Publications

Primary research papers:

  • Abu-Libdeh B, Jhujh SS, Dhar S, Sommers JA, Datta A, Longo GM, Grange LJ, Reynolds JJ, Cooke SL, McNee GS, Hollingworth R, Woodward BL, Ganesh AN, Smerdon SJ, Nicolae CM, Durlacher-Betzer K, Molho-Pessach V, Abu-Libdeh A, Meiner V, Moldovan GL, Roukos V, Harel T, Brosh RM Jr, Stewart GS. RECON syndrome is a genome instability disorder caused by mutations in the DNA helicase RECQL1. J Clin Invest. 2022 13:e147301.
  • Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet. 2022 54:1238-1247.
  • Basu S, Mackowiak SD, Niskanen H, Knezevic D, Asimi V, Grosswendt S, Geertsema H, Ali S, Jerkovic I, Ewers H, Mundlos S, Meissner A, Ibrahim DI, Hnisz D. Unblending of transcriptional condensates in human repeat expansion disease. Cell 2020 181:1062-1079.
  • Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V, Crosetto N. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc. 2020 15:3894-3941.
  • Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022 (In press).
  • Cao J, O’Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020 370:eaba7721.
  • Casa V, Moronta Gines M, Gade Gusmao E, Slotman JA, Zirkel A, Josipovic N, Oole E, van IJcken WFJ, Houtsmuller AB, Papantonis A, Wendt KS. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Genome Res 2020 30:515-527.
  • Chang NC, Rovira Q, Wells JN, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res. 2022 doi: 10.1101/gr.275655.121.
  • Cremer M, Brandstetter K, Maiser A, Rao SSP, Schmid VJ, Guirao-Ortiz M, Mitra N, Mamberti S, Klein KN, Gilbert DM, Leonhardt H, Cardoso MC, Aiden EL, Harz H, Cremer T. Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. Nat Commun. 2020 11:6146.
  • Elsner J, Mensah MA, Holtgrewe M, Hertzberg J, Bigoni S, Busche A, Coutelier M, de Silva DC, Elçioglu N, Filges I, Gerkes E, Girisha KM, Graul-Neumann L, Jamsheer A, Krawitz P, Kurth I, Markus S, Megarbane A, Reis A, Reuter MS, Svoboda D, Teller C, Tuysuz B, Türkmen S, Wilson M, Woitschach R, Vater I, Caliebe A, Hülsemann W, Horn D, Mundlos S, Spielmann M. Genome sequencing in families with congenital limb malformations. Hum Genet. 2021 140:1229-1239.
  • Galan S, Machnik N, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nat Genet. 2020 52:1247-1255.
  • Gao Q, Chagin VO, Cardoso MC, Rohr K. Non-rigid registration of live cell nuclei using global optical flow with elasticity constraints. Proc. IEEE Intenat Symp Biomed Imaging, Nice, France, April 13-16, 2021.
  • 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, Roukos V. Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL Translocations. Mol Cell 2019 75:267-283.
  • Hari-Gupta Y, Fili N, Dos Santos Á, Cook AW, Gough RE, Reed HCW, Wang L, Aaron J, Venit T, Wait E, Grosse-Berkenbusch A, Gebhardt JCM, Percipalle P, Chew TL, Martin-Fernandez M, Toseland CP. Myosin VI regulates the spatial organisation of mammalian transcription initiation. Nat Commun. 2022 13:1346.
  • Ing-Simmons E, Vaid R, Bing XY, Levine M, Mannervik M, Vaquerizas JM. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021 53:487-499.
  • Jaeger MG, Schwalb B, Mackowiak SD, Velychko T, Hanzl A, Imrichova H, Brand M, Agerer B, Chorn S, Nabet B, Ferguson FM, Müller AC, Bergthaler A, Gray NS, Bradner JE, Bock C, Hnisz D, Cramer P, Winter GE. Selective Mediator dependence of cell-type-specifying transcription. Nat Genet 2020 52:719-727.
  • Jakubke C, Roussou R, Maiser A, Schug C, Thoma F, Bunk D, Horl D, Leonhardt H, Walter P, Klecker T, Osman C. Cristae-dependent quality control of the mitochondrial genome. Sci Adv. 2020 7:eabi8886.
  • Kruse K, Hug CB, Vaquerizas JM. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. 2020 21:303.
  • Kuhn T, Hettich J, Davtyan R, Gebhardt JCM. Single molecule tracking and analysis framework including theory-predicted parameter settings. Sci Rep. 2021 11:9465.
  • Le Poul Y, Xin Y, Ling L, Muhling B, Jaenichen R, Horl D, Bunk D, Harz H, Leonhardt H, Wang Y, Osipova E, Museridze M, Dharmadhikari D, Murphy E, Rohs R, Preibisch S, Prud’homme B, Gompel N. Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Sci Adv. 2020 6:49.
  • Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny LA, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022 https://doi.org/10.1038/s41556-022-00847-6.
  • Maiser A, Dillinger S, Langst S, Schermelleh L, Leonhardt H, Nemeth A. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci Rep. 2020 10:7462.
  • Markowski J, Kempfer R, Kukalev A, Irastorza-Azcarate I, Loof G, Kehr B, Pombo A, Rahmann S, Schwarz RF. GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Bioinformatics 2021 37:3128-3135.
  • Melo US, Schöpflin R, Acuna-Hidalgo R, Mensah MA, Fischer-Zirnsak B, Holtgrewe M, Klever MK, Türkmen S, Heinrich V, Pluym ID, Matoso E, Bernardo de Sousa S, Louro P, Hülsemann W, Cohen M, Dufke A, Latos-Bieleńska A, Vingron M, Kalscheuer V, Quintero-Rivera F, Spielmann M, Mundlos S. Hi-C Identifies Complex genomic rearrangements and TAD-shuffling in developmental diseases. Am J Hum Genet. 2020 106:872-884.
  • Mizi A, Gade Gusmao E, Papantonis A. iHi-C 2.0: A simple approach for mapping native spatial chromatin organisation from low cell numbers. Methods 2020 170:33-37. 
  • Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V, Beli P. R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun. 2021 12:7314.
  • Noack F, Vangelisti S, Raffl G, Carido M, Diwakar J, Chong F, Bonev B. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. Nat Neurosci. 2022 doi:10.1038/s41593-021-01002-4.
  • Popp AP, Hettich J, Gebhardt JCM. Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene. Nucleic Acids Res. 2021 49:6249.
  • Ritter C, Wollmann T, Lee JY, Imle A, Müller B, Fackler OT, Bartenschlager R, Rohr K. Data fusion and smoothing for probabilistic tracking of viral structures in fluorescence microscopy images. Med Image Anal. 2021 73:102168.
  • Smajić S, Prada-Medina CA, Landoulsi Z, Ghelfi J, Delcambre S, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Antony P, Timmermann B, Sauer S, Pereira SL, Schwamborn JC, May P, Grünewald A, Spielmann M. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 2021 17:awab446.
  • Socha M, Sowińska-Seidler A, Melo US, Kragesteen BK, Franke M, Heinrich V, Schöpflin R, Nagel I, Gruchy N, Mundlos S, Sreenivasan VKA, López C, Vingron M, Bukowska-Olech E, Spielmann M, Jamsheer A. Position effects at the FGF8 locus are associated with femoral hypoplasia. Am J Hum Genet. 2021 108:1725-1734.
  • Sofiadis K, Josipovic N, Nikolic M, Kargapolova Y, Übelmesser N, Varamogianni-Mamatsi V, Zirkel A, Papadionysiou I, Loughran G, Keane J, Michel A, Gusmao EG, Becker C, Altmüller J, Georgomanolis T, Mizi A, Papantonis A. HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. Mol Syst Biol 2021 17:e9760.
  • Spilger R, Imle A, Lee JY, Müller B, Fackler OT, Bartenschlager R, Rohr K. A recurrent neural network for particle tracking in microscopy images using future information, track hypotheses, and multiple detections. IEEE Transac Image Proc. 2020 29:3681-3694.
  • Spilger R, Lee JY, Chagin VO, Schermelleh L, Cardoso MC, Bartenschlager R, Rohr K. Deep probabilistic tracking of particles in fluorescence microscopy images. Med Image Anal. 2021 72:102128.
  • Wollmann T, Rohr K. Deep Consensus Network: Aggregating predictions to improve object detection in microscopy images, Med Image Anal. 2021 70:102019.
  • Zampetidis CP, Galanos P, Angelopoulou A, Zhu Y, Polyzou A, Karamitros T, Kotsinas A, Lagopati N, Mourkioti I, Mirzazadeh R, Polyzos A, Garnerone S, Mizi A, Gusmao EG, Sofiadis K, Gál Z, Larsen DH, Pefani DE, Demaria M, Tsirigos A, Crosetto N, Maya-Mendoza A, Papaspyropoulos A, Evangelou K, Bartek J, Papantonis A, Gorgoulis VG. A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization. Mol Cell 2021 81:4907-4923.
  • Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D, Papantonis A. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv 2021 7:eabg8205.

Review papers:

  • Aboelnour E, Bonev B. Decoding the organization, dynamics and function of the 4D Genome. Dev Cell 202156:1562-1573.
  • Cavalheiro GR, Pollex T, Furlong EE. To loop or not to loop: what is the role of TADs in enhancer function and gene expression? Curr Opin Genet Dev. 2021 67:119-129.
  • Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing nuclear architecture through the eyes of nocturnal mammals. Trends Cell Biol 2020 30:276-289.
  • Galouzis CC, Furlong EE. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol. 2022 (In Press).
  • Ibrahim DM, Mundlos S. The role of 3D chromatin domains in gene regulation: a multi- facetted view on genome organization. Curr Opin Genet Dev 2020 61:1-8.
  • Ibrahim DM, Mundlos S. Three-dimensional chromatin in disease: What holds us together and what drives us apart? Curr Opin Cell Biol 2020 64:1-9.
  • Ing-Simmons E, Rigau M, Vaquerizas JM. Emerging mechanisms and dynamics of 3D genome organisation at zygotic genome activation. Curr Opin Cell Biol. 2022 74:37-46.
  • Mirny LA, Solovei I. Keeping chromatin in the loop(s). Nat Rev Mol Cell Biol 2021 22:439-440.
  • Mizi A, Zhang S, Papantonis A. Genome folding and refolding in differentiation and cellular senescence. Curr Opin Cell Biol 2020 67:56-63. 
  • Papantonis A. HMGs as rheostats of chromosomal structure and cell proliferation. Trends Genet 2021 37:986-994.
  • Rippe K, Papantonis A. RNA polymerase II transcription compartments: from multivalent chromatin binding to liquid droplet formation? Nat Rev Mol Cell Biol 2021 22:645-646

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