and Eilers M# ( 2021 ) Combined inhibition of Aurora-A and ATR kinase results in regression of MYCN-amplified neuroblastoma. Nat Cancer , 2:312–326  (*indicates joint contribution, #indicates joint correspondence)  Link

Wagner SA, Szczesniak PP, Voigt A, Gräf JF and Beli P ( 2021 ) Proteomic analysis of tyrosine phosphorylation induced by exogenous expression of oncogenic kinase fusions identified in lung adenocarcinoma. Proteomics , 21:2000283 Link


Bekbulat F*, Schmitt D*, Feldmann A, Huesmann H, Eimer S, Juretschke T, Beli P, Behl C# and Kern A# (2020) RAB18 loss interferes with lipid droplet catabolism and provokes autophagy network adaptations. J Mol Biol, 432:1216–1234 (*indicates joint contribution, #indicates joint correspondence) 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

Lowe DJ, Herzog M, Mosler T, Cohen H, Felton S, Beli P, Raj K, Galanty Y and Jackson SP (2020) Chronic irradiation of human cells reduces histone levels and deregulates gene expression. Sci Rep, 10:2200 Link


Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros AC, Woods M, Fu B, Yang F, Chen E, Ostermaier M, Stankovic T, Ponstingl H, Herzog M, Yusa K, Martinez FM, Durant ST, Galanty Y, Beli P, Adams DJ, Bradley A, Metzakopian E, Forment J V and Jackson SP (2019) ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks. Nat Commun, 10:87 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 J-Y, 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

Juretschke T, Beli P and Dikic I (2019) Quantitative phosphoproteomics of selective autophagy receptors. Methods Mol Biol, 1880:691-701 Link

Sasca D, Szybinski J, Schüler A, Shah V, Heidelberger J, Haehnel PS, Dolnik A, Kriege O, Fehr E-M, Gebhardt WH, Reid G, Scholl C, Theobald M, Bullinger L, Beli P and Kindler T (2019) Neural cell adhesion molecule 1 (NCAM1; CD56) promotes leukemogenesis and confers drug resistance in AML. Blood, 133:2305–2319 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

Dev H, Chiang T-WW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M, Herzog M, Lam J, Shea A, Demir M, Wu Q, Yang F, Fu B, Lai Z, Balmus G, Belotserkovskaya R, Serra V, O’Connor MJ, Bruna A, Beli P, Pellegrini L, Caldas C, Deriano L, Jacobs JJL, Galanty Y and Jackson SP (2018) Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Nat Cell Biol, 20:954–965 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


Borisova ME, Wagner SA and Beli P (2017) Mass spectrometry-based proteomics for quantifying DNA damage-induced phosphorylation. Methods Mol Biol, 1599:215-227 Link

Diamanti MA, Gupta J, Bennecke M, De Oliveira T, Ramakrishnan M, Braczynski AK, Richter B, Beli P, Hu Y, Saleh M, Mittelbronn M, Dikic I and Greten FR (2017) IKKα controls ATG16L1 degradation to prevent ER stress during inflammation. J Exp Med, 214:423–437 Link

Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P# and König J# (2017) Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Sci Rep, 7:16582 (#indicates joint correspondence) Link

Mahendrarajah N, Borisova ME, Reichardt S, Godmann M, Sellmer A, Mahboobi S, Haitel A, Schmid K, Kenner L, Heinzel T, Beli P and Krämer OH (2017) HSP90 is necessary for the ACK1-dependent phosphorylation of STAT1 and STAT3. Cell Signal, 39:9–17 Link

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 Link

Schunter S, Villa R, Flynn V, Heidelberger JB, Classen AK, Beli P and Becker PB (2017) Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster. PLOS One, 12:e0177408 Link


Heidelberger JB, Wagner SA and Beli P (2016) Mass spectrometry-based proteomics for investigating DNA damage-associated protein ubiquitylation. Front Genet, 7:109 Link

Richter B, Sliter DA, Herhaus L, Stolz A, Wang C, Beli P, Zaffagnini G, Wild P, Martens S, Wagner SA, Youle RJ and Dikic I (2016) Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria. Proc Natl Acad Sci USA, 113:4039–4044 Link

Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H and Beli P (2016) ATR inhibition rewires cellular signaling networks induced by replication stress. Proteomics, 16:402–416 Link

Wagner SA, Satpathy S, Beli P and Choudhary C (2016) SPATA2 links CYLD to the TNF-alpha receptor signaling complex and modulates the receptor signaling outcomes. EMBO J, 35:1868–1884 Link


Beli P and Jackson SP (2015) Ubiquitin regulates dissociation of DNA repair factors from chromatin. Oncotarget, 6:14727–14728 Link

Brown JS, Lukashchuk N, Sczaniecka-Clift M, Britton S, le Sage C, Calsou P, Beli P#, Galanty Y# and Jackson SP# (2015) Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep, 11:704–714 (#indicates joint correspondence) Link

Bursomanno S*, Beli P*, Khan AM, Minocherhomji S, Wagner SA, Bekker-Jensen S, Mailand N, Choudhary C, Hickson ID and Liu Y (2015) Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells. DNA Repair, 25:84–96 (*indicates joint contribution) Link

Chu WK, Payne MJ, Beli P, Hanada K, Choudhary C and Hickson ID (2015) FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51. Nat Commun, 6:5931 Link

Gallina I, Colding C, Henriksen P, Beli P, Nakamura K, Offman J, Mathiasen DP, Silva S, Hoffmann E, Groth A, Choudhary C and Lisby M (2015) Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control. Nat Commun, 6:6533 Link

Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, Francavilla C, Tolar P, Bishop GA, Hostager BS and Choudhary C (2015) Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol, 11:810 Link

Schmidt CK, Galanty Y, Sczaniecka-Clift M, Coates J, Jhujh S, Demir M, Cornwell M, Beli P and Jackson SP (2015) Systematic E2 screening reveals a UBE2D–RNF138–CtIP axis promoting DNA repair. Nat Cell Biol, 17:1458–1470 Link

Schölz C, Weinert BT, Wagner SA, Beli P, Miyake Y, Qi J, Jensen LJ, Streicher W, McCarthy AR, Westwood NJ, Lain S, Cox J, Matthias P, Mann M, Bradner JE and Choudhary C (2015) Acetylation site specificities of lysine deacetylase inhibitors in human cells. Nat Biotechnol, 33:415–423 Link

Tollenaere MAX, Villumsen BH, Blasius M, Nielsen JC, Wagner SA, Bartek J, Beli P, Mailand N and Bekker-Jensen S (2015) p38- and MK2-dependent signalling promotes stress-induced centriolar satellite remodelling via 14-3-3-dependent sequestration of CEP131/AZI1. Nat Commun, 6:10075 Link

Yang J, Wagner SA and Beli P (2015) Illuminating spatial and temporal organization of protein interaction networks by mass spectrometry-based proteomics. Front Genet, 6:344 Link


Oka Y, Varmark H, Vitting-Seerup K, Beli P, Waage J, Hakobyan A, Mistrik M, Choudhary C, Rohde M, Bekker-Jensen S and Mailand N (2014) UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells. EMBO Rep, 15:956–964 Link


Villumsen BH, Danielsen JR, Povlsen L, Sylvestersen KB, Merdes A, Beli P, Yang Y-G, Choudhary C, Nielsen ML, Mailand N and Bekker-Jensen S (2013) A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis. EMBO J, 32:3029–3040 Link

Weinert BT, Iesmantavicius V, Wagner SA, Schölz C, Gummesson B, Beli P, Nyström T and Choudhary C (2013) Acetyl-phosphate is a critical determinant of lysine acetylation in E. coli. Mol Cell, 51:265–272 Link


Beli P*, Lukashchuk N*, Wagner SA, Weinert BT, Olsen J V., Baskcomb L, Mann M, Jackson SP and Choudhary C (2012) Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. Mol Cell, 46:212–225 (*indicates joint contribution) Link

Mosbech A, Gibbs-Seymour I, Kagias K, Thorslund T, Beli P, Povlsen L, Nielsen SV, Smedegaard S, Sedgwick G, Lukas C, Hartmann-Petersen R, Lukas J, Choudhary C, Pocock R, Bekker-Jensen S and Mailand N (2012) DVC1 (C1orf124) is a DNA damage–targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks. Nat Struct Mol Biol, 19:1084–1092 Link

Povlsen LK*, Beli P*, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N and Choudhary C (2012) Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. Nat Cell Biol, 14:1089–1098 (*indicates joint contribution) Link

Wagner SA*, Beli P*, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen J V., Brakebusch C and Choudhary C (2012) Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues. Mol Cell Proteomics, 11:1578–1585 (*indicates joint contribution) Link


Wagner SA*, Beli P*, Weinert BT, Nielsen ML, Cox J, Mann M and Choudhary C (2011) A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics, 10:M111.013284 (*indicates joint contribution) Link


Beli P, Mascheroni D, Xu D and Innocenti M (2008) WAVE and Arp2/3 jointly inhibit filopodium formation by entering into a complex with mDia2. Nat Cell Biol, 10:849–857 Link